1. Introduction to Genomics BL 3300/FW 3300 Welcome Syllabus available at http://forest.mtu.edu/faculty/joshi/web/course%20Fall%202008.html

2. Who is your instructor? Shekhar Joshi (Chandrashekhar P. Joshi) Dr. Joshi Professor of Plant Molecular Genetics, SFRES Over 20 years of research experience –Molecular Genetics, Biotechnology, Bioinformatics 45 papers, 16 book chapters,80 presentations Teaching molecular genetics at MTU since 1998 This class is offered since 2001.

3. Where and when can you find me? Room # 168, Forestry Building Office Hours: I am generally available between 9 am to 6 pm on all weekdays except –MWF between 3-4 pm when I teach this BL3300/FW3300 class (better to take my appointment). Phone: 906-487-3480 Email: cpjoshi@mtu.educpjoshi@mtu.edu Web site: http://forest.mtu.edu/faculty/joshi/ For those who walk up from the main campus: Do call me or email me before walking up the hill to meet me!

4. Why was this course proposed? Genomics is the study of genome structure and function. This is a new and exciting area that has recently witnessed many conceptual and technical advances. This information is vital to our day-to-day living in this century. Such a course would also make our students competitive in current job market Bioinformatics majors needed this type of class and now all molecular biology major students will need this class too.

5. Course Description The main purpose of this course is to introduce concepts of human genomics that can also be applied to microbial, plant and animal genomes. The topics covered are: Genes and genome organization Genome mapping DNA fingerprinting Gene tagging Bioinformatics Legal and Ethical aspects of genomics Genome evolution

6. Essential Details Credits: 3 Time: Monday, Wednesday and Friday 3 pm-4 pm Place: Forestry G002 Class Paper: –Genomics meets Hollywood! (more on this later) Note: Class paper presentations will be held between December 8th and 12th, 2008.

7. Required Text Book Genomics –Philip N. Benfey and Alexander D. Protopapas (Pearson Prentice Hall) (For 2006 updates go to http://wps.prenhall.com/esm_benfey_genomics_1) http://wps.prenhall.com/esm_benfey_genomics_1 2005 –Recent book –Up to date –Real genomics book –Ready made slides and space for notes –Updates available

8. Additional Reading Optional Reading material (No need to buy it) Genomes by T.A. Brown, 1999, John Wiley & Sons, NY Genes VIII by Benjamin Lewin, 2003, Oxford University Press Molecular Biology by Robert F. Weaver, 1999, McGraw-Hill Press Genome by Matt Ridley, Harper Collins, 2000

9. Grades Grading Point System 100-95A 94-90AB 89-85B 84-80BC 79-75C 74-70CD 69-60D < 59F Course point distribution Class participation10% (attendance and attention) Home work, quizzes etc20% Class paper10% (essay and Powerpoint presentation) Mid-term exam30% (October 27th or 29th, 2008) Final exam30% (during December 15-19, 2008)

10. Class paper Each discussion group will consist of four-five students (you form your own group) Each of you will see a movie that uses DNA, genes, genomics or genetic engineering as a theme (e.g. Jurassic park) and write a 3-5 page overview of that movie and submit to me electronically by November 7, 2008. You will discuss the movie that you selected with the group You ALL will select one movie that you want to present to the class and one of you will present it Tell the class about your movie selection: its main theme, the plot and how it fits with the topic of the class. Provide your interpretations about accuracies and discrepancies of science depicted in those movies. If you were the writer/director, how would you improve it to portray the science more accurately (but not making it a complete flop) One representative per group will present a 10 minute powerpoint talk sometime between December 8-12, 2008. Questions?

11. University Policies http://www.admin.mtu.edu/urel/studenthandbook /policies.html or student handbookhttp://www.admin.mtu.edu/urel/studenthandbook /policies.html –Academic Integrity: plagiarism –Attendance Policy: email me if absent –Code of Conduct: follow the laws of the land –Computer Use Policy: use responsibly Please visit this site and make sure that all your actions in the class are within the bounds of these policies.

12. Class coverage Chapter 1: Introduction Chapter 2: Technical Foundations of Genomics Chapter 3: Fundamentals of Genome Mapping and Sequencing Chapter 4: Genome sequencing Chapter 5: RNA expression analysis Chapter 6: The Computational Foundations of Genomics Chapter 7: High-Throughput Genetics Chapter 8: Proteomics Chapter 13: The Structure of Genomes Chapter 15: Genomics and Medicine Chapter 19: Genomics and Agriculture Chapter 20: Ethical issues of genomics

13. BL4400/FW4400?? (Spring) Advanced genomics Remaining chapters of this book plus Sequenced genomes and what we learnt Future of genomics

14. What is genomics? Study of genomes

15. What is the genome? Entire genetic compliment of an organism

16. How many types of genomes exist? Prokaryotic genomes Eukaryotic Genomes Nuclear Genomes Mitochondrial genomes Choloroplast genomes

17. Why we should study genomes? Life’s little book of instructions DNA blue print of life! Human body has 10 13 cells and each cell has 6 billion base pairs (A, C, G, T) A hidden language determines which proteins should be made and when This language is common to all organisms

18. What can genome sequence tell us? Everything about organism's life Its developmental program Disease resistance or susceptibility History Where you are going?

19. How are human genomes organized? 3% coding and rest of it junk (repetitive DNA). Nuclear and mitochondrial You are 99.99% similar to your neighbor

20. Why human genome? We want to know about ourselves How do we develop? How do we struggle, survive and die? Where are we going and where we came from? How similar are we to apes, trees, and yeast?

21. How will we change in this century because of the Genomics? You will control the destiny of this planet Big changes in our life Biotechnology: more products GMOs: More food-More problems? Our society will not be the same! Individualized medicine Gene therapy Immortality? Disease free life?

22. Are we playing GOD? Central dogma in Molecular Biology