1 BIO 4174: TOPICS IN BIOTECHNOLOGY PROFESSOR: Dr. D.A. Johnson. E-mail : djohnson@science.uottawa.ca. Office: MCD 338L Lab: GNN 222 SCHEDULE: (September 5 - December 2) Tuesday 13:00-14:30 CBY B012 Thursday 11:30-13:00 CBY B012 COURSE OBJECTIVES FOR 2002 "Topics in Biotechnology" is a lecture/seminar course designed to introduce you to Biotechnology from the basic to the applied. The basic techniques used in molecular cloning will be described during the introductory lectures along with examples of how the technology is used. More advanced work will be introduced during student seminars and by guest lecturers. By the end of the course you should be able to 1. Understand the basic cloning strategies and why they are used; 2. Understand some examples of how more advanced techniques are used to identify and isolate genes; 3. Through the seminar programme, have gained an appreciation for a broad range of research areas within biotechnology and some aspects of the business of biotechnology. 4. Each year we focus on a special topic. This year s topic is transgenics. Several invited speakers will talk about the impact of transgenic technologies in plants and animals. COURSE FIGURES CAN BE DOWNLOADED THROUGH http://www.uottawa.ca/academics/online/index.html MARKING SCHEME ( Beginning on page 2 the marking scheme is explained ) Midterm examination 25% Seminar or Essay or Review** 25% Seminar Participation (reports) 5% Examination, Take Home ( December 2002) 45% ** Due to the high enrollment in 2002, the number of seminars in limited to 16. Students not giving seminars will be required to write an essay of write a review.
2 ATTENDANCE Please be aware of the Faculty regulations concerning absences from examinations and other tests as described on pp 4-5 in the 2001-2003 Faculty of Science calendar. It is the policy of the Department of Biology that these regulations are enforced and that this policy be explicitly stated in the course outlines. PLAGIARISM Students should be clear as to the meaning of plagiarism. You may copy a short section of one or two lines from another publication if the material copied is in quotation marks and referenced. If you copy extensively or without attribution, this is PLAGIARISM and will be heavily penalized. The penalties may include total loss of the mark. For a general discussion on what is acceptable, look at the Faculty of Graduate and Postdoctoral Studies website ( http://www.uottawa.ca/plagiarism.pdf ) COMMENTS CONCERNING THE COURSE MATERIALS AND MARKING SCHEME 1. When presenting material, the majority of the work chosen must be published within the last 3 years. Read the literature! There are biotechnology-oriented journals that can be read, e.g., "Trends in Biotechnology", "Biotechnology". Most molecular 'journals will have relevant material. Also there are relevant books in the library, many purchased within the last year. And there is the INTERNET! 2.THE MIDTERM EXAMINATION The examination will be limited to the material covered in the lectures. It is a normal examination in that you will be asked to recall material from the lectures and use it to solve problems. There will be choice. A typical short question is. ddrt-pcr displays differences on a sequencing gel. What is the origin of these differences? 3.THE SEMINAR (LIMITED TO 16) The seminar will give an overview of the subject designed to familiarize the intelligent audience with the topic while at the same time describing a few chosen experiments at the cutting edge. I am testing both your breadth and depth on the topic! Your one page abstract will be followed by a list of key references. By the end of the seminar the audience will have answers to questions such as "why is this important?", "how can biotechnology help to solve these problems?", "do their experiments justify their approach and optimism?", "where is the field going in the future", AND "what is going on in Canada?". Seminar topics are listed beginning on page 6.
3 The audience will also have additional questions or comments for you following your presentation (5-10 minutes). If our schedule is crowded, we may need to limit questions. Your mark will suffer if you take up more than 30 minutes (aim for 25 and time yourself), if you do not answer these 5 questions or if you read your seminar from the overheads (acetates). An abstract for your seminar is due October 11, 2002. If you have not given seminars before (or even if you have), I suggest you read a compilation of hints from the Biology profs that can be found at the end of this document. 4. THE ESSAY(LIMITED TO 20) For many of you, fourth year is first time you will have been given formal essays to write. Listed below, we have tried to offer some ideas about how to organize an essay. The most important advice we could offer is to begin immediately, choose a topic and write an abstract and an outline. You may use the outline as a guide to the writing of the essay itself (see number ii. below). Having an outline will help you to think about the topic, to formulate questions and to answer them. Some students find it beneficial to divide the essay into sections, others have used the "one page summary" technique. For this approach, try to write one sentence which summarizes the arguments in each paragraph of the essay and then read this new "mini-essay" to determine whether it makes sense. If it does not, then the original version probably does not either. After you have written a draft, take time to edit the document. Check the spelling. Add page numbers. Does it make sense? The essay will include the following elements: i. COVER PAGE: You will include the Title, with your name and student number. ii. ABSTRACT: You will be required to provide a ONE page ABSTRACT and a ONE page OUTLINE (similar to a table of contents which divides your essay into sections and, in point form, lists what you will describe) of your essay. We will read them for corrections and/or suggestions and return them you for improvement. They may be used as a guide to the writing of your essay and to how we mark. Return BOTH the original copy OF THE ABSTRACT and the improved version with the rest of your essay. We will also comment on the outline but this does not need to be corrected or returned. It is intended to make you think before you write. iii. TABLE OF CONTENTS
iv. INTRODUCTION: introduce the area of research and the importance of the paper within the framework of the area of research. Relate to topics discussed in class. End this section with a statement indicating what the paper attempts to prove. v. A DESCRIPTION of the paper: briefly describe the methodology and results. You may draw your own Figures or refer to ones in the paper ( eg. see Figure of the paper on page ). Drawing your own figures e.g. to describe the assay systems used, really forces you to understand the methodology. For experiments which you think are the ones central to understanding the paper and which you chose to describe, stress what was the objective, how the experiment was done and the conclusion(s) which can or cannot be drawn. This is rarely done in student essays but can be crucial to understanding the paper. vi. CONCLUSIONS: the most important section. Summarize the results and analyze the paper. Did the authors really demonstrate what they stated? vii. FUTURE RESEARCH: If you were to continue to research this area what would you do NEXT, how might you do it, why is this next step important and what results might you expect to find. Start by writing an hypothesis that you would test. viii. REFERENCES: Only include papers which you have read. Use any format found in one of the journals but include the title of the publication. ix. PUBLICATION: Include copies of up to two key publications. In recent years, these suggestions have been correlated with an increase in the quality of the writing. It should not be too surprising that this has lead directly to an increase in the average mark. For those of you who are still unsure as to what is an excellent essay, we have examples on file. You may read them. The essay will be about 15 pages (excluding Title Page, Abstract, Table of Contents and References), typed, paginated, double-spaced with 2 cm margins and with print size of 12 point. The essays will NOT be returned, however, you may come to discuss your essay and its marking. Essay topics are listed beginning on page 6. The Abstract and Outline Are Due on October 11. 4
5 5. THE REVIEW The review is similar to the essay but does not focus on a narrow topic. You should discuss suitable topics with me but some suggestions are i. Are GMO foods safe? ii. The tale of the butterfly and BT corn. What can we conclude after the science? iii. The tale of the deadly potato. What can we conclude after the science? iv. Do GM crops really reduce pesticide usage? v. Biotechnology in Ottawa, what s really going on? Can it succeed? 6. SEMINAR PARTICIPATION (REPORTS) The Abstract is Due on October 11. The audience will participate in the seminar too! For ONE of the seminars per session, you must answer the same five questions listed above-as if you were a journalist reporting on the speaker. Your less than 1 page submission must be sent to me by E-mail before 16:30 on the Monday following the seminars. You Are Also Required to Prepare a Report on All External Speakers. 7. THE FINAL EXAMINATION The examination will be taken from a list of questions that I will distribute by the end of October. Work on them in advance! To do them properly, you will need the material in class, your expertise from previous courses and your hard work and imagination. On December 3, I will select the questions that will constitute the exam. They will be posted outside of my office and sent by E-mail. THIS MEANS THAT I COULD, AND WILL, ASK YOU TO ANSWER QUESTIONS NOT SPECIFICALLY ADDRESSED IN CLASS! There is no single correct answer to any of the questions. You will be marked on your ideas, your research plan(s) that you use to implement your ideas, the experiments that you propose to test or validate your ideas and your proposed analysis of the data that you would collect. A typical answer would be about 5-6 double-spaced, printed pages. You may add figures or flow charts as you think necessary. In the past I have received some excellent answers. Finally after 3 years, someone is asking you to think seriously about scientific problems.
6 BIO 4174: TOPICS IN BIOTECHNOLOGY IMPORTANT DATES TO REMEMBER 1. ON OR BEFORE 17:00, SEPTEMBER 27, 2002: Your choice of the topic for your seminar (16) or the essay (20) or review is due (STATE WHICH ONE!). You must include at least one reference. Send the information to me via E-mail. 2. ON OR BEFORE 17:00, OCTOBER 11, 2002: A completed Abstract for the seminar or essay or review is due. Your Abstract will include your name, the title, the description of the material you intend to present (<200 words) and two up-to-date references. You must submit the Abstract to me by E-mail. 3. MIDTERM EXAMINATION, TUESDAY OCTOBER 29, 2002: The examination is worth 25% of your final mark and covers the material described in class. 4. NOVEMBER: Scheduled seminars worth 25% of your final mark. There is a participation mark, worth 5%, based upon your reports. 5.NOVEMBER 22: All written work (essays or reviews) is due. 6. FINAL EXAMINATION, DECEMBER 2002: The examination is worth 45% of your final mark and may cover material NOT described in class. It is due December 10. This time hand in a paper copy. PENALTIES 1. The Late Penalty for Missing a Deadline is 10% of the Assigned Mark per Working Day, i.e., an Abstract that is One Day Late Will Reduce the Maximum Mark to 22.5. 2. The Penalty for Not Sending in a Seminar Report (Student and External Speakers) is 0.5 Marks. DO NOT SEND IN A REPORT UNLESS YOU ATTENDED THE CLASS! BIO 4174: TOPICS IN BIOTECHNOLOGY
This list is not an exhaustive one, but outlines some general suggestions for your seminar and poster topics. Once a topic has been chosen and registered, then a schedule will be prepared. Register your choice ( and a second in case it has been chosen) by E-mail to djohnson@science.uottawa.ca SEMINARS WILL BE PRESENTED IN THE ORDER THAT THE TOPICS ARE LISTED! MEDICAL BIOTECHNOLOGY M-1. Germ line therapy in animals. M-2. Human somatic gene therapy. M-3. Vaccine production using recombinant techniques. M-4. Production of blood products by genetic engineering. M-5. Synthetic oligonucleotides: potential as therapeutic agents. M-6. Production of human hormones. M-7. Antisense RNA or RNAi and its use in medical therapy. M-8. Growth factors and wound healing. M-9. Alternative forms of immunization ( e.g. DNA, bacteria). M-10. Biomaterials. M-11. The human genome project. M-12. Carbohydrate technology. M-13. Genetic diseases: detection, gene cloning. M-14. Towards a rational drug design (protein or DNA level). M-15. Anti-pregnancy vaccines. M-16. Intracellular immunization in animals. M-17. Animal systems as models for the study of disease. M-18. Ribozymes. M-19. Antibodies and their use in therapy. M-20. Molecular approaches to the study of parasitic diseases. AGRICULTURAL BIOTECHNOLOGY A-1. Transgenic plants as a vaccine source-edible vaccines. A-2. Molecular assisted breeding strategies. A-3. Insect control. A-4. Freezing (salt, heat, water) tolerance in plants. A-5. Improving plant nutrition. A-6. Biotechnology and the forestry industry. A-7. Herbicide resistant plants and their use in agriculture. A-8. Control of fruit ripening. A-9. "BIOPharming"-transgenic plants expressing pharmaceuticals.. A-10. "BIOPharming"-transgenic farm animals expressing pharmaceuticals. A-11. Plants as Chemical Factories(plastics, oils, chemicals). A-12. Engineering improved pest (pathogen) resistance in transgenic plants. BIO 4174: TOPICS IN BIOTECHNOLOGY IMPROVING TECHNOLOGIES 7
8 I-1. Metabolic engineering. I-2. Improved synthesis of antibiotics. I-3. Combinatorial chemistry I-4. Chips for measuring gene expression. I-5. DNA fingerprinting-forensic analysis. I-6. Proteins from bacteria living in extreme environments. I-7. Protein engineering: improving enzymes. I-8. Heterologous regulation systems. I-9. Production of antibodies in bacteria. I-10. The production of fuels from waste. I-11. Maximizing the expression of foreign proteins. I-12. Improved drug delivery systems eg. liposomes. I-13. New sources of drugs or antibacterial agents e.g. frogs, insects. I-14. Computers in genomics. I-15. Biotechnology and the food industry. 1-16. SNPs and designing drugs for individuals. ENVIRONMENTAL TECHNOLOGIES E-1. The release of recombinant organisms: environmental aspects. E-2. Molecular techniques in conservation biology. E-3. "Bioremediation": engineering of bacteria for waste control. E-4. Phytoremediation: use of plants to control toxic metals or chemicals. E-5. Identification of individuals, populations and species. E-6. Insect control by recombinant means. OTHERS O-1. Toxicity testing: alternatives to animals. O-2. Biotechnology: legal and regulatory aspects. O-3. Biotechnology and the recovery of minerals e.g. Phytomining or the use of bacteria. O-4. Ethics of mass screening programmes. O-5. BIO-Fear and GMOs. There are hundreds of possible topics to stir your imagination (and thicken your wallet). Therefore we will allow you to pick "a topic of your choice with permission of instructor". Or why not take a contrary position? THE ORDER OF PRESENTATIONS WILL BE THE ORDER IN THE LIST!
9 BIO 4174 SCHEDULE FOR 2001 For 2002 the focus will be How can we use transgenic organisms (This is a PRELIMINARY SCHEDULE and subject to change. Updates may be distributed by E-mail) Update : August 6, 2002 Sept 17 Sept 5 Introduction Objectives Marking Scheme Role of Computers Sept 19 Sept 10 Basic Cloning Methods I: Plasmid Vectors in vitro and in vivo Sept 24 Sept 12 Basic Cloning Methods II: From 8 to YACs, HACs and BACs Sept 26 Advanced PCR Techniques Oct 1 DNA MARKERS: RFLPs, RAPDs, AFLPs Oct 15 Advanced PCR Techniques Oct 3 POSITIONAL CLONING I: Linking Molecular and Genetic Data. Oct 17 Gene Hunting Oct 8 POSITIONAL CLONING II: Identifying THE GENE Oct 22 Gene Hunting Oct 10 Dr. S. Molnar Molecular Mapping Crop Plants Oct 24 Functional Genomics: CHIPs and SAGE Functional Genomics: Tn s and Interactions Dr. D. Simons Transgenic Plants Dr. C. Martin Transgenic Fish Oct 29 Midterm examination Oct 31 Dr. D. Gray Transgenic mice Nov 5 Nov 7 Nov 12 Nov 14 Nov 19 Nov 21 Nov 26 Nov 28:
10 SOME WEB ADDRESSES OF INTEREST: BIO 4174: TOPICS IN BIOTECHNOLOGY Site Databases GenBank DDJB - DNA Data Bank of Japan EMBL - European Molecular Biology Laboratory Bioinformatics EBI - European Bioinformatics Institute Canadian Bioinformatics Resource URL http://www.ncbi.nlm.nih.gov http://www.ddbj.nig.ac.jp/ http://www.embl-heidelberg.de/ http://www.ebi.ac.uk/ http://www.cbr.nrc.ca/ Biotechnology/Employment InfoBiotech Canada http://www.ibc.nrc.ca/ibc/ Biotech Info (Ag/USA) http://www.nal.usda.gov/bic/ BHRC Home Page http://www.bhrc.ca/english/index.html The Biotechnology Human Resource Council Ottawa Life Sciences Council http://www.olsc.ca/ News and newsgroups BioMedNet BIOSCI (News Groups) Patent Information US Patent and TradeMark Office Canadian Intellectual Patent Office Access to on-line journals NCBI/Entrez (some available) HighWire Press BioMedNet (free membership) Electronic journals U.of O. Interlibrary loans U. of O. http://www.bmn.com/ http://www.bio.net http://www.uspto.gov/ http://strategis.ic.gc.ca/sc_mrksv/cipo/ http://www.ncbi.nlm.nih.gov/entrez/ http://highwire.stanford.edu/lists/freeart.dtl http://www.bmn.com/ http://www.uottawa.ca/library/ej.html (For hard copies) http://www.genengnews.com/top100.asp The top 100 Biotechnology Sites
11 What Makes a Good Seminar? Organization -should be straightforward and logical -include a brief introductory summary of what will be covered -provide sufficient background to help the audience understand the relevance of paper -use lots of visual aids (flow charts are often useful, esp. for methods) -at the end, recap main findings with conclusions and take-home message * Clarity -speak clearly and audibly -make the objectives and rationale clear; state them at the outset -relate the work to the larger context -make it understandable to the non-experts -provide a clear take-home message (taking no more than a few sentences) -be sure you understand the work Visual aids -use text slides to summarize major points * -use diagrams to illustrate protocols/results; if necessary redraw them (photocopies from articles are generally too small)* -slides (overheads) should not be too cluttered * -details large enough to see clearly (font size 24 pts. minimum) -talk to the slides, doesn't read from them -slides should be left up long enough for the audience to read Content -make sure there is sufficient review of background material -be selective in the material you present (every detail of a paper need not be presented) -provide enough material for the audience to follow, but don't bore them with trivial details -emphasize what you feel are the major points -evaluate the material critically; don't be afraid to offer alternatives to interpretations of the authors Delivery -give your presentation a trial run to see if it is too long or short -do not read or recite from memory -avoid nervous mannerisms -show enthusiasm for the topic -try to provoke questions and discussion -be prepared to respond to questions * points we feel, from previous experience, deserve particular attention.