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MOCB 630 Fall 2004 |
| MOCB | CBMG | Textbooks | Syllabus | Library |
| WebCT | NCBI | Model Organisms | Bioinformatics | Steve Mount |
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Homework, Handouts, Papers, etc.. Homework and handouts
Quiz answers
Textbooks Hawley and Walker Scott Hawley and Michelle Walker: "Advanced Genetic Analysis: Finding Meaning in a Genome." Required. The only book I could find that covers several important topics addressed in this course. Hartwell Hartwell, Hood, Goldberg, Reynolds, Silver and Veres: "Genetics: From Genes to Genomes." This book provides important background on each of the model organisms.
Miscellaneous readings Steve
Mount |
Note: This page is from the Fall of 2004, which is the last time MOCB630 was taught. The graduate curriculum for MOCB and CBMG is being changed. MOCB 630 is being replaced with a two-course sequence to be taught in the Spring. It will be two 2 credit courses, each spanning half the semester (4 credits altogether, but they can be taken separately). The first (CBMG 688F) will emphasize gene expression and will be taught by Jon Dinman. The second (CBMG 688I) will be advanced genetics and willl be taught by Steve Mount. These courses are being scheduled for Tuesdays and Thursdays 4-6.. ----------------------------------------------------------------------------- Instructor Steve Mount smount@umd.edu 301-405-6934 Meetings MWF 9:00 PLS 1117. Aug. 30 . through December
10. Prerequisites: Readings 11 papers from the primary literature in molecular genetics are required reading. Papers and supplemental readings will be on available online; I will provide links through the course web page (this page). They will be listed on the syllabus at the beginning of the term, and individual papers can be downloaded through links on the left panel and syllabus sections that should appear several weeks in advance. Texts and background literature To be purchased: - Hawley and Walker Advanced Genetic Analysis: Finding Meaning in a Genome. 2003. required. A WebCT page has been requested for this course. WebCT will be used for posting grades and for answering questions. I like to address questions in writing so that I can disseminate my answers to the entire class. Post your question directly to WebCT or send your question to me at smount@umd.edu, in which case I will generally remove your name and post my answer so that everyone can see the question and its answer. Please tell me if are asking a question that you don't want to see posted. Permission is required for this course. The class had only two open slots as of Aug. 30. After those slots are filled, only Ph.D. students in the MOCB or CBMG programs will be granted permission to oversubscribe. The policy is explained in detail at www.life.umd.edu/classroom/MOCB630/permissions.html . Keeping the class small is important for the paper presentations. Coverage. Methods of genetic analysis in various species commonly used for molecular genetics (model organisms) will be discussed. The primary species are the yeast Saccharomyces cerevisiae, the worm Caenorhabditis elegans, the plant Arabidopsis thaliana, the fruit fly Drosophila melanogaster, the mouse, and humans. For each species we will consider methods for the identification of informative mutations revealing new genes or new gene functions. We will also discuss methods for testing the expression of modified genes, usually by genetic transformation of organisms. We will bear in mind throughout the application of information from model organisms to organisms which are not among this select group. The course will also involve a great deal of information about gene expression, cell biology and development (especially gene expression). These topics will be woven into a survey of methods for genetic analysis. Grading Your grade will be determined as described below. +/- grading will be used (i.e. grades of A+, A-, B+, C-, etc. are possible). In general, you will not be directly tested on the lecture material except as it applies to the papers, or is reflected in the homework. You are encouraged to write the Honor Pledge on your assignments (see www.jpo.umd.edu/aca/honorpledge.html). I encourage you to work together to prepare your presentations and to discuss the papers and homework, but you are expected to prepare your own homework and you are responsible for your own answers. Papers The goal is to learn how to extract from a paper: - what claims are being made - how the results were obtained (i.e. which experiments were done) - why the experiments were done the way they were - whether the data justify the conclusions and what caveats remain - why these experiments were done at all; and why we should care On the date that a paper is to be discussed, come to class familiar with the paper, and with a copy of the paper in hand. Your familiarity with the papers will be judged by your presentations, your contributions to the overall discussion, and by your grade on quizzes. Presentations (25%) When papers are covered in class, I may call on you to present a defined section of the paper (usually one figure, or a part of a figure). Your presentation will be graded based on the clarity with which you cover the following four things: Many of the presenations will be given a specific time limit (e.g. 5 minutes), and you will know this in advance. I will give you a grade on a your presentation and a summary by email after class (within a few days). Everyone is subject to being called on at every paper presentation, except that you will be called on only once for a single paper, and you are exempt from presentation on the very next paper. For example, if you are selected to present a figure in paper 2, you will be exempt from presentation for paper 3. This will exempt you from presentations on that day, but not from quizzes. Those scheduled to present on a particular day will be informed at the beginning of class. The selection of students for presentation will be essentially random except that I will insure that everyone presents at least two times during the course of the semester, and you can be removed from the list (if you want to be), when and if you have presented four times. Figures assigned to specific presenters chosen for the first day of a paper scheduled for presentation over two days will be reassigned if they are not presented. Those who present on the first day will be removed from the pool for the second day and for the next paper (but will not be exempt from quizzes). Quizzes (40%) A quiz may be given on a paper on presentation day. In some cases, there may be a brief quiz before our discussion of the paper. In other cases, the discussion may be replaced by a full one-hour quiz, or the quiz will come at the end. Some quizzes will count more than others. This weighting will be reflected in the total number of points in the quiz. Discussion (10%) Contributions to the discussion that aid everyone's understanding of the paper will help your grade. Good questions are especially encouraged. I will never grade anyone down for asking honest questions about the paper. Homework (25%). Homework will be assigned at least four days (two class meetings) before the due date. Homework is due at the beginning of class. In many cases, homework questions will direct your reading to essential points of the paper. However, not all papers will have homework, and not all homework will be specifically related to a paper. There will be about 14 homework assignments, each of which will count 20 points. Your lowest four grades (including any not turned in) will be dropped before averaging. Whether or not I accept late homework, and how much it is discounted, will vary depending on many factors, including whether the homework was discussed in class before the late homework was turned in, and why it was not turned in on time. Each of you will be assigned a gene by email or WebCT. I will send you the accession number for the yeast version of the gene, and you will be required to answer questions about that gene and its homologs in other species on subsequent homework assignments. At the end of the year, the overall scores for homework and quizzes will be normalized before summing. Presentation grades will be averaged as is. I generally give roughly equal numbers of A's and B's and only a few C's, but I do have a sense of what it takes to get an A that is independent of your performance relative to the rest of the class. Being there! Evaluation during class when papers are presented will count for 75% of your grade. You should be sure to attend class on those days. If you must be absent from class on days when papers are presented (dates in bold on the syllabus) you should let me know (by email or telephone) and explain your absence. If there is a legitimate reason why you cannot present on a particular day, you will be taken out of the pool. If you are assigned a presentation and are not present, or decline to present, you will be given a presentation grade of C. In the case of conflicts that you know about in advance, try to let me know as soon as you know that you will be missing the class. Unanticipated absences (e.g. car trouble, traffic, oversleeping) will be dealt with on a case-by-case basis; but explain your absence as soon as you can, regardless of what you hear from other students about what transpired in class. The exact time of your email or voicemail message will be noted. If you simply want to be excused from a particular paper, you can be taken out of the pool for one paper in exchange for a grade penalty equivalent to one-third of a grade (e.g. A- instead of A, or B+ instead of an A-) on another presentation. You must ask for this before the assignments are made (by email or voice mail [x5-6934] prior to 8:30 a.m., or when I arrive at the room). This will exempt you from presentations on that day, but it will not exempt you from quizzes. Appointmnents outside of class: I will normally be available immediately after class. We can chat in the hall or walk back to my office. I am also happy to set up an appointment to meet with you at other times. Please send an email after consulting my online calendar. WebCT will be used for posting grades and for answering questions. I like to address questions in writing so that I can disseminate my answers to the entire class. Post your question directly to WebCT or send your question to me at smount@umd.edu, in which case I will generally remove your name and post my answer so that everyone can see the question and its answer. Please tell me if are asking a question that you don't want to see posted. 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