PMB 220 Fall 2006
Critical Thinking in Microbiology
Tuesdays and Thursdays 12:30 - 2:00, 106 Mulford Hall
| Instructors: | ||||
| Tom Bruns web site |
Louise Glass web site |
John Coates web site |
John Taylor web site |
Dan Portnoy web site |
Course Description, Grading, Etc.
Lecture Schedule
| READING LIST | ||
| 8/29 week 1 | lecture 1.pdf | Outline of genetics lecture #1 |
| questions 1.pdf | Questions for discussion from lecture #1 | |
| problems 1.pdf | Practice Genetic Problems PMB 220 | |
| Fink 2005.pdf | Intragenic tandem repeats generate functional variability | |
| Srikhanta 2005.pdf | The phasevarion: A genetic system controlling coordinated, random switching of expression of multiple genes | |
| 9/05 week 2 | lecture 2.pdf | Prokaryotic genomes and genetics |
| questions 2.pdf | bacterial genetics questions | |
| Branda 2004.pdf | Genes involved in formation of structured multicellular communities by Bacillus subtilis | |
| 9/12 week 3 | Eichenberger 2004.pdf | The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis |
| Richard 2005.pdf | Candida albicans Biofilm-Defective Mutants | |
| lecture 3 notes.pdf | Nuclear genome characteristics of microbial eukaryotes | |
| questions 3.pdf | Questions on “The program of gene transcription for a single differentiating cell type during sporulation in Bacillus subtilis” by Eichenberger et al. | |
| 9/19 week 4 | lecture 04 [pdf] [doc] | Bacterial pathogenesis |
| Hensel 1995.pdf | Simultaneous identification of bacterial virulence genes by negative selection | |
| Mahan 1993.pdf | Selection of bacterial virulence genes that are specifically induced in host tissue | |
| Sasetti 2003.pdf | Genetic requirements for mycobacterial survival during infection | |
| Valdivia 1997.pdf | Fluorescence-based isolation of bacterial genes expressed within host cells | |
| 9/26 week 5 | Decatur 2000.pdf | A PEST-Like sequence in listeriolysin O essential for Listeria monocytogenes pathogenicity |
| Lety 2001.pdf | Identification of a PEST-like motif in listeriolysin O required for phagosomal escape and for virulence in Listeria monocytogenes | |
| 10/03 week 6 | Montminy 2006.pdf | Virulence factors of Yersinia pestis are overcome by a strong lipopolysaccharide response |
| 10/10 week 7 | lecture 07 [pdf] [doc] | the Hydrogen Threshold |
| Coates 1996.pdf | Anaerobic hydrocarbon degradation in petroleum-contaminated harbor sediments under sulfate-reducing and artificially imposed iron-reducing conditions | |
| Cunningham 2001.pdf | Enhanced in situ bioremediation of BTEX-contaminated groundwater by combined injection of nitrate and sulfate | |
| Thamdrup 1993.pdf | Bacterial disproportionation of elemental sulfur coupled to chemical reduction of iron or manganese | |
| 10/17 week 8 | lecture 08 [ppt] [pdf] | Bioremediation |
| homework 08 [pdf] [doc] | ||
| 10/24 week 9 | lecture 09 [ppt] [pdf] | Microbial Fuel Cells |
| homework 09 [pdf] [doc] | due November 7th | |
| 10/31 week 10 | handout 10 [pdf] [doc] | Phylogenetics, the big tree of life |
| Berbee Tayor 1999.pdf | Fungal Phylogeny | |
| Bauldauf 2003.pdf | Phylogeny for the faint of heart: a tutorial | |
| Lewis 2001.pdf | Phylogenetic systematics turns over a new leaf | |
| Walsh 2005.pdf | The real 'domains' of life | |
| Brown 1997.pdf | Archaea and the Prokaryote-to-Eukaryote Transition | |
| Rokas 2003.pdf | Genome-scale approaches to resolving incongruence in molecular phylogenies | |
| Jeffroy 2006.pdf | Phylogenomics: the beginning of incongruence? | |
| 11/07 week 11 | handout 11 [pdf] | Microbial species concepts |
| lecture 11 [pdf] [ppt] | Species concepts in microbes | |
| 11/14 week 12 | handout 12 [pdf] [doc] | Microbial genetic exchange |
| lecture 12 [pdf] [ppt] | Microbial reproductive modes | |
| 11/21 week 13 | handout 13 [pdf] | Microbial community analysis |
| lecture 13 [pdf] | Functional vs Organismal views of Ecology | |
| homework 13 [pdf] | Papers to read for Thursday Nov 30 | |
| 11/28 week 14 | handout 14 [pdf] | Detection of activity or function |
| lecture 14 [pdf] | T-RFLP (terminal restriction fragment length polymorphism) | |
| 11/30 week 14 | Eckburg 2005.pdf | Diversity of the human intestinal microbial flora |
| Fierer 2006.pdf | The diversity and biogeography of soil bacterial communities | |
| Obrien 2005.pdf | Fungal community analysis by large-scale sequencing of environmental samples | |
| 12/05 week 15 | Hughes 2001.pdf | Counting the uncountable: Statistical approaches to estimating microbial diversity |
| Landeweert 2003.pdf | Quantification of ectomycorrhizal mycelium in soil by real-time PCR compared to conventional quantification techniques | |
| Singleton 2001.pdf | Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples | |
| 12/07 week 15 | Tringe 2005.pdf | Comparative metagenomics of microbial communities |
| Tyson 2004.pdf | Community structure and metabolism through reconstruction of microbial genomes from the environment | |
| Venter 2004.pdf | Environmental genome shotgun sequencing of the Sargasso Sea | |
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class photo |
last updated: November 28 2006