Transcript Lecture_1_2005

Microbial Genomics 433
Robert Britton - Instructor
Tom Schmidt - Instructor
Pat Venta - Instructor
Kristi Whitehead - TA
Uri Levine - TA
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. 11:50-2:40 Chem 121
• You can attend either lab - must hand in
homework to TA for lab you are assigned.
– Tues. - U. Levine
– Thurs.- K. Whitehead
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
• A Primer of Genome Science, second
edition. Gibson and Muse
• Week 1 reading - p. 1-4. 22-24, 47-59. Box
1.2.
What’s new for 2005?
• Additional lectures on eukaryotic genomics.
• Final project - we will be annotating a new
genome sequence.
– Lactobacillus reuteri
– Another organism sequenced by the JGI for a
laboratory at MSU.
Additional MMG433 information
• All lectures, labs, syllabus, etc. is posted on
my website at
http://www.msu.edu/~rbritton/mmg433/index.htm
• Each week we will cover a different
microbial genome - genome of the week.
What is genomics?
The -omics revolution of science
Functional genomics
Structural genomics
Physiological genomics
Toxicogenomics
Proteomics
Metabolomics, etc., etc.
What does it all mean?
Genomics
• Philosophical - New way to approach
biological problems.
• Practical - High-throughput methods for
analyzing biological systems.
• FAST evolving field
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).
The informatics problem
• NCBI contains 28 billion basepairs in 22
million DNA sequences
• Over 50 million PubMed searches are
performed each month
• Microarrays, proteomics, networks
• How does one handle all of the data?
Lab - NCBI
• NCBI - National Center for Biotechnology
Information
• GenBank exercises - delve right into many
different databases.
• PubMed tutorial
Web Access
Text
Entrez
Sequence
BLAST
Structure
VAST