BICH464 & BCH689 Bacteriophage Genomics
Spring 2013
Instructors:
Dr. Ry Young
Dr. Gabriela Kuty
Sadie Hatfield Professor of Agriculture
Research Associate
Center for Phage Technology
Center for Phage Technology
Department of Biochemistry &
Room 312A, BioBio
Biophysics
gabbykuty@tamu.edu; 845-6839
Room 311A, BioBio
ryland@tamu.edu; 845-2087
Course website:
http://sites.google.com/a/tamu.edu/bich-464/
(current official class schedule is kept on the website.)
Course secretary: Daisy Wilbert, room 308 BioBio; daisy@tamu.edu; 845-9427
Lectures: Tues (& some Thurs) 1110 – 1235, 106 BioBio
Computer laboratory sessions: Thurs (& some Tues) 1110 – 1235, 106 BioBio
Bench Laboratories: Fridays, 0910 – 1200 or 1400 - 1650. 243 BioBio or CPT
Laboratory, (312 BioBio) as announced.
Note: BICH689 enhancements noted in italics
Overview of the course:
This course is a 3-credit lecture-laboratory course focused on the genomics of
bacteriophages, the viruses of bacteria. It has two broad aims: to equip the students
with a basic understanding of the fundamentals of bacteriophage biology and to provide
a real basic research experience in modern genomics, culminating in the writing of a real
scientific paper on the genomics of a novel bacteriophage. The focus on bacteriophage
biology is chosen not only because of the tractable size of phage genomes but also
because phage biology is an important factor in ecology, evolution, and health, as well
as being the original and still powerful model system for the development of molecular
biology. The course has been funded by the National Science Foundation for more than
a decade.
The graduate version of the course, BICH689, is appropriately enhanced, as
noted below by italicized text.
Pre-requisites and background:
Success in this course requires a unique combination of classroom performance,
computer analysis, and laboratory ability. The lecture material is focused on the biology
of bacteriophages, the viruses of bacteria, to provide each student with the basic
understand and vocabulary needed to complete a de novo genomic analysis of a novel
phage. Enrolled students should have already taken a course that covers fundamentals
of the bacterial genetic code, gene structure and expression, DNA replication and
genetic recombination, as well as basic microbiology (i.e., bacterial cell structure). The
best preparation would include BICH/GENE431 (Molecular Genetics) and BIOL351
(Fundamentals of Microbiology). BIOL406 (Bacterial Genetics), BIOL438 (Bacterial
Physiology) and BIOL445 (Biology of Viruses) would also be advantageous, even as
concurrent registration. Although not required, previous exposure to genomics and
bioinformatics would also be useful, especially BIOL/BICH450 (Introduction to
Genomics), BIOL451 (Bioinformatics), and a new Biology course, Functional Genomics
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(temporarily BIO489). Previous research in a lab where you worked with bacteria or with
DNA and/or DNA sequences also provides useful background. The instructors will take
the full range of courses and academic performance into consideration when selecting
the registrants, as generally there are more students interested in taking the course than
the slots that are available. Preference will be given to juniors and seniors who have
had the best background for the coursework and the project. However, feel free to
express your case about why you should be allowed to enroll even if you don't have the
recommended background. Enthusiasm and energy count for a lot!
The course may also be taken by graduate students, either as BICH464 or
BICH689. Extra responsibilities for BICH689 graduate students are detailed below in
italics. Enrolled students should have already taken a course that covers fundamentals
of the genetic code, gene structure and expression, DNA replication and genetic
recombination, as well as basic microbiology (i.e., bacterial cell structure). Examples
would be BIO213, GENE302, and BICH/GENE431. A basic microbiology course is also
highly recommended; e.g., MICR351. Although there will be a brief review of
fundamentals as needed during the course, some prior experience in these areas is
important. Please consult the Instructor if you have comparable course-work or
experience that would qualify you for this course.
The course may also be taken by graduate students. If the student enrolls in
BICH689, there are two main differences between the BICH464 and BICH689 versions
of the course. First, the take-home portion of the two exams are more intensive and
require accessing literature. Second, the required genome paper is a full-paper format,
including Abstract, Introduction, Results and Discussion. Third, graduate students are
required to conduct more extensive characterizations of the phages isolated in the bench
laboratory sessions. Graduate requirements different from the BICH464 requirements
are in italics below.
Organization:
The course will be limited to 20 students and will meet, on average, for one 75
min lecture period per week. Students will also have 75 min computer laboratories and
bench laboratory sessions, estimated to occupy a total of ~ 4.5 hours per week.
However, during the semester, the amount of class time devoted to these three activities
(lecture, computer lab and bench lab) will vary considerably.
Grading: (BICH464 enrollees)
Grades will be assigned as follows, based on 1000 total possible points. The
initial grading scale is: 850+ = A; 650-850 = B; 500-649 = C; 400-499 = D; <400, F.
Grading will be based on a curve determined at the end of the semester. This is
necessary due to the variable nature of the novel phage genomes that are assigned to
the student roster. Basically this is a “degree of difficulty” issue.
Grade components:
Exams: two exams, each 100 points, total maximum 200 pts.
1. Each exam will have in-class, closed book and take-home, open book
components. Generally this will be done on a 65% - 35% split. The BICH689
take-home segment will be more intensive and require accessing the literature.
2. If necessary, each exam will subjected to a curve so that the average grade is
raised to 70 points (70%). However, if the average is higher than that, no curve
will be applied.
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3. Make-ups for excused absences held on next class day in Instructor's office, at
time TBA.
Quizzes: 6 quizzes, maximum 100 pts.
(Note Quiz schedule may change; if so, you will be notified, but ALWAYS check
class schedule on web.)
1. Each quiz counts 25 points; only the four highest quiz grades count, so
maximum total is 100 points.
2. No make-ups.
3. Each quiz is 5 m/c, t/f or fill-blank questions based on the reading
assignment for that day, or material as specified by the instructor.
Bench Lab: total 200 points
1. Notebook readability & organization = maximum 50 points
2. Results (quality of work in phage hunts, phage processing and
characterization) = maximum 150 points. In the BICH689 version, a more
extensive characterization of the phage DNA will be required, including a
Pulsed Field Gel analysis that must be done out of class hours.
Genome annotation and paper: 350 points (maximum)
See handout describing the Genome Annotation and Paper requirements.
In general this grade will be assigned by the instructor on the quality of the
annotation, including the depth and originality of the gene analysis, the graphics
prepared to describe the genome, and the exploitation of the most significant or
unusual features of the annotation. In general, the BICH464 paper requirement
will be in the form of a Journal of Virology Genome Announcement and will be
submitted to the journal, with minimal editing, at the end of the semester. For
BICH689 enrollees, the paper will be a full length paper modeled on a
submission to the Journal of Bacteriology or Virology.
Class attendance and participation: 150 points.(maximum).
50 points will be awarded for perfect attendance. 5 points will be
deducted for each unexcused absence.
0 - 100 points will be awarded based on Instructors’ assessment of your
participation in the class lecture, computer lab and wet lab activities. If
you make a good faith effort to answer questions in class, but nothing
else, expect approximately 50 points for this. Higher scores in this
category reflect above-average participation.
Presentation bonus points (maximum 15 pts added to an exam grade):
One exam grade can be increased up to 15 points for the presentation of
a 10 minute Powerpoint talk summarizing the important and/or most
interesting features of your genomic analysis. This is entirely voluntary.
Instructors will be available to help design and implement your
presentation. Presentations will be scheduled during a C period, TBA,
during late April. Limited to first 5 volunteers.
Textbooks:
The instructor will provide a textbook-formatted set of class notes that will be
used as the textbook for the lecture portion of the course. In addition, Snyder and
Champness’s "Molecular Genetics of Bacteria" is recommended as a background text.
However, copies of this book will be on reserve in the secretary's office.
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