Transcript Introduction to Genomics

Welcome
Introduction to Genomics
BL 3300/FW 3300
Syllabus available at http://forest.mtu.edu/faculty/joshi/web/course%20Fall%202008.html
Who is your instructor?
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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: [email protected]
• 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:
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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
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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
Grades
Grading Point System
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100-95
94-90
89-85
84-80
79-75
74-70
69-60
< 59
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Course point distribution
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Class participation
Home work, quizzes etc
Class paper
Mid-term exam
Final exam
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B
BC
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F
10% (attendance and attention)
20%
10% (essay and Powerpoint presentation)
30% (October 27th or 29th, 2008)
30% (during December 15-19, 2008)
Class paper
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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
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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
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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)
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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 genomes
Eukaryotic Genomes
Nuclear Genomes
Mitochondrial genomes
Choloroplast 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?
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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?
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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?
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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