BIO 440 Genetics Lab
Spring 2008
Dr. Mark S. Wilson
msw13/ 826-5557/ Office Sci B 222 / Office Hours: M/T/R
(2-3) W (12-1).
Course Description: The primary objective is for you to gain hands-on experience with fundamental techniques in Classical and Molecular Genetics. The breadth and depth of genetics is immense, and consequently the approaches that we will take are diverse. They include laboratory exercises with a wide range of organisms as well as significant use of internet-based analysis tools used by modern geneticists. Doing research can be exciting--in order to hopefully communicate some of this feeling, many of the basic molecular genetics projects that we will do have genuinely experimental components--tangents of ongoing research projects at HSU. 6 (+) hours laboratory/wk. Prerequisites: BIO 340
Textbook: None. Prior to each weekÕs lab, protocols, background, and discussion material should be downloaded from the BIO440 Moodle site
Lab Notebooks: You are required keep a three-ring binder as a lab notebook. This notebook is not a traditional research notebook. Instead it will consist of lab handouts, notes from the lectures, observations taken during the experiments, and calculations. Each experiment will have an 'observations and analyses' section that needs to be turned in.
Attendance: Is required and monitored --15 points will be deducted from that week's project for absences not pre-arranged with the instructor. Multiple absences will be penalized with increasingly larger deductions. In addition to being in the lab ON TIME, attendance includes being prepared, and remaining long enough to fully complete the work.
Quizzes: Before each lab session begins, you are required to have read the material that relates to that dayÕs exercise. By having pre-read the information, you can maximize the use of your in-lab time -- if you are not prepared, we will never be able to complete the exercises within the three-hour period. These quizzes will cover material that you are to have read for that dayÕs lab.
Exams: Exams will test your understanding of the material in a more extensive fashion than the quizzes. The first exam, on 1/31/08, will be focused on how to use dilutions and how to prepare solutions. Subsequent exams will cover the laboratory projects that we carry out.
Research Projects: You will research a contemporary topic in genetics. These can be focused on ethical legal or social issues, such as genetic privacy or the impacts of genetic technologies, or they can be focused on a new genetic approach or methodology. Alternatively, you may want to look at some aspect of the history of genetics. You will write a 6-10 page paper (double-spaced). Your initial submission (80 points) will be reviewed by two other students (10 points each), and your revised, final submission is worth 50 points.
Student Presentations: You will give a 15 minute Powerpoint presentation on a contemporary topic in genetics (as described above, in ÔResearch projectsÕ). This presentation may be developed from your research project or it may be on a new topic.
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Date |
experiment
(* denotes a quiz on that date) |
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1/22-24 |
Introduction to Molecular Genetics -bacterial culture and dilution plating Intro MolGen - isolation and spectrophotometric characterization of DNA |
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1/29 1/31 |
* Plasmid DNA isolation test 1 - solutions, dilutions - 60 points |
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2/5 2/7 |
* Transformation, student-designed transformation experiments Research Paper Discussion, Genome
Transplantation in Bacteria: Changing One Species to Another |
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2/12 2/14 |
* PCR I - determination of insert size in recombinant plasmids Agarose gel electrophoresis of DNA Research project - initial submission of topic – 1 paragraph |
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2/19 2/21 |
Gel Interpretation Genetics
Problem set handed out Plasmid purification using silica gel columns,
quantification |
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2/26-28 |
DNA sequencing and sequence analysis Bioinformatics I / Introduction to the National Center for Biotechnology Information |
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3./4- 3/6 |
* Human DNA isolation / PCR II - human DNA fingerprinting PCR product purification/quantitation haplotype
introduction |
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3/11-13 |
PCR II - human DNA fingerprinting – population genetics analysis |
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3/18-20 |
Spring Break |
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3/25 3/27 |
Human migration and human haplotype analysis RT-PCR / Research Paper Discussion |
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4/1- 4/3 |
Test 2 – 100 points * Southern hybridization/molecular cloning final research papers due Thursday |
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4/8-17 |
Southern hybridization/ – peer reviews due 4/17 Bioinformatics III – PCR primer design |
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4/22-24 |
Bioinformatics IV Serial Analysis of Gene Expression Bioinformatics V
Microbial Genomics |
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4/29-5/8 |
student presentations Research project – revised submission due 4/30 |
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5/15 |
final exam 100 points 10:20 – 12:10 Thursday |
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Due Dates for Laboratory Assignments
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Assignment |
Date Due |
Points |
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Introduction to Molecular Genetics |
2/5 |
30 |
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Plasmid Isolation |
2/14 |
20 |
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Transformation |
2/21 |
20 |
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PCR I / Agarose Gel Electrophoresis |
2/28 |
25 |
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Genetics Problem set |
3/4 |
50 |
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Bioinformatics I and II |
3/11 |
40 |
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DNA Sequencing and Sequence Analysis |
3/13 |
25 |
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PCR II - human DNA fingerprinting |
3/27 |
30 |
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Research Project (written paper) |
4/3 |
80 |
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Human Haplotype analysis |
4/8 |
20 |
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RT-PCR |
4/10 |
20 |
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Peer reviews of research papers |
4/17 |
20 |
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Southern hybridization |
4/30 |
25 |
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Revision of paper |
4/30 |
50 |
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Bioinformatics III/IV/V |
5/6 |
60 |
Grades:
|
Points |
Component |
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515 |
Lab Assignments |
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260 |
3 exams -- 1 for 60 points, 1 for 100 points, final for 100 points |
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40 |
Student presentations |
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50 |
Quizzes (5 quizzes @ 10 points each) |
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865 |
Total |