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Molecular Evolution (BIO 325)

Course Outline

Lecture Text:
W.H. Li and D. Graur. Fundamentals of molecular evolution.
---Additional reading will be provided throughout the course.

Class Meets:
Lecture: 5.00-6.00 p.m. T-Th
Lab: Variable to accomodate experiments and demostrations
Meeting Place: S-111

Attendance and Honor Code:
Students are expected to attend both lectures and lab on a regular basis. Students in this course will comply to the University of Richmond Honor Code.

Course Format:

• Exams:
  There will be two exams worth 100 points each.
• Oral presentation:
  Each student must present one research paper that used a molecular technique. The presentation will last 10-15 minutes. It will be worth 100 pts.
• Research Proposal:
  Each student will write a research proposal that will address a problem that requires the use of a molecular technique. It will be worth 200 points.
• Poster Presentation:
  The research proposal will be presented in a poster format at the end of the semester. It will be worth 100 points.
• Notebook:
  Each person will maintain a current laboratory notebook which will be examined regularly. Guidelines for the laboratory notebook will be provided.

  Grading:
  

  • Exams-200 points
  • Oral presentation-100 points
  • Research Proposal-100 points
  • Notebook-100 points
  • Poster-100 points
  • TOTAL OF 600 POINTS

Grades will be assigned on a 90-80-70-60% basis; there is no "curve".

• A = 600-541
• B = 540-481
• C = 480-421
• D = 420-360

No makeup quizzes, lab or lecture tests will be given.

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SYLLABUS
Molecular Evolution (BIO-325)
Spring 1995

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Date	Day	Lecture
Jan. 12	Th	Introduction.
Jan. 17	T	What is molecular evolution?. Gene structure, Mutation, Genetic codes.
Jan. 19	Th	Dynamics of gene populations: Hardy-Weinberg Equilibrium and assumptions.
Jan. 24	T	Dynamics of gene populations: Allele frequencies, Natural selection, Random genetic drift.
Jan. 26	Th	Dynamics of gene populations: Population size and Genetic polymorphims.
Jan. 31	T	Dynamics of gene populations: Population size and Geneticpolymorphims.
Feb. 2	Th	Evol. Changes: Rates of nucleotide substitutions, causes of variation.
Feb. 7	T	Evol. Changes: Rates of nucleotide substitutions, causes of variation.
Feb. 9	Th	Evol. Changes: Molecular clocks: assumptions and controversy.
Feb. 14	T	Evol. Changes: Molecular clocks: assumptions and controversy.
Feb. 16	Th	Evol. Changes: DNA sequences alignments, statistical methods.
Feb. 21	T	Evol. Changes: DNA sequences alignments, statistical methods.
Feb. 23	Th	Evol. Changes: DNA sequences comparisons, statistical methods.
Feb. 28	T	Evol. Changes: DNA sequences comparisons, statistical methods.
Mar. 2	Th	MID TERM EXAM
Mar. 7	T	Evol. Changes: Gene duplication, gene families.
Mar. 9	Th	Evol. Changes: Gene duplication, gene families.
Mar. 21	T	Evol. Changes: Exon shuffling, concerted evolution.
Mar. 23	Th	Evol. Changes: Exon shuffling, concerted evolution.
Mar. 28	T	Evol. Changes: Transposition and transposable elements.
Mar. 30	Th	Evol. Changes: Transposition and transposable elements.
Apr. 4	T	Genome organization: Genome size, compostion in bacteria and eukaryotes.
Apr. 6	Th	Genome organization: Genome size, compostion in bacteria and eukaryotes .
Apr. 11	T	Molecular Phylogeny: Phylogenetic trees.
Apr. 13	Th	Molecular Phylogeny: Phylogenetic trees.
Apr. 18	T	Molecular Phylogeny: Phylogeny of humans and apes.
Apr. 20	Th	Molecular Phylogeny: Phylogeny of humans and apes.
Apr. 25	T	POSTER SESSION

Laboratory:

Week 1. Introduction. Preparation of basic media and solutions, concentrations, calculations, safety regulations.

Week 2. Genomic DNA preparation. Isolate and purify intact high molecular weight DNA from eukaryotic cells. Vector DNA preparation.

Week 3. Restriction Fragment Mapping. Understanding restriction undonucleases. DNA restriction reactions. Full and partial digestions. Effects of: temperature, reaction time, salt concentrations. Gel preparation, pouring, and effects of gel concentration. Restriction Mapping: RFLP analysis and fingerprinting. Applications and limitations of technique.

Week 4. DNA-DNA hybridization. Principles and concepts associated, e.g., DNA denaturation and renaturaltion. Electrophoresis of cleaved DNA. DNA Denaturation, transfer to membrane through Southern Blot. Nick translation and Hybridization. Applications and limitations of technique.

Week 5. Construction of a genomic library. Restriction digestion of genomic DNA and vector. Ligation: principles and conditions.

Week 6. Genomic library. Transformation and library screening for ribosomal DNA genes.

Week 7. Genomic library. Library screening, identification, and purification of ribosomal DNA .

Week 8. Cloning into bluescript. Ligation and transformation.

Week 9. Bacterial growth and Plasmid preparation. Minipreparations and CsCl preparations.

Week 10. Understanding the Polymerase Chain Reaction (PCR) method. Principles and applications. PCR reaction and run. Isolation of PCR products.

Week 11. DNA sequencing. Understanding the Dideoxy Chain Termination method. Principles and applications. Double vs Single stranded DNA sequencing. Annealing and sequencing reactions.

Week 12. Sequencing gel preparation. Sequencing electrophoresis. Gel drying and autoradiograph.

Week 13. Sequence Analysis. Gel reading, manually and with gel reader. Entering sequence data in computer and comparison of DNA sequences with those of the GENBANK database on CD-ROM, using a microcomputer.

Week 14. Poster Session.