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BL 3300/FW 3300
Teaching molecular genetics at MTU since 1998 This genomics class is offered since 2001.
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) or Blogging about Genomics! Note: Class paper presentations will be held between December 6th and 10th, 2010.
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 Introduction to Genomics by Arthur M. Lesk, 2007, Oxford University Press
Grades
Grading Point System
100-95 94-90 89-85 84-80 79-75 74-70 69-60 < 59 A AB B BC C CD D F
Course point distribution Class participation Home work, quizzes etc Class paper Mid-term exam Final exam 10% (attendance, attention & participation) 20% 10% (class paper or blogging) 30% (October 13th or 15th, 2010) 30% (Take home due before December 13)
Class paper
Each discussion group will consist of four-five students (you form your own group and let me know by email) 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 8, 2010. You will discuss the movie that you selected with the group You ALL in each group 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 6-10, 2010. 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 (new name) Chapter 6: The Computational Foundations of Genomics (new name) Chapter 7: High-Throughput Genetics (not included) Chapter 8: Proteomics Chapter 13: The Structure of Genomes (not included) Chapter 15: Genomics and Medicine Chapter 19: Genomics and Agriculture (not included) Chapter 20: Ethical issues of genomics (not included) Chapters in red are not included in Essential of genomics book
(Either I will teach the chapters in red or will replace those with other topics in genomics)
DNA sequence
1 61 121 181 241 301 361 421 gtcgacccac gcgtccgtct tgaaagaata tgaagttgta aagagctggt aaagtggtaa taagcaagat atgatgcaaa cttgtttcga atgatgagaa catctcacct ccactgtgga agagctgtaa
Protein coding regions of Genes begin with ATG and end with either TAG, TGA or TAA
M M E S G A P ..* Study function of proteins and expression of genes in different organs and tissues
DNA
to
RNA
to
Proteins
transcription
translation
Why horse is a horse and duck is a duck? It is in their genes! DNA structure was discovered in 1953 DNA replicates by making a copy of itself and passes to next generation of cells or organisms Purity of lineages maintained Biotechnology: fish genes in plants
Now look at your neighbor and say Hi! What do you see? Someone is different than you! Could be that your friend differs in his/her sex, looks, nature, smartness, or simply the way he/she dresses and talks How much similarity you think you share with your friend at the gene level? 99.9% so we could fix genes if we want
Origin of terminology
The term genome was used by German botanist Hans Winker in 1920 Collection of genes in haploid set of chromosomes Now it encompasses all DNA in a cell In 1986 mouse geneticist Thomas Roderick used Genomics for mapping, sequencing and characterizing genomes New terms: Functional genomics, transcriptomics, proteomics, metabolomics, phenomics (Omics)
What is genomics?
A marriage of molecular biology, robotics, and computing Tools and techniques of recombinant DNA technology
High-throughput technology
e.g., robotics for sequencing
Computers are essential for processing and analyzing the large quantities of data generated
Origin of Genomics
Human Genome Project
Goal: sequence 3 billion base pairs High-quality sequence (<1 error per 10 K bases) ACGT
. . .
Distance
High-throughput genetics
ABI3700
2002 Paradigm Genetics, Inc. All rights reserved. Used with permission.
Genome sequencing
Analogy: Complete works of an author
in partially understood language
Two approaches
Page by page All at once
Functional genomics
Once we know the sequence of genes, we want to know the function The genome is the same in all cells of an individual, except for random mutations However, in each cell, only a subset of the genes is expressed
The portion of the genome that is used in each cell correlates with the cells differentiated state
Gene expression
Whats loaded into RAM (shortterm memory) Subset of genome used in each cell
Evolutionary mechanisms
Comparative genomics
Expression microarrays
Global expression analysis RNA levels of every gene in the genome analyzed in parallel Compare with Northern blot
Microarrays contain more information by many orders of magnitude
Neuronal network
Food chain
Transcriptional network
Comparative genomics
Mechanisms of evolution What is conserved between species? Genes for basic processes What makes closely related species different? Their adaptive traits
Superfluous parts
Wristband
human
chimpanzee
gorilla
orangutan
Identify those who will suffer harmful side effects from particular drugs
2
Treat Responders and Patients Not Predisposed to Toxic
Farm-animal genomics
Genome sequencing of pigs, cows, sheep, and poultry EST sequencing Agricultural pathogens
Potential bioterrorism agents
Future of sequencing We have the genome! Whats next? (post genome era)
Sequencing costs
Dropping each year Could go down to $1,000/genome