University of Delaware
Department
of Biological Sciences
BISC667:
"Molecular Mechanisms of Pathogens"
This course
will introduce advanced topics in mechanisms of pathogenesis in relation to the
primary scientific literature.
Suggested textbook: Bacterial
Pathogenesis: A molecular approach by Salyers and Whitt (ASM Press). In addition, the class will discuss all
topics in relation to the primary scientific literature. Notes for the class and the papers to be
discussed will be found on Web CT.
Coordinator: Dr. E. Fidelma Boyd
Schedule: Monday/Wednesday Room Wolf 318, 1.45pm - 3.00pm
Grading
50% Two
cumulative one hour exam on course material (25% mid-term and 25% Final exam to give 50% total)
20% Two
class presentations per student of research papers (10% each)
20% Four
written critiques of research articles (5% each)
10% Class
participation
Prerequisites:
BISC 300 (or equivalent). In addition, a
working understanding of microbial molecular biology and microbial genetics is
expected. If you have any doubts about
your preparation please discuss this with Dr. E. Fidelma Boyd the first week of
class.
Professor: E. Fidelma Boyd, Ph.D.
Department of Biological
Sciences
328 Wolf Hall
fboyd@udel.edu
Course policies:
Attendance: Attendance will not be taken and is
not figured into the final grade.
However, students are responsible for all material covered in class
(which may or may not be found in the materials posted on WebCt).
EXAMS: Two
cumulative one hour exams will be given to test your understanding of the
material presented in lecture. All exam
questions are either short answer format or multiple choice questions. Make-up exams will only be given under the
most unusual and very rare circumstances (such as medical emergency or family
crisis), which must be accompanied by documentation. You must contact Dr. E. Fidelma Boyd in
writing at least two days ahead of the exam to be missed, to stand any chance
of being granted a make-up exam.
Presentations: There are four paper sets,
with each student presenting twice during the semester. I will assign papers
after the first week of class. Each paper set consists of four papers, and each
student with be assigned two papers to present and two papers to write a critique
on (see below for details on written critique).
When it is your turn to present,
you should give 1) a short introduction to the topic, 2) major findings and 3)
overall conclusions of how the research has advanced the field. Then open the floor for discussion. 10
presentations plus 5 minutes of discussion.
Every student is expected to have read all papers and therefore
participate actively in discussion.
During the discussion, you should make sure
as presenter that everyone gets a chance to participate, and should also
recognize when the discussion is dwelling on minor points or bogging down and
pose questions that will get things back on track.
To present visual information as part of
your presentation, you may use the chalkboard, overheads, PowerPoint (for
Windows or Macintosh). If you are going to use PowerPoint, e-mail the file to
me by 1 p.m. on the day of your presentation, and if possible, bring the file
to class on a flash drive or CD as a backup in case the e-mail doesn't work.
Each presentation will be worth 10 percent
of your grade (20 per cent total), based on the thoroughness of your
preparation, your effective use of visual aids (note that "effective"
does not mean "flashy"; sometimes a simple chalkboard drawing is all
you need), and your ability at leading a discussion.
Papers: You are required to submit a critique of each paper
set presented (4 in all), at the end of class on the day of the discussion of
each paper set. Each paper must be typed
and at least one-and-a-half single-spaced pages long (maximum word count 1000)
and must identify the major question or questions each paper was trying to
answer, discuss how well the papers addressed their main questions, mention one
or two good and bad points about each paper, and suggest further research.
Points are awarded to papers with more opinions then papers that merely
summarize the contents of papers. These
papers will count for 20 percent of your grade.
Remember, it is more difficult than you may think to write a synopsis of
paper, it takes time and effort. You
will not be able to start on your paper the night before it is due and expect
to do a passing job. Late papers will not be accepted. If you have a conflict on the day a paper is
due, I expect to receive it EARLY.
Participation: Your participation in the class discussions will
count for 10 percent of your grade. If
you say something in every discussion class, you'll get the full 10 percent; to
encourage uninhibited discussion, I'm not going to grade the content of your
comments.
I will be
happy to discuss your paper and presentations with you and help you put it
together in the correct form if you are uncertain what is expected. However, it is your responsibility to contact
the course instructors with your problems.
If I do not hear from you, I will assume that you understand the
assignments fully.
Office hours: I will not have formal office hours; if you'd like to
talk to me, feel free to e-mail me to make an appointment or I'm generally at
my office or lab from 8 a.m. to 6 p.m.
Academic dishonesty/plagiarism: It is the student’s responsibility
to ensure that all work for this class is their own (you may discuss possible
paper topics among yourselves). We will
prosecute any and all instances of cheating to the fullest extent allowable by
the university.
Copying someone else's writing and
pretending that it is yours is a serious violation of the University's Code
of Conduct. If you copy text
from a book, article, web page, or other source, or from another student or
former student, you will receive a 0 for the assignment. If the copying is
particularly extensive or egregious, you will receive a harsher penalty, up to
an F for the course. In some cases, you
may also be required to take university mandating courses on appropriate
academic conduct to remain a student at UD.
To illustrate the difference between
plagiarism and acceptable paraphrasing, here's a passage from Hudson et al.
(1987):
The
presence of a balanced polymorphism in the coding region of Adh could
explain the relatively high level of polymorphism observed in that region. The
existence of a balanced polymorphism at a single site can lead to higher levels
of neutral polymorphism at linked sites (Strobeck 1983). The reason this can
occur is that during the time that the balanced polymorphism is maintained by
selection, new mutations will tend to accumulate in the region tightly linked
to the selected site.
Copying these words exactly is
plagiarism, even if you put "(Hudson et al. 1987)" at the end. It's
also plagiarism if you just change a few words, like this:
A balanced
polymorphism in the coding region of Adh could explain the high level of
polymorphism in that region. The existence of a balanced polymorphism at a
single site can cause higher levels of neutral polymorphism at linked sites
(Strobeck 1983). This is because during the time that the balanced polymorphism
is maintained by selection, new mutations will accumulate in the region tightly
linked to the selected site (Hudson et al. 1987).
Instead of copying or trying to
rewrite a passage, you should paraphrase it, summarizing the information in
your own words:
There is an
area around an amino acid polymorphism in Adh that has a relatively high
level of silent polymorphism. This may be caused by balancing selection (Hudson
et al. 1987).
NOTE: All
statements of fact must be substantiated by a reference in correct format,
preferably from the primary scientific literature. Failure to reference your sources is also
plagiarism. (For instance, this statement on plagiarism is liberally lifted
from John McDonald’s course syllabus with permission :).
Direct
quotes
In papers in other fields, such as
English or history, it is common to use direct quotes, putting phrases or
sentences from sources in quotation marks. This is because the exact words are
important; if you're writing a paper on "Entomological ambiguities in
Kafka's Metamorphosis," it's important to quote exactly what Kafka
wrote about Gregor Samsa's carapace. As long as you cite the source correctly,
using quotes in quotation marks is not plagiarism.
In scientific writing, however, we
rarely use direct quotes. Partly, this is just a cultural tradition; partly,
it's because when scientists cite another paper, it's because they're writing
about the information in the paper, and the exact words used to convey that
information are not important. You may use a quotation or two, if you come
across a particularly pithy statement of an important concept, but you will get
points off for excessive use of direct quotes.
Disabilities: Students suspected of having a
learning disability must seek an accommodation from the office of academic
enrichment http://www.aec.udel.edu/LD_ADHD_students.html.
BISC667:
"Molecular Mechanisms of Pathogens"
Date Lecture
Topic
2/11 Introduction/course outline. Bacterial Cell and
Genome Structure
2/13 Molecular Bacterial Genetics I
2/18 Molecular
Bacterial Genetics II Horizontal transfer & integrative elements
2/20 Methods
in Molecular Pathogenesis I
2/25 Methods
in Molecular Pathogenesis II
2/27 Paper
Presentations. Articles 1 to 4.
3/3 Water-borne
Diseases I. The Players, Bacteria, viruses, protozoa
3/5 Water-borne
Diseases II. Molecular mechanisms (Vibrio cholerae)
3/10 Water-borne
Diseases III. Molecular mechanisms (Salmonella)
3/12 Food-borne Diseases I. The Players,
Bacteria, viruses, protozoa
3/17 Food-borne Diseases II. Molecular
mechanisms (Escherichia coli)
3/19 Food-borne
Diseases III. Molecular mechanisms (Listeria monocytogenes)
3/24 Paper Presentations. Articles 5 to 8.
************************* End of
material for Exam 1*************
3/26 MID-TERM EXAMINATION
3/29- 4/6 SPRING BREAK
4/7 Airborne
Diseases I. The players, Bacteria and viruses
4/9 Airborne
Diseases II: Molecular mechanisms (Legionella
pneumophila)
4/14 Airborne
Diseases III: Molecular mechanisms (Bordetella
pertussis)
4/16 Vector-borne
Disease I: Bacteria,
viruses, protozoa
4/21 Vector-borne
Disease II. Molecular
mechanisms (Borrelia burgdorferi)
4/23 Vector-borne
Disease III. Molecular
mechanisms (Yersinia pestis)
4/28 Paper
Presentations. Articles 8 to 12.
4/30 Sexually
transmitted diseases I: The players, Bacteria and viruses
5/5 Sexually
transmitted diseases II. Molecular mechanisms (Chlamydia trachomatis)
5/7 Sexually
transmitted diseases III. Molecular
mechanisms (HIV)
5/12 Emerging
Infectious Diseases (Staphylococcus aureus)
5/14 Origins
of major human infectious diseases
5/19 Paper
Presentations. Articles 12 to 16.
************************* End of
material for Exam 2*************
5/21 FINAL EXAM
Research Papers: The following are a list of
research papers that students are expected to read (articles 1 to 18) and
present (articles 1 to 12) to supplement their notes from class.
1.
Hacker J and Carniel E. Ecological fitness, genomic islands and
bacterial pathogenicity. A Darwinian view of the evolution of microbes. EMBO Rep. 2001 May;2(5):376-81.
2.
Wagner PL, Waldor MK. 2002. Bacteriophage control of bacterial virulence.
Infect Immun. 2002 Aug;70(8):3985-93.
3.
Faruque SM and Mekalanos JJ. Pathogenicity islands and phages in Vibrio
cholerae evolution. Trends Microbiol.
2003 Nov;11(11):505-10.
4.
Burrus, Vincent , Joeli Marrero and Matthew K.
Waldor. 2006. The current ICE age:
Biology and evolution of SXT-related integrating conjugative elements. Plasmid
55:173-183.
5.
Heithoff DM, Conner CP, Hanna PC, Julio SM, Hentschel U,
Mahan MJ. Bacterial infection as assessed by in vivo gene expression. Proc Natl
Acad Sci U S A. 1997 4;94(3):934-9.
6.
Saenz HL, Dehio C. Signature-tagged mutagenesis:
technical advances in a negative selection method for virulence gene
identification. Curr
Opin Microbiol. 2005 Oct;8(5):612-9. Review.
7.
Merrell DS, Camilli A. Acid tolerance of
gastrointestinal pathogens.Curr Opin Microbiol. 2002 Feb;5(1):51-5.
8. Nielsen, Alex Toftgaard
, Nadia A Dolganov, Glen Otto, Michael C Miller, Cheng Yen Wu, and Gary K
Schoolnik. 2007. RpoS Controls the Vibrio cholerae
Mucosal Escape Response. PLoS Pathogen. 2(10): e109.
9. Elahi, Shokrollah , James
Holmstrom and Volker Gerdts. 2007. The
benefits of using diverse animal models for studying pertussis. Trends in
Microbiology, 15(10):462-8.
10. De Buck, Emmy , Jozef Anné and Elke
Lammertyn. 2007. The role of protein secretion systems in the
virulence of the intracellular pathogen Legionella pneumophila. Microbiology,
153(Pt 12):3948-53.
11. Hovius JW, van Dam AP, Fikrig E. 2007.
Tick-host-pathogen
interactions in Lyme borreliosis. Trends Parasitol.23(9):434-8.
12.
Riedel CU, Monk IR, Casey PG, Morrissey D, O'Sullivan GC,
Tangney M, Hill C, Gahan CG.
2007. Improved luciferase tagging
system for Listeria monocytogenes allows real-time monitoring in vivo and in
vitro. Appl Environ Microbiol73(9):3091-4
13. Ohnishi M, Tanaka
C, Kuhara S, Ishii K, Hattori M, Kurokawa K, Yasunaga T, Makino K, Shinagawa H,
Murata T, Nakayama K, Terawaki Y, Hayashi T. Chromosome of the
enterohemorrhagic Escherichia coli O157:H7; comparative analysis with K-12
MG1655 revealed the acquisition of a large amount of foreign DNAs.DNA Res. 1999
Dec 31;6(6):361-8.
14. Baker S, Dougan G.
The genome of Salmonella enterica serovar Typhi.Clin Infect Dis. 2007 Jul
15;45 Suppl 1:S29-33.
15. Sirand-Pugnet P, Lartigue C, Marenda M, Jacob D, Barre A,
Barbe V, Schenowitz C, Mangenot S, Couloux A, Segurens B, de Daruvar A,
Blanchard A, Citti C. Being pathogenic, plastic,
and sexual while living with a nearly minimal bacterial genome. PLoS Genet. 2007 3(5):e75.
16.
Terekhova D, Iyer R, Wormser GP, Schwartz I. Comparative genome hybridization reveals
substantial variation among clinical isolates of Borrelia burgdorferi sensu stricto with different pathogenic
properties. J Bacteriol. 2006 Sep;188(17):6124-34.
17.
Bryant JE, Holmes EC, Barrett AD.Out of Africa: a molecular
perspective on the introduction of yellow fever virus into the Americas. PLoS Pathog. 2007 May 18;3(5):e75.
18.
Wolfe ND, Dunavan CP, Diamond J. Origins of major human infectious
diseases. Nature. 2007 447(7142):279-83.
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