Introduction to Genomics

BL 3300/FW 3300

Welcome

Who is your instructor?

• Shekhar Joshi (Chandrashekhar P. Joshi)

• Associate Professor of PMG, SFRES

• Over 20 years of research experience– Molecular Genetics, Biotechnology, Bioinformatics

• 44 papers, 14 book chapters,65 presentations

• Teaching molecular genetics at MTU since 1998

• This class is offered since 2001.

Where and when can you find me?

• Room # 167, Forestry Building• Office Hours: I am available between 9 am to 6

pm on all weekdays except – MWF between 3-4 when I teach this BL3300/FW3300

class.

• 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!

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:

– How will Genomics change my life?– Genomics meets Hollywood!

• Note: Class paper presentations will be held between December 3rd and 7th, 2007.

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 22nd or 24th, 2007)• Final exam 30% (during December 17-21, 2007)

Class paper: Option 1• First, you will come up with a theme for your class paper• You choose articles from the following magazines (or make

your own choice) and find out some interesting articles related to Genomics that are published during last five years. – Time, Life, Discover, Science, Nature, Scientific American,

Genetic Engineering News, National Geographic, US News….

• You will copy ten genomics articles, review them and prepare a 10-minute power point presentation that will be presented to the class during the December 3rd and 7th, 2007. Your peers and I will evaluate your presentations.

• You will also write an essay (~10 pages long) based on all such recent news items that you have collected and submit it to me along with your Power point presentation by December 3rd.

Class paper: Option 2

• You choose and see 4 movies that use genes or genomics or genetic engineering as a theme (e.g. Jurassic park).

• Tell the class about one such movie: its major theme, the plot and how it fits with the topic of the class.

• Provide your own interpretations about accuracies and discrepancies of science in those movies.

• You will present a 10 minute powerpoint talk and write a 10-page review paper on all 4 movies selected.

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 14: Human Origins• Chapter 15: Genomics and Medicine• Chapter 19: Genomics and Agriculture • Chapter 20: Ethical issues 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