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

ANNOUNCEMENTS

1. Intersting story: check this out! http://www.hani.co.kr/arti/science/science_general/577186.html

2. 취업특강 안내   생물학과의 93학번 선배인 양명주 강사가 후배들을 위한 특강을 해 줄 계획이니 많은 학생들의 참여 바랍니다. 양명주 강사는 현재 전문 carrer consultant 로서 활동 중이고 생물학분야의 채용동향, 잡서치 전략, 면접전략, 자기소개서 작성 등에 대해 강의해 줄 예졍임.   일시: 2013년 4월 11일 목요일 5:30PM   장소: 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: 김보경 (99/110), 이은진(89/110), 차수연(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. 방학중 국립생물자원관 인턴쉽 프로그램 안내 http://www.nibr.go.kr/board/article_view.jsp?board_no=17&article_no=50155&menuTop=3&menuSub=03-01-00-01

CONTENTS

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    

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

          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.

        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

               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.