Fall Semester 2006
Activities subject to the uncertainties of science.
Deadlines are firm.
Updated Aug 9, 2006

NOTE:  Readings and handouts are available by direct link or via e-res, the electronic reserve system of the CONSORT libraries.

Aug. 30 Course introduction; pipettor verification; quantification of nucleic acids by spectrophotometry; intro. to degenerate primer design Morrison et al. (1995)
Morrison et al. (1998)
Iwata and Stegeman (2000)
Wilkie and Simon (1991)
Sept. 6 Total RNA Isolation, quantitation.  RNA isolation protocol  
Sept. 13 RNA gels, photography; Figure preparation;
Workshop: Primer design.
 Wilkie and Simon (1991) Homework:  primer sequences
Sept. 20
(Meet in  Computer Lab, FSH 009)
Computer Workshop: Bioinformatics  BLAST searches, sequence alignment, phylogenetic trees.

Handout:  DNA and Protein Sequence analysis.
also, Molecular Evolution Readings

Lab Report 1:  RNA Isolation
Also:  Notebook check.
Sept. 27 RT-PCR for CYP1A cDNA fragments RT-PCR Protocols  
Oct. 4 Agarose gel analysis of PCR products  
Oct. 11 Purification of RT-PCR products from gels; ligation of products into plasmid cloning vector. Gene Clean protocol
Ligation protocol
Lab Report 2:  Sequence analysis exercise.
Oct. 18 (and 19) Transformation of competent E. coli cells.     
Oct. (24 and) 25 Plasmid minipreps; restriction enzyme digestion. Miniprep protocol
Restriction ezyme protocol
Notebook Check by request.
Nov. 1 Gel analysis of miniprep digests.
Nov. 8

Workshop: Intro to Real-Time PCR;
Primer design for CYP1A expression experiment

Real-Time PCR Data Analysis Tutorial. Lab Report 3:  RT-PCR and cloning
Nov. 15 Real-Time PCR Reactions on ABI 7500 Real-Time PCR Protocol  
Nov. 22
Thanksgiving Break
Nov. 29 Real-Time PCR Data Analysis ABI 7500 Tutorial Lab Report 4: Analysis of YOUR sequence
Dec. 6 Course catch-up and wrap-up:  discussion of results and check-out.  
Dec. 16 (Saturday) FINAL REPORT AND NOTEBOOK ARE DUE:  4:30 PM (corresponds to the end of the schedule exam time).    FINAL REPORT DUE 4:30 PM

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Last Modified Aug. 9, 2006