Course Outline and Philosophy
Biology 524
Strategies of Host-Microbe Interactions
Spring Semester, 2008 M,W
2.00-3.15 Coker 119
Jeff Dangl
email: dangl@email.unc.edu
office hours by appointment, please email
Statement of Purpose: In this course, we will be exposed
to the richness of strategies that microbes use to access the nutrients
afforded by their hosts. We will discuss pathogens that cause disease and also
more subtle forms of host-microbe interaction such as mutualism and symbiosis.
We will cover topics that are areas of active research, and we will therefore
rely on recent reviews and primary research papers, as well as more basic text
readings. We will largely concentrate on bacterial and fungal systems. This
course will be very challenging, and there will be a heavy reading load. I hope
to instill in students an appreciation for the breadth of this topic and the
excitement that exists in this area. We will by no means cover it all!
Expect to spend at least 3 hours
reading for each lecture. But there are few other homework assignments.
Required
(1) Book Chapters from
a text called Bacterial Pathogenesis by Salyers and Whitt, 2nd edition (American SM Press,
2002) (denoted SW on the syllabus; these chapters will be made
available as electronic reserved reading as pdf files).
To view
your paper reserve items, click:
http://webcat.lib.unc.edu/search/a?searchtype=r&searcharg=biol524&submit=Search
The stable
link that you requested to your electronic reserve items is:
http://laconia.lib.unc.edu/eres/coursepage.aspx?cid=3093
You can
also try the direct connection at:
http://eres.lib.unc.edu.libproxy.lib.unc.edu/eres/coursepage.aspx?cid=3093&page=docs
(2) a variety of Research Publications
and News Stories are all available as pdf files on the course web
site.
Course Web Site: http://www.bio.unc.edu/Courses/2008Spring/Biol524/
Mode of presentation: This course is intended for highly
motivated people and I want it to be largely discussion oriented. I want you to
learn to talk and write about science, and be able to understand and present
scientific results.
This REQUIRES
that you do the reading BEFORE each class. I hope that the course will
be discussion-style, question and answer driven. I will give short,
introductory lectures and then we will turn to dissection of a research
problem. I want you to ask questions, and answer each other’s questions. I will
facilitate the discussion and try to give the “facts” for you to operate on. If
things slow down, I will call on people to answer questions in class. The goal
is to stimulate you to not only read the material, but to learn and practice
oral scientific critique.
Class
participation is a must. Please don’t be shy about joining the
discussion. If you have a question, it is highly likely that someone else in
the group has the same one. There is no such thing as a “stupid question”; just
ask.
Exams and Grading: Your participation in discussions and attendance
will count for 25% of your grade. It will be obvious to me if you are not
prepared, and that will detract not only from your learning experience and fun,
but also from your final grade. The will be a midterm exam, also counting for
25% of your grade. I will give you two hours for this exam, and you will be
required to sign an honor pledge for it. The remainder of your grade will be
determined by an oral presentation (25%) and a “research proposal” style term
paper (25%). These three participatory items are each described below.
Student Presentations and “Research Proposal”: In a month or so, we will draw
dates for the presentations. Your written research proposals are due on Tuesday May 6,
For the Presentation and Research Proposal, each of you should choose either a
topic covered in the course, or a very similar one. You will have some time to
think about what you are interested in, but note from the syllabus that
OUTLINES of no more than 2 pages double spaced are DUE by email to me on
Friday, March 14. I will be happy to receive them earlier, and to
discuss them with you. Do not be afraid to choose a topic that we will not
cover until near the end of the semester. There are certain advantages to
approaching these topics without being biased. The reading lists will be
available, and I will be happy to discuss the topics informally before we cover
them in class with those of you in this position.
Each Presentation will be a 15 minute presentation of your term paper
using overheads and / or slides, followed by a 5 minute discussion period. Both
your talk and the “research proposal” have the following goals:
(1) To
educate your classmates and me as to the nature of the biological problem under
study and (2) to convince them that your proposed experiments have merit, and
(3) will add to the knowledge base in that field. In real terms, get the
proposal funded! This requires clarity, homework, and some exuberance for the
subject.
I think you
will find this format useful, and it will encourage each of you to develop
ideas, read independently and find strategies that allow you to communicate
complex topics in simple language.
Both your
talk (15-20 Powerpoint slides MAXIMUM) and the Research Proposal should be
arranged as follows (numbers in parentheses refer to upper page limits, double
spaced, for each section)
1) summarize your overall goals
(best done in “bullet” or “outline” form). (0.5)
2) briefly summarize the current
status of the research area covered by your proposal. (3)
3) state the Specific Aims of your
proposal (one or two clearly stated aims are sufficient).
4) Describe in simple terms a set of
experiments to address your Specific Aims.
Discuss the
possible outcomes of each experiment and how you would interpret them. (5)
5) list of full references, use the
format of the journal
This is the
typical organization of all graduate and post-doctoral fellowship applications,
as well as a normal grant proposal. Citation of references and any figures,
graphs, tables, or schematic representations of experiments proposed and
possible outcomes or interpretations DO NOT count in these page limits.
Tutorials: You will see from the schedule that we will take one class
week off before these presentations begin. During this time, I will schedule
meetings with each of you separately to “coach” you a bit and help with ideas
as to how to effectively communicate your ideas to the class. Consider this a
“dry run”. Note that if you are one of the “early presentations” it will
probably be advantageous to you if we schedule this meeting before the
“tutorial period”.
Texts and Reading Lists: As stated above, you will be
expected to read quite a lot for this course. I have tried to arrange the
topics, in each case, first with a general review followed by examination of
one of two primary research papers. Those of you who do not have very much
experience reading primary research papers will find it overwhelming in the
beginning. Stick to it.
Some keys for success: Draw pictures of the experiments
described in the text--a simple re-statement in your own pictorial terms is
often worth the proverbial thousand words! So keep pencil and scrap paper handy
while you read. Always keep in mind the goal of the experiments, which are
hopefully clearly stated in the Abstract or Summary at the beginning of each
paper. Understand each figure on its own as an experiment. Pay close attention
to what the authors conclude from their results--Are the conclusions supported
by the data? Have the authors performed the correct “control” experiments to
show that their experimental conclusions are right?
Computer skills: You are responsible for learning how to use Adobe
Acrobat reader (it is free), EndNote or another reference management program,
and you will also need to know MS Word and one presentation/drawing program,
usually Powerpoint or Canvas. You may want to bring your laptop to class to
have the reading material at hand. Otherwise bring print-outs of the papers.
Learning to handle scientific publications electronically is part of this
course. If you do not know how, go to ATN help Desk and find out!
Model Presentations and Research Proposals from past
years:
Syllabus
Biology 524
Strategies of Host-Microbe Interactions
Spring Semester, 2008 M,W
2.00-3.15 Coker 119
Lecture:
1 W Jan. 9 Class
Introduction: Review of Bacterial Genetics
In this first, very short week, please review your Bio 50 (now Bio 202)
text. If you sold it, go find one in the library. There are several on Reserve for
Bio 50 (now Bio 202) and they all have a Bacterial Genetics chapter. Review of
plasmids, gene transfer (conjugation, transformation, phage transduction) and
mechanisms of Gene Regulation in prokaryotes.
Here’s the
Powerpoint slide
show for Lecture 1 and Lecture 2.
2 M Jan 14 Continuation
of Lecture 1. Guest Lecturer, Emily Fisher.
3 W Jan 16 Infection
mechanisms of bacterial pathogens and methods of analysis.
SW chapters 2 and 3 (or from the 1st edition, as posted here, chapters 3, 6).
Here’s the Powerpoint
show for Lecture 3
In addition,
go to: http://www.bio.davidson.edu/courses/genomics/chip/chip.html.
Go through this animation CAREFULLY to understand
M Jan 21 Martin Luther King Holiday
“True
compassion is more than flinging a coin to a beggar; it understands that an
edifice that produces beggars needs re-structuring."
Instead of
just going home for a long weekend and lounging around, get involved in your
community.
Honor the man.
4 W Jan 23 Strategies for
identification of virulence genes.
Here’s the Powerpoint show for Lecture 4
Heithoff,
D. M., et al. (1997) Dissecting the biology of a pathogen infection Trends in Microbiol. 5, 509-513. (an excellent systems
review).
Valdivia,
R. H., and Falkow, S. (1997) Fluroescence-based
isolation of bacterial genes within host cells. Science 277, 2001-2011.
5 M Jan 28 Comparative
Genomics and Understanding Virulence in E.
coli
SW chapters 28 and 29
Here’s the PowerPoint
show for Lecture 5
Medini, D. et al.
(2005) The microbial pan-genome. Current Opin. In Genet. and Develop.
15, 589-594.
Dobrint,
U. et al. (2004) Genomic islands in pathogenic and environmental
microorganisms. Nature Rev.
Microbiol. 2, 414-424.
Brzuszkiewicz,
E. et al. (2007) How to become a uropathogen: Comparative genomic analysis of
extraintestinal pathogenic Escherichia
coli strains. Proc. Natl. Acad. Sci.,USA 103, 12879-12884.
Extra reading, if interested:
Welch,
R.A. et al. (2002) Extensive mosaic structure revealed by the complete genome
sequence of uropathogenic Escherichia
coli. Proc. Natl. Acad.
Sci., USA 99, 17020-107024.
6 W Jan 30 Commonalities
in bacterial pathogenesis: Type
Here’s the PowerPoint
slide show for Lecture 6
He,
S. Y. et al. (2004) Type
(a long
review—do not get bogged down with the gene names; focus on the principles)
He, S.-Y., et
al. (2001) The Hrp pilus in Type
Anderson,
D., et al (1999) Reciprocal secretion of proteins by the bacterial type
7 M Feb 4 Recognizing
pathogens by recognizing virulence factor action: the plant immune system.
Here’s the PowerPoint
show for Lectures 7 and 8.
Jones,
JDG and JL Dangl (2006) The Plant Immune System. Nature 444, 323-329.
Shao,
F. et al. (2003) Cleavage of Arabidopsis PBS1
by a bacterial type
Ade
J. et al. (2007) Indirect activation of a plant
nucleotide binding site–leucine-rich repeat protein by a bacterial protease. Proc. Natl. Acad. Sci., USA 104, 2531-2536.
8 W Feb 6 The plant immune
system, part 2.
9 M Feb 11 A broad host pathogen: The Pseudomonas aeruginosa
system.
SW Chapter 16
Here’s the Powerpoint
show for Lecture 9
Rahme,
L.., et al. (2000) Plants and animals
share functionally common bacterial virulence factors. Proc. Natl.
Acad. Sci. 97, 8815-8821. (a good
review).
Rahme,
L.., et al. (1995) Common virulence factors for bacterial pathogenicity in
plants and animals. Science 268,
1899-1902. (see also short news article at the end of this pdf.)
Extra reading, if interested;
He,
J. et al. (2004) The broad host
range pathogen Pseudomonas aeruginosa strain PA14 carries two
pathogenicity islands harboring plant and animal virulence genes. Proc. Natl. Acad. Sci., USA 101, 2530-2535.
11 M Feb 18 The Genesis of Cholera epidemics.
Here’s the PowerPoint show for Lectures 11 and 12.
SW Chapter on Cholera (skim!)
Faruque, S. H. and Mekalanos, J. J. (2004) Pathogenicity islands and phages in Vibrio cholerae evolution. Trends Micrbiol. 11, 505-1510.
Waldor, M. K. and Mekalanos, J. J. (1996) Science, 272, 1910-1914.
Lysogenic conversion by a filamentous phage encoding cholera toxin.
Faruque, S. H. et al. (2004) Genetic diversity and virulence potential of environmental Vibrio cholerae population in a cholera-endemic area.
Proc. Natl. Acad. Sci., USA 101, 2123-2128
12 W Feb 20 Same as Lecture 11.
13 M Feb 25 Intracellular entry, growth and spread: How
Salmonella
usurps host cell biology.
Here’s the PowerPoint
show for Lecture 13
SW Chapter 26 (skim)