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Molecular Approaches
to Biological Oceanography

Instructors: Senjie Lin

3 credits, one 2-hr lectures per week (Wed, 2:00-4:00 pm), one 3hr lab per week (Fri, 9:30 am-12:30 pm). Offered at Avery Point

In general, this course will introduce all major molecular biological techniques that are useful for ecological studies. Lectures will cover theories and principles behind the techniques and highlight some technical difficulties often encountered. Labs will offer hands-on experience for students. Typically, students will work in groups of 2 to 3 on biological samples students choose.

• Lecture 1: Introduction: Why molecular techniques?

• Lab 1: Preparation of reagents and samples

Lecture 2: Nucleic acid properties and DNA isolation

• Lab 2: DNA isolation

• Lecture 3: PCR*

• Lab 3: PCR

• Lecture 4: DNA fingerprinting (RFLP, AFLP, VNTR, etc)

• Lab 4: DNA restriction digestion and gel electrophoresis.

• Lecture 5: Molecular cloning and sequencing

• Lab 5: Gene cloning

• Lecture 6: Basic informatics

• Lab 6: Gene cloning (continued)

• Lecture 7: Molecular phylogeny

• Lab 7: Isolation of plasmids

• Lecture 8: Population genetics

• Lab 8: BLAST, alignment, and phylogeny

• Lecture 9: Gene transcription and mRNA detection

• Lab 9: Isolation of RNA and synthesis of cDNA

• Lecture 10: Translation and protein detection

• Lab 10: RT-PCR and real-time qPCR

• Lecture 11: Genomics and proteomics

• Lab 11: RT-PCR and real-time qPCR (continued)

• Lecture 12: Metagenomics

• Lab 12: Immunofluorescence

• Lecture 13: Application to Oceanography

• Lab 13: Work on project

• Lecture 14: Application to other marine organisms

• Lecture 15: Study for final and work on project

• Lab 14: Work on project

* PREMIER Biosoft International Developers of Intuitive Software for the Molecular Biologist kindly provides Beacon Designer for primer and probe design in this course. To learn more about this software, please check out their website http://www.premierbiosoft.com/molecular_beacons/index.html.