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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?. Hands on experience with many of the tools that are used to perform genomic science.

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Microbial Genomics 433

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  1. Microbial Genomics 433 Robert Britton - Instructor Tom Schmidt - Instructor Pat Venta - Instructor Kristi Whitehead - TA Uri Levine - TA

  2. 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

  3. 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

  4. 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

  5. Textbook • A Primer of Genome Science, second edition. Gibson and Muse • Week 1 reading - p. 1-4. 22-24, 47-59. Box 1.2.

  6. 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.

  7. 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.

  8. What is genomics? The -omics revolution of science Functional genomics Structural genomics Physiological genomics Toxicogenomics Proteomics Metabolomics, etc., etc. What does it all mean?

  9. Genomics • Philosophical - New way to approach biological problems. • Practical - High-throughput methods for analyzing biological systems. • FAST evolving field

  10. Functional Genomics B. subtilis DNA microarray

  11. Proteomics 2-D gel electrophoresis

  12. Structural genomics Structure of the YlqF GTPase of B. subtilis

  13. 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).

  14. 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?

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

  16. Web Access Text Entrez Sequence BLAST Structure VAST

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