MOLECULAR TECHNIQUES FOR FIELD BIOLOGY
ZOO 4353/5353, Sec. 050, 3 credit hours
Slide Show from 2009 Class
Syllabus - PDF
This is an outline of the lecture, discussion, and laboratory activities planned for this intensive two-week course. Details on general classroom policies, what to turn in at the end of the course, and additional requirements for graduate credit are provided at the end of this syllabus. The class environment will be active, but informal. Please never hesitate to interrupt to ask questions or offer recommendations. Since many of the planned activities are complex or have multi-day components, we will almost certainly need to modify this schedule as we go along. That is part of the research process. If you have never had a lab class in which you had some noticeable degree of control or independence, this will be a pleasant new experience for you. But be prepared to be confused a little (or a lot!) from time to time. We sometimes let you wander about on your own for a while so you can learn what is needed to keep yourself organized. We believe you can learn by mistakes as well as by successes. We may even thank you for making a mistake that can help others learn what to do (or not to do). If you only feel comfortable in lab when you have specific minute-to-minute guidance, then be prepared to be uncomfortable. This will be an important experience in learning self-direction and laboratory independence. One guaranty is that it will be a learning partnership. If you take it half-heartedly, your performance assessment will disappoint all of us. The only way you can fail is by failing to take this learning partnership seriously.
General Background Reading: Articles from Scientific American: Evolution
For a literary experience: Sean Carroll, 2006, Making of the Fittest, W.W. Norton & Company, New York. [Note: These paperback copies are the property of Jim Thompson and are on loan for the duration of this summer session. Thank you.]
Week 1:
Monday, 24 May
Morning
Overview of the Course and Organization of Lab Manual
Introduction to Molecular Biology (L) Primer, Chap. 1
Biotech. Explorer, Appdx A
Introductory Laboratory
a. Introduction to major equipment
b. Safety
c. Use of pipettors
d. Practice loading of agarose gels
Overview of Molecular Techniques (L)
Afternoon
Protein Electrophoresis Avise, pp. 55-63
a. Introduction to techniques (L) Manual, A12 – A44
b. Cellulose acetate: Drosophila ADH Manual, A1 – A4
Protein Polymorphism in Natural Populations (L)
Tuesday, 25 May
Morning
Morning Meeting (D)
Introduction to Evolution (L)
Cellulose Acetate: Hemoglobin Manual, A5 – A11
DNA Electrophoresis Protocol Discussion (L) Manual, C15 – C16
Make an Agarose Gel for DNA Electrophoresis
Local “Field Trip”: Seining for Minnows
Afternoon
Set up DNA Gels:
a. lambda DNA
b. lambda/HindIII ladder
c. 1 kb DNA ladder
Cellulose Acetate with Minnow Tissues
Staining and Examination of DNA Gel
Wednesday, 26 May
Morning
Morning Meeting – Protein Polymorphism and Genetic Distance (L)
Avise, ref. pp. 107-110
DNA Electrophoresis and Restriction Digestion Protocol Discussion (L)
Avise, pp. 67-78
Manual, B1 – B27
Set Up Restriction Digests of Unknowns Manual, C12 – C14
DNA Isolation Protocol Discussion (L) Manual, C1 – C8
Begin DNA Isolation of Drosophila Genomic DNA
(complete up to 30+ min incubation-on-ice point)
Set Up DNA Gels to Run Digests
Afternoon
DNA Isolation (continued)
Stain and Photograph DNA Ladder Electrophoresis Gels
Individual Projects (All organism materials must be approved before collection begins.)
Thursday, 27 May
Morning
Morning Meeting: Data Interpretation (e.g., estimating DNA fragment sizes) (L)
Turn in Title of Paper to be Discussed in Class
Introduction to Population Genetics (L)
Run Gel on Drosophila Genomic DNA
Afternoon
Individual Projects
-- Including Isolation of Genomic DNA from Organisms of Choice
Discuss Assigned Journal Article (Group Reading #1) (D)
Friday, 28 May
Morning
Morning Meeting (D)
Contrast Nuclear and mtDNA Isolation Protocols (L) Manual, C24 – C28
Discuss DNA Isolation Using Commercial Kits (L) Manual, C6 – C7
Collect Tissue from Individual Project Organisms and Discuss
Kit DNA Isolation Protocol
Afternoon
ADH Allele Survey from UOBS Population
Hardy-Weinberg (continued): Effects of Deviations from H-W Assumptions (L)
Finish Kit Isolation of DNA
Individual Projects
Week 2:
No Class on Saturday, Sunday, or Monday (Memorial Day)
Tuesday, 1 June
Morning
Morning Meeting: Review Earlier Techniques (D)
Discuss PCR Protocol and Supporting Articles (D) Avise, pp. 87-92
Manual, C21 – C23, C29
Set Up PCR for white
Run Gel on DNA Isolated by Kit
Isolation of Individual DNA Samples for PCR and Sequencing
Set up Electrophoresis of DNA Markers for Southern Blots
Afternoon
Discuss Southern Blot Protocol (L) Manual, C17 – C20
Set Up Group Southern Blots
Generating Restriction Maps (L)
Digest white PCR Product
Set Up PCR for Segregation Distortion (SD) to Run Over Night
Individual Projects
Wednesday, 2 June
Morning
Morning Meeting: How to Make a Phylogenetic Tree (D)
Change Paper on Group Southern Blots
Set Up Gels for white PCR Digest and SD PCR Products
Introduction to Conservation Genetics and Applying Molecular Techniques to Population
Problems (L and D)
Individual Projects
Afternoon
Set Up PCR for Microsatellites
Individual Projects
Discussion of Assigned Journal Article (Group Paper #2) (D)
Thursday, 3 June
Morning
Morning Meeting (D) Avise, pp. 84-87, 92-104
Discussion of DNA Sequencing and Other Techniques (L)
Stain and View Southern Blot Gels
Run Gel on Microsatellites
Afternoon
DNA Fingerprinting (D)
Set Up Additional PCR (optional)
Individual Projects
Friday, 4 June
Morning
Morning Meeting (D)
Complete Analysis of PCR Results (D)
Discuss: Carroll, Making of the Fittest
Individual Projects
Afternoon
Begin Individual Presentations of Research Article (T)
Complete Individual Projects
Clean Lab Area and Begin Packing Lab Equipment
Saturday, 5 June
Morning
Complete Individual Presentations (T)
Final Discussion and Overview of the Course (D)
Turn in Package of Materials To Be Evaluated; Evaluations Must Be Completed by
Either Jim Thompson or Ron Woodruff Before You Leave
The program will be concluded at 12:00.
Key:
L = lecture
D = discussion
T = student talks
Other periods are primarily laboratory time.
Protocols in this guidebook have been derived from many sources, which should be clear from the copied material. Molecular Cloning: A Laboratory Manual by J. Sambrook and D.W. Russell (3rd edition, 2001. CSHL Press, Cold Spring Harbor, NY) is an excellent general source. Others will be available for your use in class.
Other Important Course Information
All students are responsible for knowing and following proper laboratory safety practices and safety rules at all times. This includes following guidelines prohibiting eating or drinking during lab or wearing contact lenses during class periods in which volatile chemicals and preservatives are in use. The safety rules and fire exit procedures are posted in the classroom.
Any student in this course who has a disability that may prevent him/her from fully demonstrating his/her abilities should contact me personally as soon as possible so we can discuss accommodations necessary to ensure full participation and facilitate your educational opportunity.
The OU Academic Misconduct Code is available as a link from the Provost’s student academic integrity page, www.ou.edu/provost/integrity. In 2004, UOSA adopted an Honor Pledge, “On my honor, I affirm that I have neither given nor received inappropriate aid in the completion of this exercise.” Each student should be aware of the University regulations in regard to cheating on class examinations or other work. It is also important to understand the various kinds of plagiarism, all of which will be considered forms of cheating. Additional information about such things as what constitutes plagiarism and the advantages and limitations of using internet sources will be discussed in class. Any instance of cheating will be dealt with seriously, under the guidelines set out by the University. I sincerely trust that this will not be necessary.
Molecular Techniques for Field Biology
What To Turn In at the End of the Course
1. Summary of Individual Projects
A. "Diary" style summary of protein and DNA results and your interpretations
B. Drawings and/or original plates to illustrate your results
(Cross-reference to your samples on another person's plates (we expect you to share lanes on plates); this can be done easily by having each person number the plates sequentially and use these numbers to reference data in the notes)
2. Problems and Unknowns
A. Restriction Digest Unknowns: your interpretation and explanation, including your estimates of each fragment size
B. Protein Polymorphism Data Set: calculation of levels of polymorphism and average heterozygosity for examples provided
C. Restriction Mapping Problem and Other Problems as Assigned During the Session
3. Journal Article Presentation
A. Prepare a 1-3 page handout that includes:
1. Authors, date, title, source (journal name, volume, and inclusive page numbers)
2. Brief summary (or photocopy the article abstract)
3. Key figures and tables that can be used by each person to follow your presentation
4. Note: These handouts will yield a set of 12 useful journal article summaries on which you can take notes
during a presentation and then refer to in the future when you need examples of research in this field.
B. Prepare a written outline of your presentation, using any style you choose. This will be the set of lecture notes from which you will give your talk. But during your presentation, you should know the material well enough that you can use your notes for quick reference but still talk through the study rather than read your notes. For students enrolled for graduate credit, a formal paper summarizing and critiquing the research article will also be required. Guidelines for its format will be provided individually.
C. PowerPoint Talk: Your presentation of the journal article to the class is important. You should plan to spend 15-20 minutes providing an introduction to the question studied by the authors, an outline of their methods (although we do not expect tedious detail -- we can help guide your planning of this if you want to ask us), and most importantly a detailed discussion of their results and conclusions. The results should refer to specific data in tables and figures and their interpretation. Any ideas you personally have for improving or expanding upon the study will also be welcome. The PowerPoint presentations should be transferred to a ZIP disk or memory stick so all are loaded onto the same computer to be used during the presentation sessions.
4. Finally, in all appropriate sections, critique your own performance and results. What did you learn from the experience and what, if anything, would you do differently next time to improve?
Massive length is neither expected nor needed, but it is important that you think about what you did and what it means. You will not be graded to any significant extent on whether your data look great or your gels are beautiful. You will, however, be evaluated on your involvement and attempts to learn and improve. There is no reason to put this off until the last minute. Good students (and we know all of you are good students) will want to develop this written critique/diary as you go along. In addition to making the learning experience richer, this will keep you from having a heavy project to complete at the end of the course. We have no doubt you are motivated to excel, and we look forward to helping you do so. The full collection of written work must be reviewed by either Jim Thompson or Ron Woodruff on Saturday before you leave.
James Thompson, Jr.
University of Oklahoma
Department. of Zoology
314 Richards Hall
Norman, OK 73019-1024
Phone: (405) 325-4821 or 2001
Fax: (405) 325-7560
Bio page: faculty-staff.ou.edu/T/James.N.Thompson-1.Jr/
Ron Woodruff
Bowling Green State University
Department of Biological Sciences
417 Life Science Building
Bowling Green, OH 43403-0001
Phone: (419) 372-2332
Fax: (419) 372-2024
Bio Page: www.bgsu.edu/departments/biology/people/faculty/woodruff/publications.html
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