Biology 41005100 Advances in Agricultural Biotechnology Spring 2009 by nwr27961


									                                  Biology 4100/5100
                        Advances in Agricultural Biotechnology
                                     Spring 2009
                              Course outline - tentative
Instructor: Dr. Alicja Ziemienowicz
Office: HH120, tel. 8327155
Laboratory: HH129, tel. 3292628
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
+ biochemistry (Core and Prerequisites)
        - clear understanding of chemical structure, chemical reactions, functional groups,
        - 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

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.

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
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.

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