Biol 14A: Genetics and Genomics Fall 2016 Dr. Rachel Woodruff woodruff@brandeis.edu Introduction Think for a moment about inheritance. What did you get from your biological parents? What do you know about your own genome? The fields of genetics, genomics, and molecular biology have been developing rapidly over the last few decades: PCR, gene cloning, anti-retroviral therapy, next-generation DNA sequencing, RNAi, somatic cell nuclear transfer (animal cloning), induction of pluripotent stem cells, CRISPR to name but a few advances! We can expect these fields to continue to advance, and to affect more and more aspects of our lives. How will doctors use their patient s genomic information in a few years? What discoveries will alter our fundamental understanding of molecular biology? How will genetic engineering be adapted to cope with global warming? The super-goal of this course is for you to be able to understand and interpret such new developments and applications, as they affect your own life and career, throughout your life. The Learning Goals for this course encompass the skills and knowledge that will enable you to interpret past, present, and future findings in genetics. These are the large goals we will work toward all semester: - You should have a conceptual understanding of the molecular mechanisms that result in phenotypes and biological inheritance. If you have a strong framework of understanding what the key components and processes are, you will be able to use this to interpret new information. - You should understand many of the common tools and approaches currently used by researchers in genetics, genomics and molecular biology. If you understand how these approaches work, and how they are interpreted, you will be able to understand how they have been used to reach new conclusions, and you will also be better equipped to figure out experimental approaches that are unknown to you. - You should know strategies and information sources you can use to make sense of new observations relating to molecular biology or genetics. When you have met these goals, you will be ready to begin being an informed reader of primary research articles in the field. You will be able to question and discuss experimental
results and interpretations. Some of you will go on to use these skills and concepts to become researchers, creating the future of the field; and all of you, I hope, will use them to be betterinformed voters and advocates for yourself, your families and your communities. Course structure Schedule: A typical week in BIOL 14a Like any 4-credit course, this should take you about 12 hours per week, including class time (4 hours, in this case) and out-of-class time. Success in this 4 credit hour course is based on the expectation that students will spend a minimum of 9 hours of study time per week in preparation for class (readings, papers, discussion sections, preparation for exams, etc.). There is some variation, but a typical week includes: - Readings: I recommend that you take time to read the week s readings ahead between and Monday. This is also a great time to do your Self Test (see below) - Monday Homework: one Self Test homework assignment to help prepare you for upcoming classes (online, through LATTE or the textbook LaunchPad site), due on Mondays - Lecture: three 50-minute Lecture meetings (all 225 of us), Mondays, Wednesdays and s 9:00-9:50 a.m., in Gerstenzang 123, which will be used for lecture, discussion, a Wednesday Question Session, of your questions, - Recitation: one 50-minute Recitation meeting, often including a Practice Quiz (smaller groups). Recitation sections and the activities you do there are an integral and required part of the course. - Daily Homework: several hours of reading, study, and work on Practice Problems, - Wednesday Homework: one Weekly Response assignment (online, due Wednesdays). - Testing: Some weeks will include Quizzes (given on s, approximately every other week). Some weeks will include additional homework ( special assignments ), which are sporadic. You will get the most out of this class if you come to both lectures and recitations prepared to actively engage in thinking, questioning, and problem solving. By its nature, the material you will learn in this course is all inter-related. It will not be presented in separate units with breaks in between, but will be presented in a continuous format. That means, for example, that we will continue working on new material right up until each quiz, though quizzes will not cover the last couple of days of newest material. On attendance: You should attend every class. I know that everyone has extenuating circumstances sometimes, but if circumstances make you miss class more than 3 times during the semester, you may have overextended yourself, and you should consider dropping the class. Lecture meetings are not just for traditional listen-and-take-notes lectures. On some days (usually Wednesdays), we will spend part of our 50-minute meetings in Question Sessions in which you will work, often in groups, to answer and ask questions related to current course material. These sessions are intended to give you supervised practice in applying the concepts you are learning, which really is the hardest aspect of this course. Your work in Question Sessions will be graded based on your effort and participation.
Every, we will also have a portion of lecture explicitly devoted to Review. Exactly what we review will be up to you: part of your Weekly Response homework will be to describe your current confusions and questions about the material, so that your instructors can choose the most helpful things to spend more time reviewing. Recitation groups meet weekly, and are led by TAs who have research experience in genetics or related fields. It is important that you attend the recitation section you are registered for. You registered for one of these on SAGE when you signed up for the class: Section 1: Mondays, 5:30 6:20 pm Section 2: Mondays, 6:30 7:20 pm Section 3: Mondays, 7:30 8:20 pm Section 4: Mondays, 7:30 8:20 pm Section 5: Tuesdays, 5:30 6:20 pm Section 6: Tuesdays, 5:30 6:20 pm Section 7: Tuesdays, 6:30 7:20 pm Section 8: Tuesdays, 7:30 8:20 pm Section 9: Mondays, 4:30 5:20 pm How will recitation time be used? They will be a mix of practice and review. Many recitation section meetings will include a Practice Quiz. These are much shorter than the Quizzes given as assessments during lecture, but they will be composed of questions similar to those you ll see in the actual Quizzes. Unlike the Quizzes themselves, you will work through these Practice Quizzes in groups. This will help you to learn from and teach each other, and to gain experience in discussing genetics concepts. Part of each recitation section will also be devoted to review, primarily focusing on concepts you have raised in your Weekly Response or in emails to your TA, or on new questions you raise. It is fine to email your TA over the weekend, with questions you d particularly like them to go over in section. Of course, you can also ask questions in class on the spur of the moment. Homework will be listed in the course schedule on the course LATTE site. You should expect to spend about 8 hours each week in homework and studying for BIOL 14a. There are five types of homework assignments. Readings are primarily from the textbook Biology: How Life Works (edition 1 or 2). You should read each reading assignment before the class date it is associated with, and may also need to review it after lecture. Practice Problems are posted as PDFs on LATTE. Doing these problems is essential to success in the course. They are similar to those you will see in Practice Quizzes, Quizzes, and the Final Exam. You are responsible for doing all the practice problems, as they are posted, but you will not hand these in for grading. Answer keys will be posted on LATTE to allow you to check your own work. Weekly Responses are online questions you will answer each week (by 3pm Wednesday). These are graded credit/no-credit, based on whether you put in thoughtful effort in answering the questions. If you are keeping up with your other work, they should not take you long to answer. Here, you will communicate your interests and confusions to instructors, so that we can adapt course content accordingly. You are expected to complete at least 9 of these responses over the course of the semester. Note that there will be 14 opportunities, so you can miss 5 of them, but keep track so you don t miss more!
Self Tests are on-line assessments, composed of sets of basic questions. Though each has its due-date, you can start on them as early as you like. These are intended to help you test your own reading comprehension to prepare for upcoming activities in class. These questions typically are not representative of the types of questions you ll see on Quizzes. They are graded for correctness, but most questions allow you multiple tries, so you really ought to aim for getting 100% on every Self Test. Self-tests will be administered through LATTE or the textbook s LaunchPad site. Special Assignments are occasional other assignments, such as the chat-group meetings, and journal club preparation. They are not regularly occurring, but are graded. Resources: Course website: Essential resources are posted for you on LATTE. Check the course website on LATTE frequently for course announcements, lecture notes, assignments, practice problems, and answer keys, as well as updates to the course schedule. In addition, you will find it helpful to sign up for the course Q&A forum on Piazza (the link will be available through LATTE). This is a place where you can ask questions, and likely receive a faster response than if you email Dr. Woodruff directly. You can also see what questions other students have asked (anonymously), and what answers they received from instructors. Office Hours: Please come! Dr. Woodruff and every TA have weekly office hours listed at the top of the course LATTE page. Even though you have one recitation TA, you may attend any one s office hours. You are also welcome to set up appointments with us outside of office hours if needed. Textbook: Morris: Biology, How Life Works. either 2 nd or 1 st Edition. Reading assignments are listed on the syllabus and on the course LATTE site. It is expensive, but you can use it for BIOL15 and BIOL16 as well! The textbook will be a very useful reference for you; however, there will not be an exact correlation between topics covered by the textbook and topics covered in class. Use the textbook as a reference, but use the practice problems, recitation activities, and lectures as the defining resources in your studying. The textbook also comes with an online resource, LaunchPad. If you have purchased a version of the book that includes LaunchPad, you ll be able to use this site for reading and reviewing textbook material. In particular, I have assigned specific LearningCurve Self Test which you can do, instead of Self Tests on LATTE. It is not required that you have LaunchPad access; however, if you bought LaunchPad access for the first edition of the textbook, you should still be able to access our course LaunchPad site, even though it is the 2 nd edition version. Learning Catalytics: This is a response system that we use to facilitate active learning and group activities, such as the Question Sessions, in lecture. Please buy a subscription for $12 for the semester (or $20 for the year) and use it in this class and any others that use this technology. You use it from your own device (smartphone, computer, etc). If you do not have an internet-enabled device, or if you think it will be too distracting to you to use it during class, please talk to Dr. Woodruff and we will make accommodations so that you can do the same activities without this tool.
Quizzes and Exams: Instead of midterm exams, we will have 5 shorter Quizzes, given in lecture, generally occurring on alternate s over the course of the semester. These are distinct from the Practice Quizzes which you will take in recitation sections: both are composed of similar types of problems to solve, but Quizzes have more problems than Practice Quizzes, and you must work alone on Quizzes. Quiz dates are given in the course schedule below. There are no make-up quizzes. Your one lowest quiz grade will be dropped. There will also be one cumulative Final Exam. Students with excused absences from the final exam will be able to take a make-up final exam next semester. (By design, the Quizzes ask you to solve a lot of problems in a short time-frame. Those of you who find this stressful will appreciate that the final exam is different: you should have more than enough time to complete the final exam.) Disabilities: If you are a student with a documented disability on record at Brandeis University and wish to have a reasonable accommodation made for you in this class, please contact me during the first week of class. Cell phones and laptops should only be used in class when they are part of a classroom activity. Use common sense, and don t waste your class time trying to multitask. If your use of a phone or laptop is perceived as disruptive by anyone in the room, you will be asked to put it away or to leave. Academic Integrity: For goodness sake do not cheat! It can only harm your education. You are expected to be familiar with and to follow the University s policies on academic integrity (see http://www.brandeis.edu/studentlife/sdc/ai ). Faculty may refer any suspected instances of alleged dishonesty to the Office of Student Development and Conduct. Instances of academic dishonesty may result in sanctions including but not limited to failing grades being issued. Preliminary Course Schedule: The specific order and content of lectures and readings is subject to change. However, Quiz dates are set! Notes: 1) assigned readings should be done before the day of class they are listed with. Date Daily Topic Readings to do before this meeting, and assignments due this day. Aug 24 No class, but get ready! Read course Syllabus and LATTE page. Sign up for Learning Catalytics before first class meeting! Weekly response 1 due by 3pm. Aug 25, 1 Introduction: Relevance of Genetics & Question Session 1 Abstracts (on LATTE), Chapter 1 & Chapter 2 Aug 29 Molecular biology 1 2 Molecular structures and geneticists favorite molecules: nucleic acids and proteins Chapter 2: 2.1-2.5 Chapter 3: 3.1 and 3.2 Chapter 4: Section 4.1 Self-test 1 due (online), or LaunchPad Ch1,2,4
Aug 29/30 Recitation meeting #1: Intro to recitation & Molecular Basis of Inheritance Activity Aug 31 Sept 1, Sept 5 Sept 6/ Sept 8 (Mon groups) Sept 7 Sept 8, 3 DNA Replication, Chromosomes, Chromatids, and Chromatin & Question Session 2 4 Molecular Techniques: hybridization, electrophoresis, and Sanger Sequencing intro NO CLASS Recitation meeting #2: Sequencing Activity 5 Molecular Techniques continues: PCR and Question Session 3 6 Molecular Techniques. Blots: Southerns, Notherns, and Westerns Chapter 12: 12.1 and 12.2 Chapter 13: section 13.4 Weekly Response 2 due Chapter 12: 12.3 Self-test 2 due (online), or LaunchPad Ch3,12 Chapter 3: 3.3 Korf pp12-13 Weekly response 3 due Special Assignment: Chat-group 1 responses due Review Chapter 12: 12.3 Strachan excerpt on hybridization assays Sept 12 Note: Brandeis Monday: Monday recitations meet. 7 Molecular Biology 2: Using genetic information Following the genetic information: transcription, translation, and RNA splicing Sept 12/13 Recitation meeting #3: Central Dogma and Practice-Quiz (short) Sept 14 8 Translation, Protein Structure and Function & Question Session 4 Chapter 3: 3.4 Chapter 4 (all) Watch animation on LATTE Self-test 3 due (online), or LaunchPad Ch4* Review Chapters 3 & 4 Weekly response 4 due Sept 15, Sept 19 9 Quiz 1 10 Alleles to Phenotypes: Protein structure and applications Chapter 15: 15.1 Self-test 4 due, or LaunchPad Ch15
Sept 19/20 Recitation meeting #4: Practice Quiz Special Assignment #2 due in recitation section Sept 21 Inheritance 11 Chromosomes and Cell Division & Question Session 5 Chapter 11: 11.2 11.3 Chapter 19, p19-8 to 19-9 Chapter 42: p42-1 to 42-4 Weekly response 5 due Sept 22, Sept 26 12 Experimental Crosses, Modes of Inheritance,* and Classes of Alleles (Horizontal gene transfer in bacteria) 13 Modes of inheritance and Classes of Alleles. Begin pedigree analysis, sex linkage. Chapter 16: 16.1 16.4 Flies as Model Organisms (on LATTE) Self-test 5 due, or Launchpad Ch16 Sept 26/27 Recitation meeting #5: Practice Quiz 4 Sept 28 14 Pedigree analysis,* Sex Linkage, and cytoplasmic inheritance. Begin Genetic Linkage and Recombination. & Question Session 6 Chapter 16: 16.5 Chapter 17: 17.1, 17.2, and 17.4, 17.5 Pierce pp139-143 Weekly response 6 due Sept 29, 15 Quiz 2 Oct 3 No Class, and no recitations this week Self-test 6 due, or LaunchPad Ch17 Oct 5 Middle of term! Oct 6, Oct 10 16 **Genetic Linkage, Recombination, Genetic Mapping & Question Session 7 17 Genetic hypotheses, and hypothesis-testing with statistical analysis: chi-square test!** Genomes 18 Genomes, genome Structure & Question Session 8 (probably on linkage and/or statistical analysis) Chapter 17: 17.3, 17.5 mid-term Weekly response 7 due Pierce p174-83 Pierce p61-63 Pierce p113 Chapter 13: 13.1-13.2 Korf p 84 Optional: Pierce p302 Self-test 7 due, or LaunchPad Ch13 Oct 10/11 Recitation meeting #6: Practice Quiz Oct 12 No class Weekly response 8 due Oct 13, 19 Genome Sequencing (physical vs. genetic maps) and Viral genomes Chapter 13: 13.3-13.5 Pierce pp312-316, and optionally pp303-306
Oct 17 No class Oct 19 20 Viruses: Genomes and and Viral life-cycles Article posted on LATTE Oct 20, Oct 24 Oct 25 Brandeis Monday (but no recitation) Oct 26 21 Quiz 3 No Class: no recitations this week. 22 Genetic interactions and pathways,** complementation and epistasis** 23 Complementation & Question Session 9 Weekly response 9 due Chapter 16: 16.4 Self-test 8 due Special Assignment: Chat-group 2 due Weekly response 10 due Oct 27, Oct 31 Molecular Biology 24 Mutations, origins of genetic variation: Germline vs. Somatic 25 DNA Damage and Repair, Reverse Genetics, and Gene Cloning and Genetics of Halloweeen Oct 31/Nov1 Recitation meeting #7: Short Practice Quiz 6 (genetic interactions) Chapter 14, all Chapter 15, all Chapter 12: 12.4 Self-test 9 due, or LaunchPad Ch14,15,*12* Nov 2 26 Gene cloning, Transgenic organisms, and intro to Gene Editing by CRISPR/Cas9* & Question Session 10 Pierce pp519-523 Pierce pp541-546 Article posted on LATTE Weekly response 11 due Nov 3, 27 Quiz 4 Nov 7 28 Gene Therapy Online interactive readings Self-test 10 due, or LaunchPad Ch18 Nov 7/8 Recitation meeting #8: Practice Quiz 8 Nov 9 Inheritance and genomics 29 Complex Traits and Genome-wide association studies (GWAS) & Question Session 11 Chapter 15: 15.3 Chapter 18: all Weekly response 12 due Nov 10, Nov 14 30 Cancer genetics, GWAS, and personal genomics* 31 Cancer, GWAS, personal genomics, and Metagenomics Case 2 Chapter 11: 11.5 Case 5
Nov 14/15 Recitation meeting #9: Short Practice Quiz 8 Nov 16 Regulation of Gene Expression and the Genetics of Development 32 Regulation of Gene Expression I: Introduction & Question Session 12 Self-test 11 due, or LaunchPad Ch11,19,20* Chapter 19, section 19.1 Pierce pp463-65 ncrna Reading online Weekly response 13 due Nov 17, Nov 21 Nov 22, 23,24 Nov 28 33 Quiz 5 34 Regulation of Gene Expression, II: epigenetic phenomena and transcriptional regulation in eukaryotes No Class. Happy Thanksgiving! No recitation meetings this week. 35 Regulation of Gene Expression, III: alternative splicing, RNAi, and C. elegans as model developmental organism Chapter 19: 19.2 & 19.3 Research article: lin-4 mirna commentary (on LATTE) RNAi perspective: Nobel Prize reading (link on LATTE) Pierce p442-45 Nov 28/29 Recitation Meeting #10: Journal Club!! Self-test 12 due, or LaunchPad Ch19*,20* Research article: lin-4 mirna commentary (on LATTE) Nov 30 Dec 1 36 Prokaryotic transcriptional regulation; Development: Stem Cells and Cell Differentiation & Question Session 13 37 Genetics of Development continues Chapter 20: 20.1 and 20.2 Weekly response 14 due Chapter 20: 20.3 through 20.5 Dec 5 38 Current research: TBA Special assignment: Questionnaire 2 Dec 7 39 Final Class: Conclusions Date TBA Final Exam: Cumulative, 3-hour exam *These are some of past students favorite topics. **These are some of the most challenging parts of the course.
GRADING: Description Quizzes (your lowest 1 score is dropped: 4 remaining quizzes each contribute 11%) Final Exam (no substitutions) Homework: - Weekly responses: You are expected to do at least 9 of the 14. - Special Assignments - Self Tests: Complete all Self Tests online. Your final scores on all Self-tests will be averaged. Lecture Participation: Question Sessions (approximately 13 of these), and other activities. (your lowest 1 score will be dropped) Recitation: Practice quiz, activity, journal club, or attendance graded for each of 10 meetings (lowest 1 score is dropped) Percentage of Final Grade 43% 30% 7% 2% 9% 9% About the professor, Rachel Woodruff: I grew up in Texas, and got my PhD at MIT. When I was in college, I almost majored in Chemistry and History before choosing Molecular Biophysics and Biochemistry halfway through my Junior year. Ironically, I never took genetics as an undergrad! Now, I have been teaching at Brandeis for 4 years, and have taught genetics here 6 times (not including this semester). I love teaching here. Every semester, I learn more from my students. In addition to teaching, I like to play with my 2 young daughters, ride my bikes (only one at a time), and drink an excessive amount of tea. I hope you will come to my office hours and help me put a face, and a story, to your name this semester.