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Lecture_1_-_2011
Course: MMG 433, Spring 2011School: Michigan State University
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Genomics Microbial 433 Robert Britton - Instructor Tom Schmidt - Instructor Pat Venta - Instructor Stephanie LaHaye - Lab instructor - Tues Devin Dobias - Lab instructor - Thur Click to edit Master subtitle style What you should expect from MMG433? Hands on experience with many of the tools that are used to perform genomic science. Discussion of the concepts behind the use of genomics in science....
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Genomics Microbial 433
Robert Britton - Instructor Tom Schmidt - Instructor Pat Venta - Instructor Stephanie LaHaye - Lab instructor - Tues Devin Dobias - Lab instructor - Thur Click to edit Master subtitle style
What you should expect from MMG433?
Hands on experience with many of the tools that are used to perform genomic science. Discussion of the concepts behind the use of genomics in science. Applications
Science Everyday life
Important info about the schedule
Meet Tues. and Thurs. 10:20-11:10 Lab is Tues. or Thurs. 11:45-2:15 2245 BPS You must hand in homework to TA for lab you are assigned. Due at the beginning of class one week after the assignment.
Tues. - Stephanie Thurs.- Devin
Exams and Labs
Two exams - 2/3 of the grade Lab - 1/3 of the grade
Individual labs = 1/2 lab grade Final lab project = 1/2 lab grade
Textbook (Optional)
A Primer of Genome Science, second edition. Gibson and Muse Week 1 reading - p. 1-4. 22-24, 47-59. Box 1.2.
Final project we will be participating in a new genome annotation project CACAO (Community Assessment of Community Annotation with Ontologies)
Still working on which genome to annotate. Annotation competition that will allow students (you) to judge the quality of each others annotations. James Hu and Brenley McIntosh (Texas A&M).
Additional MMG433 information
All lectures, labs, syllabus, reading assignments, etc. will be available on Angel, or directly emailed to you (do not go to my website). Each week we will cover a different microbial genome - genome of the week.
Computers
Using MacBook Pro laptops. You will be assigned a laptop to use during class period. You may use your own MacBook if you wish with the exception of two labs that have preinstalled software on the computers. Use the same laptop each time so remember your assignment. You can save information on the computer
What is genomics?
The -omics revolution of science Functional Structural genomics genomics Physiological genomics Toxicogenomics Proteomics Metabolomics Personal genomics What does it all mean?
Genomics
Philosophical - New way to approach biological problems. Practical - High-throughput methods for analyzing biological systems. FAST evolving field focus on concepts
DNA sequencing
1392 complete bacterial genomes currently in the Entrez Genome database.
Over 3500 draft genomes in the database, probably over 50,000 done but not deposited. Goal - $1000 human genome = $1 bacterial genome Genetic mapping in bacteria obsolete. PacBio= 10Gb/hr sequencing technology
New sequencing methods on the horizon
Functional Genomics
B. subtilis DNA microarray
Proteomics
2-D gel electrophoresis
Structural genomics
Structure of the YlqF GTPase of B. subtilis
High-throughput genetics
Determine the function of every gene in a genome Determine the genes essential for life
Minimal genome concept Mycoplasma - 500 genes ~256 genes estimated for life. Can we build a bacterium (phage recently completed).
High-throughput sequencing
Personalized genomics
http://www.nytimes.com/2010/03/11/health/research/11gene.html?ref=research
The informatics problem
There are approximately 106,533,156,756 bases in 108,431,692 sequence records in the traditional GenBank divisions and 148,165,117,763 bases in 48,443,067 sequence records in the WGS division as of August 2009
There are approximately 85,759,586,764 bases in 82,853,685 sequence records in the traditional GenBank divisions and 108,635,736,141 bases in 27,439,206 sequence records in the WGS division as of February 2008.
Over 50 million PubMed searches are performed each month
PubMed (19 million articles). PubMed Central (>2 million articles must be freely accessible). Different search capabilities.
Lab
NCBI - National Center for Biotechnology Information Familiarize ourselves with MacBooks PubMed tutorial
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