Biology 4100/5100 Advances in Agricultural Biotechnology Spring 2009 Course outline - tentative Instructor: Dr. Alicja Ziemienowicz Office: HH120, tel. 8327155 Laboratory: HH129, tel. 3292628 Email: email@example.com Office Hours: Open. Students are advised to first arrange an appointment via Email or phone. Alternatively, you may also drop by my office/lab weekdays from 12:00 a.m. to 2:00 p.m. Lectures: Tuesday and Thursday in room UH E575 Section A: 3:05 - 4:20 pm Course Description and Rationale: This is course is designed to be a capstone course for the Agricultural Biotechnology program at the University of Lethbridge. Senior students will be exposed to recent and advanced aspects of molecular biology and biotechnology related to agricultural applications through critical reading, discussions and seminars on current research problems in these areas. Specific Objectives: Students in this course will: • expand their working vocabulary and knowledge of agricultural biotechnology, • develop an in depth appreciation for specific topics in agricultural biotechnology • develop oral and written communications skills • apply information learned in the classroom to real life problems. Expected Background: + cell biology (Core and Prerequisites) - clear understanding of cellular structure, function, reproduction and regulation + diversity of life (Core) - clear understanding of taxonomy, systematics and current classification systems + ecology (Core) - a basic understanding of ecosystems; the interactions between organisms and their environments + biochemistry (Core and Prerequisites) - clear understanding of chemical structure, chemical reactions, functional groups, macromolecules - protein structure and function - enzymes - understanding of metabolic processes + genetics (Core and Prerequisites) - clear and detailed understanding of DNA and RNA structure and function - DNA replication, transcription, translation - clear and detailed understanding of gene structure function and regulation - clear and detailed understanding of genetic variation, including mutation, recombination - clear understanding of heredity and evolution Reference Material: Textbook: Glick, B.R. and J.J. Pasternak. 2003. Molecular Biotechnology: Principles and applications of recombinant DNA. 3rd edition. ASM Press, Washington D.C. Students are responsible for reading and mastering all the material in the chapters specified in the course outline. Course Website: detailed lecture notes and other relevant course material will be posted available to download at the Biology 4100A course website located at the University of Lethbridge, Web Tools, Class Web Sites for Spring 2009. Lecture notes covering each part of the course content will be posted in advance. However, it also means that the posted notes may not always present the final version of the lecture. GRADE COMPOSITION 10% - Homework (due January 29th, 2009) 12% - Minor Assignment 1 (due February 24th, 2009) 10% - Minor Assignment 2 (due March 12th, 2009) 15% - Midterm Exam 1 – February 3rd, 2009 15% - Midterm Exam 2 – March 3rd, 2009 20% - Seminar (oral presentation) 18% - Final exam – April 16th, 2009 ADDITIONAL IMPORTANT NOTES Students are responsible for mastering both the information presented in the lectures and the relevant assigned chapters of the textbook as well as the assigned additional materials (papers). Since this is a senior level course, the lectures will not cover every detail of every topic – they will rather highlight the most important aspects of the textbook chapters will also provide additional material from alternative sources. Therefore, attendance at all lectures is strongly recommended. A grade of zero will be assigned for any missed oral presentation, midterm or final exam unless a valid official excuse is provided. Supplementary exams will be given only upon presentation of a doctor’s certificate of illness dated on or before the date of the missed exam/presentation. No retroactive documentation will be accepted as valid excuse. GRADING SYSTEM Letter Grade Percent Grade Point A+ 91-100 4.0 A Excellent 86-90.9 4.0 A- 80-85.9 3.7 B+ 77-79.9 3.3 B Good 74-76.9 3.0 B- 70-73.9 2.7 C+ 67-69.9 2.3 C Satisfactory 64-66.9 2.0 C- 60-63.9 1.7 D+ Poor 56-59.9 1.3 D Minimal Pass 50-55.9 1.0 F Failure 49 or less 0 Homework and Minor Assignments: You will be required to complete two written assignments (5-10 pages) and one homework for evaluation. You will be notified of the written assignments/homework well in advance of due dates. These assignments will require you to address specific questions or problems on a relevant topic whereas the homework will require you to employ bioinformatics’ tools for gene cloning. The details of each assignment/homework will be posted on the class website. Your work will be evaluated for content, grammar, originality and style. You may not recycle assignments or research papers from other courses. Late assignments/homework will be accepted without penalty only if you have received prior approval from the instructor or in the case of an applicable official excuse. Prior approval is given only under exceptional circumstances and requires your written application giving detailed reasons at least 2 days in advance. Marks for late assignments/homework will be reduced by 20% of the total mark value for that assignment and for an additional 20% for each day (24 h) overdue. All written assignments/homework will be typed in a 12-point font on one side of the page with 1-inch margins and 1.5 line spacing. Oral presentations You will select a relevant research paper and lead the class in a discussion of this paper. You will have the entire class period on your assigned day to deliver you presentation and lead a discussion on the subject. It is up to you to decide on the most efficient way to use your allotted time. You may use any of a number of A/V aids in your presentation (e.g., handouts, overheads, Powerpoint). If you require special A/V equipment or aids please notify the instructor well in advance of your presentation. As the resource person you should also be prepared to answer any questions that may arise during the lecture. You will present your oral presentation during one of the predetermined slots on the lecture schedule. Assignment of lecture slots is on a first come first serve basis. Oral presentations missed without an official excuse or prior approval will be assigned a grade of zero. If you have an official excuse or prior approval, your oral presentation grade will be based on a written report and material (e.g., overheads) to be used for the oral presentation. Your work will be evaluated for content, grammar, originality and style. You may not recycle oral presentations or research papers from other courses. Midterm exams and Final examination The exams will cover the topics presented during lectures and seminars, as well as additional materials from the assigned book chapters and papers. Exams are non-cumulative. Attendance/Participation: Regular attendance and participation are critical to the success of this course. Students are expected to attend lectures regularly and take an active role in this course. Class participation will be assessed through contributions to class discussions and attendance. At the discretion of the instructors, final grades may be reduced by up to 10% for poor attendance (without an official excuse) and not participating in class discussions. Searching the Scientific Literature: It is suggested that you spend some time in the library reviewing research papers on the theme that interests you. You might start by searching through some of the journals in the library (Refer to list below). Alternatively, you may use electronic databases that are available through the U of L library. While you are searching the literature you should also be looking for appropriate background material that will help you understand papers of interest. This may often be found through reading the references listed in the reference section of a paper. Review papers are also an excellent place to start. As the name suggests, review papers provide the reader with an overview of the published literature on a particular subject. You will often find reviews published in journals such as those listed below or in journals specializing in the publication of reviews, such as the Annual Review or Trends in series (e.g., Annual Review of Entomology, Annual Review of Genetics, Annual Review of Microbiology, Annual Review of Phytopathology, Annual Review of Plant Physiology and Plant Molecular Biology, Molecular and Microbiological Reviews, Trends in Biotechnology, Trends in Genetics...). Your may find that some good references are not readily available in the library and an interlibrary loan will be necessary. Remember that interlibrary loans may take up to 2 weeks to receive, so start early!!!! Partial List of Peer Reviewed (refereed) Journals Applied and Environmental Microbiology Biochemistry Biotechnology Canadian Entomologist Canadian Journal of Animal Science Canadian Journal of Microbiology Cell Crop Science EMBO Journal Gene Genetics Insect Biochemistry and Molecular Biology Journal of Animal Science Journal of Bacteriology Journal of Biochemistry Journal of Biotechnology Journal of Dairy Science Journal of Insect Physiology Journal of Invertebrate Pathology Livestock Production Science Microbiology Molecular and General Genetics Molecular Microbiology Nature Planta The Plant Journal Plant Molecular Biology Plant Physiology Proceedings of the National Academy of Science Science Course Themes: Agricultural biotechnology covers a very broad selection of research areas. It would be impossible to cover all aspects of this subject. The material for the first half of the course has been established. The remaining one half of the course will consist of student presentations on selected topics decided upon during the first lecture. Tentative Lecture Topics and Schedule: Date Topic January 8 Introduction: Course and participant introductions. Discussion of course emphasis, topics and assignments. Section 1: Fundamental of Molecular Biotechnology and Agriculture January 13 - Lectures covering the basic methods, applications and ethics of gene cloning and March 3 expression in microbes, plants and animals. This section will also cover the major recombinant DNA technologies and molecular techniques used in cloning. (Assigned readings in Chapters 1 through 8 as well as a number of research papers) February 16-21 Reading Week – No classes Selected topics March 5 - Potential topics may include Antibiotic resistance, BSE, Crop diseases and April 14 strategies for control, Insect pests and strategies for control, Metabolic engineering, Nutraceuticals, Molecular pharming, Nitrogen fixation, Proteomics, Metabolic Engineering, Weed control strategies, Bioremediation, Whole animal cloning, Xenotransplantation, GMO food, legal and bioethical issues in agricultural biotechnology. .