Download BIOMI/PLAA 608 Bacterium

Genomics of Bacterium-Host Interactions: BIOMI/PLPA 6080
Lecturers: Alan Collmer, Dave Schneider, Steve Winans, Magdalen Lindeberg
Syllabus for Fall 2010
9:05-9:55 MWF
9/27 – 10/25
336 Plant Science Building
The genomics revolution began in 1995 with the determination of the first complete genomic
sequence of a free-living organism, the pathogen Haemophilus influenzae, by The Institute for
Genomic Research (TIGR). Interest in pathogens has continued to motivate genomics efforts,
and knowledge gained through genomics has revolutionized our understanding of pathogenesis.
These activities have combined to spawn the new discipline of "pathogenomics". In essence,
pathogenomics involves identifying and characterizing the subset of genes in a pathogen that
confer virulence, the "virulome". Because pathogen-host coevolution drives the development of
multifactorial virulence systems featuring redundancy and system robustness, the seemingly
simple mission of pathogenomics employs a powerful suite of bioinformatic tools and addresses
major concepts in pathogenic microbiology. Thus, this course will introduce and employ tools for
annotating, visualizing and aligning whole bacterial genomes, sequence similarity searches,
protein family classification, and protein and RNA structure prediction. In addition, the course
will address concepts such as the pan-genome, horizontal gene transfer, bacterial genome
structure, and the "eco-evo" view of bacterium-host interactions. The course will draw examples
from both animal and plant pathogens. Students will gain experience with key bioinformatic tools
through a class project based on newly deposited, but unpublished Pseudomonas syringae
genomes.
Course Schedule
Date
9/27
9/29
10/1
10/4
10/6
10/8
10/11
10/13
10/15
10/18
10/20
10/22
10/25
Topic
Introduction to pathogenomics
Genome annotation, visualization and alignment
Classification and structure prediction for RNA and proteins
Key experimental tools in pathogenomics
Key structural features of pathogen genomes
Introduction to bioinformatics project
Fall Break
Mechanisms of horizontal gene transfer and genome change
Pathogenomic lessons from the Rhizobiaceae
Pathogenomic lessons from the Enterobacteriaceae
Pseudomonas aeruginosa and clinical applications
Review of lessons in the context of systems biology
Reports on bioinformatics project
Presenter
Collmer
Schneider
Schneider
Collmer
Collmer
Lindeberg
Winans
Winans
Winans
Collmer
Class and staff
Class and staff