Department of Biology

Biology 522 Course Website

Bacterial Genetics
Spring 2008
 

 

Syllabus (html)

Syllabus (PDF)

 

Lecture 02/18/2004 (html)

Lecture 02/18/2004 (ppt)

 

Lecture 02/20/2004 (html)

Lecture 02/20/2004 (ppt)

 

Lecture 03/01/2004 (html)

Lecture 03/01/2004 (ppt)

 

 

 

 

Pre-Laboratory Exercises

Lab 6 (Doc, PDF)

 

Protein Secretion Slides

Protein Secretion (ppt)
Dr. Todd Vision Phylogenetics Lecture (PDF)

 

Useful web sites 

http://www.BioCyc.org/    Bacterial metabolic pathways and genes

http://www.journals.asm.org/    American Society for Microbiology Journals

http://www.ncbi.nlm.nih.gov/genomes/MICROBES/Complete.html    microbial genomes complete sequences

http://www.ncbi.nlm.nih.gov/    National Center for Biotechnology Information 

http://www.ncbi.nlm.nih.gov/blast/Blast.cgi  NCBI blast site

http://agro.vbi.vt.edu/public Agrobacterium genome and annotation

http://us.expasy.org/    analysis tools

http://bioweb.pasteur.fr/intro-uk.html lots of nice analysis tools

http://www.umass.edu/microbio/chime/pipe/ftsz/present/    FtsZ web site

http://www.agrobacterium.org web site for annotation

http://pfam.sanger.ac.uk/ pfam site

http://www.megasoftware.net/index.html  site for mega 3.1

http://www.megasoftware.net/mega4  site for manual
 

Articles available on line

Luria and Delbruck

http://www.geocities.com/phagenoel/ClassicPapers.html

 

FtsZ and cell division review: Margolin, W. (2001). Spatial regulation of cytokinesis in bacteria. Curr Opin Microbiol 4, 647–652.
 

RNAP review

Volume 20, Issue 3 of Molecular Cell, 11 November

2005 pg 335-345

 

Holliday junctions

    J. Bacteriol. 181:5543-5550. 1999.  This review contains a good color diagram of a Holliday junction.

            Jeffery Errington, Richard A. Daniel, and Dirk-Jan Scheffers Cytokinesis in Bacteria Microbiol. Mol. Biol. Rev. 2003 67: 52-65. The most recent review.  You can look at it if you want to know what has happened to particular areas but you may find it a bit hard going.
 

Reuber and Walker, Biosynthesis of succinoglycan, a symbiotically important exopolysaccharide of Rhizobium meliloti. Cell 74:269-280 (1993).   This is an example of using molecular techniques to sort out the links between genes, proteins, and function.
 

Wang, L, Helman, J.D., and S. C. Winans. 1992. The A. tumefaciens transcriptional activator OccR causes a bend at a target promoter, which is partially relaxed by a plant tumor metabolite.  Cell 69, 659-667. 

Protein secretion

White, David  Book on reserve. Chapter 17

 

Z. Ding and P.J. Christie. 2003. J. Bacteriol. 185, 760-771. Pages 760-761 are what we need.

 

Regulation at the level of translation (paper to be rewritten)

J.R. Cole and M. Nomura. 1986. PNAS 83, 4129-4133.

 

Plasmids  

K. Geredes, T. Thistad, and J. Martinussen. 1990. Molecular Microbiology 4, 1807-1818.

 

Pathogenesis

Kaper, JB, Nataro, JP, and HL Mobley.  Pathogenic Escherchia coli. Nature Rev. Microbiol. 2: 123-140, 2004.

 

Quorum sensing

Fuqua, C. , Parsek, M.R. , Greenberg, E.P. (2001) Regulation of gene expression by cell-to-cell communication: acyl-homoserine lactone quorum sensing. Annu Rev Genet 35: 439–468.

Fuqua, C. and Greenberg, E.P. Listening in on bacteria: acyl-homoserine lactone signalling.
Nat Rev Mol Cell Biol. 2002 Sep;3(9):685-95.  This is in Nature Reviews and is shorter and probably more fun.

Regulatory RNA

Gottesman, S. Micros for microbes: non-coding regulatory RNAs in bacteria. 2005Trends Genet. 21:399-404.

Majdalani, N. , Vanderpool, C.K. , Gottesman, S. (2005) Bacterial small RNA regulators. Crit Rev Biochem Mol Biol 40: 93–113.

Biofilms

Stoodley, P., Sauer, K., Davies, D.G., & Costerton, J.W. (2002) Biofilms as complex differentiated communities. Annu. Rev. Microbiol. 56, 187-209.

Squid-Vibrio symbiosis

Nyholm S.V. and M.J. McFall-Ngai (2004) The winnowing: establishing the quid-Vibrio Symbiosis

Nature Reviews Microbiology 2: 632-642

Ruby, E. G., and Lee, K-H. (1998). The Vibrio fischeri-Euprymna scolopes light organ association: current ecological paradigms.  Appl. Environ. Microbiol. 64: 805-812.

Nishiguchi, M. K., Ruby, E. G., and McFall-Ngai, M. J. (1998) Parallel evolution in the sepolid squid-Vibrio symbiosis.  Appl. Environ. Micro. 64 3209-3213.

http://www.medmicro.wisc.edu  then go to faculty and to McFall-Ngai or to Ruby

 

 

 

 

 

 

Phylogeny Slides

Papers for discussions: Martin, Bayliss and Moxon, van der Woude