2012 Molecular Phylogeny (NC21100) Homepage

Schedule (original)                      Prof.: Sangtae Kim: 010-2 0 4 6-1 7 6 7   TA: Hee Joo: 010-3604-0929



1. Intersting story: check this out!


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Ͻ: 2013 4 11 5:30PM   : C311

3. A book chapter for PCR

I found very very nice recent book chapter for PCR technique.  I scanned and uploaded it for you guys.  We will use this material in the class. Although entire material contains many pages (87page) please print out only the following pages and bring them to the next class (April 15): 1) INTRODUCTION (pp455-and 468), 2) one or two front page of each protocol (pp470-471, 477-478, 481-482, 484-485, 490-491, 494-495, 499, 531, 533-535), and 3) troubleshooting of protocol 1 (pp473-476).

B ook C hapter: P C R   p r o t o c o l s UPDATED


4. Result of mid-term exam


Top three students: 躸 (99/110), (89/110), (88/110)         Congratulations!

5. First assignment

Assinment I.  due date: May 6


6. Submit Personal Lab Folder

  Print out all molecular lab protocols and make a file with results of experiments.

  Due date: May 20.

7. ڿ Ͻ α׷ ȳ




Week 1 (3.4) Course introduction

            INTRODUCTION  updated

Week 2 (3.11) The book Classification

          "Classification"  BOOK  updated

Week 3 (3.18) C a m p b e l l General Biology Chap 2 6.

           BOOK chapterupdated PPT down    CLASSIFICATION MOVIE    

Week 4  (3.25) The archaeology of the genome, Trees (chap. 1 and 2)

          Chap 1 PPTupdated   Chap 2 PPTupdated The archaeology of the genome, Trees (chap. 1 and 2)

Week 5 (4.1) Genes: organization, function and evolution (chap 3.)

          Chap 3 PPTupdated  

Week 6 (4.8) (Lab.) Lab basics and DNA extraction

           Lab basics PPT

           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

                                                        An example of EXTRACTION RESULT    2013-EXTRACTION RESULT


Week 7 (4.15) (Lab.) PCR 

           B ook C hapter: P C R   p r o t o c o l sUPDATED

           PCR and purification PPT UPDATED

           Sequencing process, PCR condition, Primer informatio, endonuclease treatment

           Taq polymerase information sheet

           PCR record form

            2002: Result of extraction and PCR 

Week 8 (4.22) Mid-term exam.

             2012-Mid-term exam.       2013-Mid-term exam.

Week 9 (4.29) (Lab.) DNA sequencing, cloning, and other methodologies: RFLP, RAPD, CAPS, and AFLP

        Sequencing PPT  UPDATED

           CAPS protocol     Endonuclease information sheet

           PCR product purification protocol

           RFLP, CAPS, RAPD, ISSR, and AFLP PPT  

           Assinment I.  due date: May 6

             Oligo Program

Week 10 (5.3) Cloning.

           TA cloning protocol           

          TOPO TA colning kit protocol

         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 11 (5.13) Measuring genetic change I (chap 5)

         Chap 5. PPTUPDATED  Measuring genetic change (chap 5)  

Week 12 (5.20) Inferring molecular phylogeny (chap 6)

       Chap. 6. PPTUPDATED  Inferring molecular phylogenyI (chap 6)  

         R a d f o r d  et al Book Chapter


Week 13 (5.27) (Computer lab.) Reconstruct Phylogeny - Assignment.

               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  

         M E G A program   M P sample data

         Paper: Kim et al. 2001

Week 14 (6.3) Special Seminar

Week 15 (6.10) Final exam.