BIO 577:Advanced Molecular Biology, Spring 2009 Instructor: Dr. Kathy Szick-Miranda Office: Science I, 316 Phone: 654-6165 Email: kszick-miranda@csub.edu Web: www.csub.edu/~kszick_miranda Office hours: T Th 12:20-3:10pm Lecture and Lab: T Th 3:10-4:25pm; 4:35-7:05pm, Sci I 215 Course Philosophy/Format: This course in advanced molecular biology is designed as a rigorous introduction to the topics, terminology, techniques, methodologies and approaches of modern molecular biology that may not have been covered in an introductory molecular biology (or molecular genetics) course. This course is taught with the assumption that students have had previous courses in biochemistry, molecular biology and/or genetics and that many have already had some laboratory experience. We will examine core concepts in molecular biology including, DNA damage and repair, homologous recombination, transposition, chromatin remodeling, alternative splicing, posttranscriptional regulation of gene expression and the role of regulatory RNAs. Additional topics that contribute to our understanding of gene expression will include recent advances in genomics and proteomics. This course serves to help students make the transition from lecture-based, text book-oriented courses common in undergraduate training to independent learning organized around current research papers and seminars that are the hallmarks of advanced studies. The topics/concepts we will cover are grouped into two time block clusters. The first time block will cover the topic in the traditional lecture/powerpoint format, while the second time block will be focused on analysis and understanding of current scientific papers. Students will be assigned a discussion paper. As the discussion leader, it will be the students responsibility to provide an overview, lead the discussion and summarize the assigned paper. Students are expected to read all of the assigned literature and contribute in a significant and meaningful way to the group discussion. Discussion leaders for papers that have not been assigned to a specific person, will be chosen at random the day the paper is to be discussed. Participation in classroom discussions and student presentations is essential. Consequently, attendance is mandatory. There is no mechanism for making up discussion material or classes that are missed and no credit will be given for classes that are missed. Reading Materials: Suggested: •Weaver, R. 2008. Molecular Biology, Fourth Edition. McGraw Hill. Required: •Lab Manual Packet - To be distributed in lab and/or will be available via the web. •Discussion papers - To be distributed in lab and/or will be available via the web. Assignment Point Values: Exam I Exam II Exam III (final) Attendance/Participation Discussion Leader Research Report TOTAL 100pts 100pts 100pts 50pts 50pts 75pts 475pts Academic Policies: It is expected that your work is YOUR work. In the unexpected event of plagiarism and/or dishonesty during exams or for the research term-paper, the student will receive a zero on that activity and be referred to the campus administration for disciplinary action. Please refer to the campus 2007-2009 catalog page 81. Grading: Grades will be based on the percentage of points accumulated in the course (lecture and lab) using the scale shown below. A = 94-100 A-= 90-93.9 B+ = 87-89.9 B = 83-86.9 B- = 80-82.9 C+ = 77-79.9 C = 73-76.9 C- = 70-72.9 D+ = 67-69.9 D = 63-66.9 D- = 60-62.9 F = 0-59.9 *Missed lecture exams due to illness or other justified reasons can be made up. If you know in advance that you must miss an exam, see me and bring documentation to support your anticipated absence. LECTURE SCHEDULE & READING ASSIGNMENTS Wk 1 Date R-Apr 2 Topic Intro to the course Reading 2 T-Apr 7 R-Apr 9 Lecture 1- Molecular Tools Discussion 1 CH 5 84-119 3 T-Apr 14 R-Apr 16 Lecture 2- Genomics, Proteomics, Bioinformatics Discussion 2 CH 24 797-827 4 T-Apr 21 R-Apr 23 Lecture 3- DNA Damage and Repair Discussion 3 CH 20 660-682 5 T-Apr 28 R-Apr 30 Exam I Lecture 4- Homologous Recombination CH 22 718-738 T-May 5 R-May 7 Discussion 4 Lecture 5- Transposition CH 23 743-769 T-May 12 R-May 14 Discussion 5 Lecture 6- Chromatin Remodeling CH 13 368-398 8 T-May 19 R-May 22 Discussion 6 Exam II 9 T-May 26 R-May 28 Lecture 7- Alternative Splicing Discussion 7 CH 14 422-434 10 T-June 2 R-June 4 Lecture 8- Posttranscriptional Control of Gene Expression Discussion 8 CH 16 494-500 Lecture 9-Regulatory RNAs CH 16 501-520 6 7 10 1/2 T-June 9 R-June 11 FINAL 5:00-7:30pm DISCUSSION SCHEDULE Wk 1 Date R-Apr 2 Topic Intro to Research Component 2 T-Apr 7 R-Apr 9 Sterilize and imbibe seed; prepare plates and top agar Plate seed (allow to grow for ~10days) 3 T-Apr 14 R-Apr 16 Design primers Prepare LB plates and liquid media 4 T-Apr 21 R-Apr 23 Harvest seedlings, isolate RNA, set up RT-PCR Run gel, purify sample, clone into TOPO vector, transform bacteria 5 T-Apr 28 R-Apr 30 Set-up colony PCR, prepare agarose gel Run gel on colony PCR 6 T-May 5 R-May 7 Plasmid preps, send samples off for sequencing LR reactions, transform bacteria 7 T-May 12 R-May 14 Set-up colony PCR, prepare agarose gel Run gel on colony PCR 8 T-May 19 R-May 22 Plasmid preps, send samples off for sequencing Transform Agrobacterium 9 T-May 26 R-May 28 Set-up colony PCR, prepare agarose gel Run gel on colony PCR 10 T-June 2 R-June 4 Wiggle-room Floral Dips 10 1/2 T-June 9 Discussion 9 R-June 11 FINAL 5:00-7:30pm