Botany 662
Advanced Systematics
General Information
Strategy of the Course
This course is taught on a Tuesday-Thursday schedule with a discussion of the protocols and molecular consequences of the reactions followed by the laboratory procedures carried out by the students. As in life as a career scientist, there are no exams, but you are graded on the quality of your research, your ability to publish your results in a journal, and your ability to present your results before your peers in society meetings. As such, students have projects of their choosing from which they will be graded. The papers will be published at the end of the semester in a volume of the Hawaiian Journal of Systematic Biology (for class projects only -- not a true peer reviewed journal!), and student presentations held with other departmental faculty and students invided and conducted as in professional meetings.
Topics
- Intro to class, DNA isolation
- DNA isolation, idea's due!!
- DNA isolation cont., radiation and safety class
- DNA restriction analysis, DNA size markers
- Mapping (cloned DNA for experiment)
- Gel blotting, genome restriction ampping
- Southern Hybridization, Proposals due!!
- Cloning, Subcloning and Library construction
- Disgestion, ligations, transformation, plasmid DNA preps
- Sequencing: ssDNA and DSDNA preparation
- Sequencing: Reactions, gel preparation, gel breakdown and drying
- Sequencing: Reading and interpretting DNA sequence
- PCR: DNA amplification (ssDNA vs dsDNA)
- PCR: RAPD analysis of population variation
- PCR: RAPD analysis of population variation
- PCR: Sequencing of amplified DNA
- PCR: Sequencing of amplified DNA
- Data analysis: Introduction to GCG and sequence alignment
- Isozyme Analysis: germination of seeds, buffer systems
- Isozyme Analysis: (Class example) grinding tissue and gel loading
- Isozyme Analysis: (Class example) Slicing gel and staining
- Isozyme Analysis: Interpretation and student assignments
- Isozyme Analysis: Interpretation and student assignments
- Phylogenetic Analysis: Parsimony (MacClade)
- Phyolgenetic Analysis: Parsimony (PAUP)
- Phyolgenetic Analysis: Distance
- Phyolgenetic Analysis: Maximum Likelihood
- Phyolgenetic Analysis: Continued
- Phyolgenetic Analysis: Continued
- Prepare oral presentation, Projects due
- Prepare oral presentation
- Final - Oral presentations