2012 Molecular Phylogeny (NC21100) Homepage

Schedule (original)                                                       

 

ANNOUNCEMENT

2. The first assignment

    Read "Classification" booklet and write a page of dafinition and description about Phenetics and Cladistics.

    Due date: 9.21

3. The second assignment

        Find "THREE" new "biological" or "phylogenetic" terminologies during the Dr. Ui Wook Whang's seminar and report their definition and meaning.

  e. g., Tridigrada, bootstrap, sensu lato, ... and etc.

  - Half page per an item (Total one and half pages; A4)

  - Due date: Nov. 13

 

4. Final Exam: Dec. 14. 3:00PM  Room C209

 Note: a couple of midterm questions will be included in the final exam.

   Midterm questions.    

 

 

CONTENTS

Week 1 (9.7) Course introduction

Week 2 (9.14~5) Field trip (official departmental break)  

         HOMEWORK:  "Classification"  BOOK  <-- read this book and make one page of summary

Week 3 (9.21) Chap 1 PPT   Chap 2 PPT  The archaeology of the genome, Trees (chap. 1 and 2)

Week 4 (9.28)   BOOK chapter  PPT down  Campbell General Biology Chap 26.

Week 5  ----------

Week 6 (10.12)   Chap 3 PPT   Genes: organization, function and evolution (chap 3.)

Week 6 (10.19) (Lab.) Lab basics and DNA extraction

           Lab basics PPT    UPDATED

           DNA extraction @ general biology lab: CTAB method PPT

           DNA extraction  CTAB DNA extraction protocol I (Doyle and Doyle)  

                                CTAB DNA extraction protocol II (Sangtae Kim)

                                GeneAll DNA extraction Kit (Commercial Kit)  

                                FTA Card protocol   

                                Samples and band test

                                                        EXTRACTION RESULT

Week 8 (10.26) Mid-term exam.   UPDATED     

Week 7 (11.2) (Lab.) PCR and sequencing

           Book Chapter: PCR protocols

           PCR and purification PPT UPDATED

        Sequencing PPT  UPDATED

           Sequencing process, PCR condition, Primer information

           Taq polymerase information sheet

           PCR record form

           OUR RESULT: extraction, PCR

Week 9 (11.9) (Lab.) Other methodologies: RFLP, RAPD, CAPS, and AFLP

          Alignment, Sequence editing using SEQUENCHER

           CAPS protocol     Endonuclease information sheet

           DNA purification protocol

           TA cloning protocol           

           TOPO TA colning kit protocol

           RFLP, CAPS, RAPD, ISSR, and AFLP PPT  UPDATED

C.f. : P l a n t  S y s t e m a t i c s  C h a p .  M o l e c u l a r  P h y l o g e n y

 

Week 10 (11.16)  Chap 5. PPT   Measuring genetic change I (chap 5)  UPDATED

Week 11 (11.23) Measuring genetic change II (chap 5)

                Special seminar: Dr. Eu-wook Whang, Kyungbook Univ.

 

Week 12 (11.30)  Chap. 6. PPT Inferring molecular phylogenyI I (chap 6)  UPDATED

         R a d f o r d  et al Book Chapter

Week 13 (12.7) Reconstruct Phylogeny with RAPD and sequencing data using MEGA, PHYLIP  (computer lab.)

               PHYLIP web site  TreeView web site       

               PHYLIP program  TeeView Program     

         Phylogeny reconstruction using M E G A and P H Y L I P programs  UPDATED

         M E G A program   M P sample data

         Paper: Kim et al. 2001

 

 

 

 

Week 14 (12.14) Final exam.