Transcript Introduction to Genomics

Welcome
Introduction to Genomics
BL 3300/FW 3300
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: [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!
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:
– 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
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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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BC
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10% (attendance and attention)
20%
10% (essay and Powerpoint presentation)
30% (October 22nd or 24th, 2007)
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
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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 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 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