Biology 3355A Course Outline (2017-18) 1. General Course Information Course Information Biology 3355A (Molecular Cell Biology of Stress), Fall term 2017. Lectures are on Wednesdays and Fridays, 9:30-10:30am in NCB-117. Tutorials are on Tuesdays (1:30-2:30pm in UCC-60, section 002) and Thursdays (11:30-12:30pm in NCB-293, section 003). Prerequisite Requirements Unless you have either the requisites for this course or written special permission from your Dean to enroll in it, you may be removed from this course and it will be deleted from your record. This decision may not be appealed. You will receive no adjustment to your fees in the event that you are dropped from a course for failing to have the necessary prerequisites. The prerequisite for this course is Biology 2382B. 2. Instructor Information Dr. Alexander Timoshenko, office: BGS 3032 Office hours: Tuesdays, 10:30 am to 12:00 (noon) or by appointment. Tel.: 519-661-2111 ex. 88900, E-mail: atimoshe@uwo.ca. If you email your instructor, you must use your Western (@uwo.ca) email address and include Bio3355A in the subject line. Messages from a non-western account or those that do not include Bio3355A may be blocked by the university s anti-spam system. 3. Course Description/Syllabus Biology 3355A is an advanced course in cell biology. This course will cover a range of environmental, physiological, and pathological stresses common to animal systems. The focus will be on evolutionary conserved cell stress responses, individual signaling pathways and the molecules controlling the action of specific stress stimuli. The topics listed below may be adjusted to reflect current progress or to introduce new and exciting developments in the field. In particular, there will be several guest lectures of experts in the field of cell stress biology. By the end of the course, successful students will be able to: Describe signaling processes underlying heat shock response, endoplasmic reticulum stress and unfolded protein responses, oxidative stress, hypoxic stress, osmotic stress, metal stress, inflammatory stress, DNA damage response, and nucleolar stress. Understand the structure and properties of stress-related transcription factors and discuss molecular mechanisms of their activation in mammalian cells Apply the knowledge of cell stress biology to discuss and explain biological principles of some human diseases. Describe the experimental methods used to study cellular stress responses and understand how to apply these methods in cell biology laboratories. Develop and practice their presentation skills by performing the oral presentation of novel concepts, current methodology and techniques in cell stress biology and reviewing primary articles published in scientific journals (tutorial component). Page 1
Demonstrate competence with scientific writing and critical thinking by preparing a midterm assignment to analyse and examine regulatory factors (transcription factors and mirnas) controlling the expression of stress-related genes using available bioinformatics online tools and databases. Anticipated lecture topics Date Sept 8 (Fri) Sept 13 (Wed) and Sept 15 (Fri) Sep 20 (Wed) and Sept 22 (Fri) Sept 27 (Wed) and Sept 29 (Fri) Oct 4 (Wed) Oct 6 (Fri) Oct 11 (Wed) and Oct 13 (Fri) Oct 18 (Wed) Oct 20 (Fri) Oct 25 (Wed) Oct 27 (Fri) Nov 1 (Wed) Nov 3 (Fri) Nov 8 (Wed) and Nov 10 (Fri) Nov 15 (Wed) and Nov 17 (Fri) Nov 22 (Wed) Nov 24 (Fri) and Nov 29 (Wed) Dec 1 (Fri) Dec 6 (Wed) Dec 8 (Fri) Lecture topics Introduction and general overview Unit 1: Heat shock response and chaperones Unit 2: Unfolded protein response Unit 3: Oxidative stress Unit 4. Stress and redox regulation Unit 5: Hypoxic stress Fall study break, no classes Midterm review Midterm exam: 9:00am-10:20am Unit 6: MicroRNAs in stress responses Unit 7: Osmotic stress Unit 8: Metal stress Unit 9: DNA damage response Unit 10: Nucleolar stress Unit 11: Inflammatory stress Unit 12: Glycobiology of cellular stress responses Final review and student questions 4. Course Materials There is no specific textbook assigned to this course. The list of required reading (links to primary and review scientific articles), lecture handouts, announcements, tutorial assignments, and other important course information and handouts, will be available on the course website. As additional sources, students are advised to consider the following textbooks of basic information related to the course topics: 1. H. Lodish et al. Molecular Cell Biology, 8 th ed, New York, W.H. Freeman and Co., 2016. 2. B. Alberts et al. Molecular Biology of the Cell, 6 th ed, New York, Garland Science, 2015. Page 2
Students should check OWL (http://owl.uwo.ca) on a regular basis for news and updates. This is the primary method by which information will be disseminated to all students in the class. Students are responsible for checking OWL on a regular basis. 5. Methods of Evaluation The overall course grade will be calculated as listed below: Component Notes Value Take-home assignment Due Friday, November 10, 9:30am, submit in class 10 Tutorial presentation Individually scheduled 15 Midterm Exam Wednesday, October 25, 9:00-10:20 am (1h20min) Makeup on Monday, October 30, 5:30-6:50 pm Final Exam 2 h, TBA and scheduled by the Office of the Registrar 40 Take-home assignment A short written assignment (650 words) will be based on bioinformatics analysis of regulatory factors of stress-related genes using available online software and databases (NCBI GenBank, GeneGards, Diana Tools, and SABioscience). The purpose of this assignment is to identify and describe tentative transcription factors and mirnas that can be involved in transcriptional and post-transcriptional regulation of gene expression. The topic of your assignment has to be approved by the instructor. All assignments must be done individually and be submitted as a hard copy to instructor in class and as electronic copy on OWL. Late submissions of take-home assignment will be penalized at a rate of 5% per day (including the weekend) until the percentage of the assignment is used up. Tutorial information Students, in groups of two, are required to select one primary peer-reviewed research publication to present. This powerpoint presentation (12 min and 3 min Q&A) is intended to broaden our knowledge in animal and human cell stress biology and to provide students with the opportunity to develop their oral presentation skills. The purpose of the presentation is to convey novel concepts or findings in cellular responses to microenvironmental stress, current methodology and techniques, and their application in a specific situation. The presentation is not intended to be a critique of the paper. The tutorials will be run by our Teaching Assistant Joshua Frank (e-mail: jfrank22@uwo.ca). Students may only attend the tutorial section in which they are registered unless special permission has been granted by the instructor. Tutorial attendance is mandatory and attendance will be taken. There will be a deduction of 5% from the final tutorial mark for each unexcused absence. Midterm and final exams Both exams will have the same format and based on combined multiple choice questions and short answers. There will only be one make-up for each exam. 35 Page 3
6. Accommodation and Accessibility If you are unable to meet a course requirement due to illness or other serious circumstances, you must provide valid medical or supporting documentation to the Academic Counselling Office of your home faculty as soon as possible. If you are a Science student, the Academic Counselling Office of the Faculty of Science is located in WSC 140, and can be contacted at scibmsac@uwo.ca. For further information, please consult the university s medical illness policy at http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_medical.pdf. If you have received academic accommodation from your Dean s Office/Academic Counselling unit, the instructor may extend deadlines or provide make-up options for missing components. If you miss the Final Exam, please contact your faculty s Academic Counselling Office as soon as you are able to do so. They will assess your eligibility to write the Special Exam (the name given by the university to a makeup Final Exam). You may also be eligible to write the Special Exam if you are in a Multiple Exam Situation (see http://www.registrar.uwo.ca/examinations/exam_schedule.html). 7. Academic Policies The website for Registrarial Services is http://www.registrar.uwo.ca. In accordance with policy, http://www.uwo.ca/its/identity/activatenonstudent.html, the centrally administered e-mail account provided to students will be considered the individual s official university e-mail address. It is the responsibility of the account holder to ensure that e- mail received from the University at his/her official university address is attended to in a timely manner. No electronic devices may be used in your possession during tests and exams. Scholastic offences are taken seriously and students are directed to read the appropriate policy, specifically, the definition of what constitutes a Scholastic Offence, at this website: http:// www.uwo.ca/univsec/pdf/academic_policies/appeals/scholastic_discipline_undergrad.pdf. All required papers may be subject to submission for textual similarity review to the commercial plagiarism detection software under license to the University for the detection of plagiarism. All papers submitted for such checking will be included as source documents in the reference database for the purpose of detecting plagiarism of papers subsequently submitted to the system. Use of the service is subject to the licensing agreement, currently between The University of Western Ontario and Turnitin.com (http://www.turnitin.com). Computer-marked, multiple-choice tests and exams may be subject to submission for similarity review by software that will check for unusual coincidences in answer patterns that may indicate cheating. Page 4
8. Support Services Please contact the course instructor if you require lecture or printed material in an alternate format or if any other arrangements can make this course more accessible to you. You may also wish to contact Services for Students with Disabilities (SSD) at 661-2111 ext. 82147 if you have questions regarding accommodation. The policy on Accommodation for Students with Disabilities can be found here: www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_disabilities.pdf The policy on Accommodation for Religious Holidays can be found here: http://www.uwo.ca/univsec/pdf/academic_policies/appeals/accommodation_religious.pdf Learning-skills counsellors at the Student Development Centre (http://www.sdc.uwo.ca) are ready to help you improve your learning skills. They offer presentations on strategies for improving time management, multiple-choice exam preparation/writing, textbook reading, and more. Individual support is offered throughout the Fall/Winter terms in the drop-in Learning Help Centre, and year-round through individual counselling. Students who are in emotional/mental distress should refer to Mental Health@Western (http://www.health.uwo.ca/mental_health) for a complete list of options about how to obtain help. Additional student-run support services are offered by the USC, http://westernusc.ca/services. 9. Equal Opportunity and Evaluation Policy All individuals involved in the offering of Biology 3355A were, at one time, undergraduate students themselves. Accordingly, your professor and your teaching assistant thoroughly understand the importance of course grades and the hard work that you will invest into this course. They are there to help you achieve your goals. We want you to do well in the course, but we also have to be fair. The university is committed to academic integrity and has high ethical and moral standards. All students will be treated equally and evaluated using the criteria presented in this course outline and their respective weights. The evaluation criteria are based strictly on actual achievement, not on effort or how hard the student tried. Claims of an excellent academic history, of attendance in the course components, or of personal issues (family, relationship, financial, etc.) cannot be used to justify a higher grade in the course because they are not criteria for evaluation. There is no extra work available for extra credit or to make up another grade. We do not offer any extra assignments, essays, or other work of any kind to any student. The requirement for a higher grade in order to, for example, maintain a scholarship, enter a program, or obtain a higher GPA for various reasons, is not a justifiable reason for increasing your grade. If we increased or bumped your grade (i.e. gave you a grade that you did not legitimately earn), it would be unfair to the other students and also a great disservice to the scholarships and programs who are evaluating all students on the basis of their grades. Good Luck with your Studies! Page 5