Introduction to Genomics

BL 3300/FW 3300

Welcome

Syllabus available at http://forest.mtu.edu/faculty/joshi/web/course%20Fall%202008.html

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.

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.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!

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.

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

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.

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) • 2005

– Recent book– Up to date– Real genomics book– Ready made slides and space for notes– Updates available

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

GradesGrading Point System• 100-95 A • 94-90 AB• 89-85 B• 84-80 BC• 79-75 C• 74-70 CD• 69-60 D• < 59 F

• Course point distribution

• Class participation 10% (attendance and attention)• Home work, quizzes etc 20%• Class paper 10% (essay and Powerpoint presentation)• Mid-term exam 30% (October 27th or 29th, 2008)• Final exam 30% (during December 15-19, 2008)

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?

University Policies

• http://www.admin.mtu.edu/urel/studenthandbook/policies.html or student handbook– 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.

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

BL4400/FW4400?? (Spring)

• Advanced genomics

• Remaining chapters of this book plus

• Sequenced genomes and what we learnt

• Future of genomics

What is genomics?

Study of genomes

What is the genome?

Entire genetic compliment of an organism

How many types of genomes exist?

Prokaryotic genomesEukaryotic Genomes

Nuclear GenomesMitochondrial genomesCholoroplast genomes

Why we should study genomes?

• Life’s little book of instructions

• DNA blue print of life!

• Human body has 1013 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

What can genome sequence tell us?

• Everything about organism's life

• Its developmental program

• Disease resistance or susceptibility

• History

• Where you are going?

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

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?

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?

Are we playing GOD?

Central dogma in Molecular Biology