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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.

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microbial genomics 433

Microbial Genomics 433

Robert Britton - Instructor

Tom Schmidt - Instructor

Pat Venta - Instructor

Kristi Whitehead - TA

Uri Levine - TA

what you should expect from mmg433
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
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
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
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
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
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
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
Genomics
  • Philosophical - New way to approach biological problems.
  • Practical - High-throughput methods for analyzing biological systems.
  • FAST evolving field
functional genomics
Functional Genomics

B. subtilis DNA microarray

proteomics
Proteomics

2-D gel electrophoresis

structural genomics
Structural genomics

Structure of the YlqF GTPase of B. subtilis

high throughput genetics
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
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
Lab - NCBI
  • NCBI - National Center for Biotechnology Information
  • GenBank exercises - delve right into many different databases.
  • PubMed tutorial
slide16

Web Access

Text

Entrez

Sequence

BLAST

Structure

VAST