Genome Biology, Spr 04  Page 1
BIOLOGY 421
NICHOLLS STATE UNIVERSITY  DEPARTMENT
OF
BIOLOGICAL SCIENCES
GENOME BIOLOGY
*BIOL 421-2M——SUMMER 2004
MONDAYS THROUGH FRIDAYS  9:00 AM—10:20 AM  209 GOUAUX HALL
INSTRUCTOR: DR. JOHN P. DOUCET
OFFICE: 316 GOUAUX HALL  OFFICE HOURS: 4-5MTWH
PHONE: (985) 448-4721  EMAIL: john.doucet@nicholls.edu
COURSE DOWNLOAD SITE: http://www.nicholls.edu/biol-med/doucet/genomics
COURSE DESCRIPTION
*BIOL 421. Genome Biology. 3-0-0. Prerequisite: BIOL 203 or permission of the
department head. Results and applications of human and other genome projects. Emphasis
on new technologies and biological concepts derived from genomics, proteomics, and
bioinformatics. Includes computer experiences.
REQUIRED TEXT
There is no required text for the course. Required reading material will derive from
handouts, download site postings, websites, reading lists, and the scientific literature. Basic
concepts of some of the topics covered in the course can be found in specific chapters of the
required textbooks for BIOL 155 (General Biology) and BIOL 320 (Genetics). Students who
will be taking genetics in Fall 2004 can purchase this textbook (details below) in anticipation
of the course. A copy of the General Biology and Genetics textbooks (or pertinent chapters)
is on reserve in the library.
Klug, W. and Cumings, M. Essentials of Genetics (4 Ed.) Boston: Upper Saddle
River, NJ: Prentice Hall, 2002.
Raven, P. and Johnson, G. Biology (6 Ed.) Boston: McGraw-Hill, 2002.
COURSE GOAL
The goal of Genome Biology is to empower the student with contemporary knowledge and
investigative skills in genomics and associated disciplines in preparation for a twenty-first
century career in biological sciences.
STUDENT OUTCOME OBJECTIVES
In Genome Biology, the student will
 explain and apply basic principles underlying genomics
 appraise the significance and social implications of the Human Genome Project (HGP)
 differentiate results of animal, plant, and microbe genome projects to the HGP
 evaluate technological developments required by the HGP
Genome Biology, Spr 04  Page 2










discuss and illustrate the fine structures of chromosomes, genes, and non-gene DNA
evaluate gene discovery strategies
evaluate and discuss proteomics, pharmacogenomics, metabolomics, and transcriptomics
evaluate and apply the utility of single-nucleotide polymorphisms
appraise and predict genomic expansion by sequence repetition
appraise and predict genomic reduction by mutation and fine gene regulation
compare chromosome structure and organization between closely related species
evaluate the significance and predicted importance of new small RNA families
evaluate the usefulness of comparative genomics
design and construct a scientific synopsis of a species-specific genome project (other
than the HGP)
COURSE REQUIREMENTS
Each student is required to:
 attend all course lectures, computer laboratories, and special meetings.
 maintain access to required readings, including handouts, download site postings, and
websites.
 read and become familiar with material in required readings.
 read and become familiar with material in all out-of-class assignments.
 maintain a complete collection of class handouts.
 activate and maintain his/her personal Academic Computing Account throughout the
semester. The student must be able to access his/her computer account at any course
session. The student must memorize both the account User ID and password. For
information or problems with accounts, contact Academic Computing at 448-4224.
 check email at least once weekly for important course announcements
 participate in three lecture examinations.
 prepare and deliver an in-class presentation, complete with M.S. PowerPoint graphics,
as described in the Special Topics instructions (to be distributed after the semester
begins).
 download course study materials from the Course Download Site as assigned.
 conduct himself/herself in a manner respectful, harmless, and undisruptive to both the
instructor and fellow students in both the lecture room and the computer laboratory.
 accept and abide by all parts and provisions of this syllabus.
SPECIAL COURSE REQUIREMENTS FOR GRADUATE STUDENTS
To earn graduate credit in BIOL 421, the student is required to undertake a specially designed
exercise using strategies discussed and evaluated in the general course. Results of the gene
discovery exercise will be presented to the instructor in the form of a scientific manuscript
suitable for scholarly publication. Each student enrolled for graduate credit will be assigned a
specific exercise at the beginning of each semester.
Genome Biology, Spr 04  Page 3
SPECIAL COURSE REQUIREMENTS FOR HONORS PROGRAM STUDENTS
Students enrolled in the University Honors Program may earn honors course credit in BIOL 421
by completing (1) a Petition for Honors Credit before the end of the second week of the
semester and (2) a specially-designed assignment in genome biology. A meeting of Honors
Program students interested in earning honors course credit in BIOL 421 will be held at a
prescribed time on or before Monday, 14 June.
COURSE CONTENT
BIOL 421 is a course with both lecture and computer research components. The table on the
following page lists weekly topics that will be covered in each component. Genome biology
is a rapidly developing science, and new topics may substitute for any of the topics listed. In
addition, the sequence and content of lectures and laboratories may be changed at the
discretion of the instructor. The position of each exam in the semester is indicated.
METHOD OF EVALUATION:
The final grade in Genome Biology is based on a ten-point scale, where a minimum of 90.00
points is required to earn a final grade of A. Ranges of other grades are as follows: 80.0089.99=B, 70.00-79.99=C, 60.00-69.99=D, and <60.00 points earned = F. Evaluation in
Genome Biology is based on five componentsthree exams, a Special Topics presentation,
and a set of weekly quizzes (six)and each component is worth 20% of the final grade.
Evaluation of graduate students is based on six componentsthree exams, the presentation,
the set of weekly quizzes and the graduate exerciseand each component is worth 16.67%
of the final grade.
PRELIMINARY NOTE ON SPECIAL TOPICS STUDENT PRESENTATIONS. On 14-16
July, students will deliver presentations of their own summarization of the biomedical literature
on specific genomics topics to be assigned within the first three weeks of class. In the interim,
students will be responsible for literature research and preparation of both (i) a one-page
summary and (ii) a set of presentation graphics, all based on the specified topic. A set of
detailed instructions will be distributed within the first two weeks of the semester.
SPECIAL REGULAR LECTURE PERIODS. Two periods outside of normal class periods
are reserved in the rare event that regularly-scheduled course lectures or laboratories need to
be cancelled due to unforeseen University service required of the instructor. Note that these
periods will only be used if regularly scheduled 2M periods need to be cancelled. These
dates are as follows: Monday, 28 June and Wednesday, 14 July. Each of these periods will
last up to three hours and will occur either on the afternoons from 1:30 PM until 4:30 PM or
in the evenings from 6:00 PM until 9:00 PM. Students will be notified ahead of time if these
special lecture periods need to be used. A student will be excused from these sessions if and
only if enrolled in another Monday evening University course on any of these dates, but an
excused student remains responsible for all coursework conducted, distributed, and assigned
during these special lecture periods. To be officially excused from any of these sessions will
require a typewritten and signed request by the student and presented to the instructor in a
timely manner.
Genome Biology, Spr 04  Page 4
GENOME BIOLOGY
Summer 2004 Course Content
*Note nonstandard times.
WEEK 1 M 07 JN
T 08 JN
W 09 JN
H 10 JN
F 11 JN
WEEK 2 M 14 JN
T 15 JN
W 16 JN
H 17 JN
F 18 JN
WEEK 3 M 21 JN
T 22 JN
W 23 JN
H 24 JN
F 25 JN
WEEK 4 M 28 JN
T 29 JN
W 30 JN
H 01 JL
F 02 JL
WEEK 5 M 05 JL
T 06 JL
W 07 JL
H 08 JL
F 09 JL
WEEK 6 M 12 JL
T 13 JL
W 14 JL
H 15 JL
F 16 JL
WEEK 7 M19 JL
Course Introduction
The Human Genome Project (HGP)
Fundamental Genome Biology
Basic Techniques in Molecular Biology
How to Elucidate a Genome?
A First Glance at the Human Genome
New Biological Concepts due to the HGP
No Class
No Class
New Technology of the HGP (9AM-12 Noon)*
TEST ONE
Animal Genome Projects
Plant Genome Projects
Microbe Genome Projects
Gene Discovery and Annotation
Transcriptomics
Proteomics
Metabolomics
Pharmacogenomics
TEST TWO
No classes; Independence Day holiday
Novel Polymorphism Analysis & Application
Genome Expansion I: Repetitive Elements
Genome Expansion II: Gross Duplications
The New RNA World
Comparative Genomics
Endosymbiotic Genomics
Special Topics Presentations 1-5
Special Topics Presentations 5-10
Special Topics Presentations10-15
TEST THREE (10 AM-12 Noon)*
Genome biology is a rapidly developing science, and new topics may substitute for any of the
topics listed. In addition, the sequence and content of lectures and laboratories may be
changed at the discretion of the instructor.
Genome Biology, Spr 04  Page 5
MAKE-UP POLICY & PROCEDURE
The instructor makes extraordinary efforts to ensure that students facing unforeseen and
urgent problems have an opportunity to succeed in the course. As you can imagine, however,
this privilege is too often abused, and abuse causes the establishment of stipulations for all
students. Understanding that personal problems can arise on dates and occasions important
in this course, the instructor has developed the following policy for remediation (make-up
work):
(1) Discretion. All make-up work is allowable only at the discretion of the instructor. This
discretion supersedes any and all components of the make-up procedure listed below.
(2) Request for Remediation. Any and all make-up work must be requested by the student.
Within 24-hours of missing an exam, a due date, or a laboratory session, the student must
contact instructor either by phone, email, or in person during office hours to request
remediation. In all cases, acceptable reasons for requesting remediation are (i) personal
illness, (ii) illness of dependent, or (iii) death of immediate family member. In times of
national emergency, military service is also an acceptable reason to request remediation. In
all cases, requests for remediation must be accompanied by documentation substantiating the
reason for missed work, to include photocopies of either doctors visit receipts or published
death notices when applicable; this documentation can be submitted to the instructor when
the student returns to the University.
(3) Exam Remediation. Participation in each exam is an absolute requirement of the course
(see Course Requirements above). Following initial contact of the instructor and receipt of
documentation (as described above), the instructor will schedule with the student a make-up
exam to be administered during the week of University Final Exams (21-22 July 2002). The
make-up exam will cover the same course material as the missed exam but will not be
identical in either content or format to the missed exam.
(4) Presentation Remediation. Participation in the Special Topics presentation is an absolute
requirement of the course (see Course Requirements above). Following initial contact of
the instructor and receipt of documentation (as described above), the instructor will schedule
with the student a make-up presentation time, and the student will present before an
appropriate audience.
(5) Quizzes Remediation. There is no remediation of a missed quiz.
Because they are absolute requirements of the course, failure to participate in any exam or
failure to participate in the presentation will result in an F grade. An incomplete grade in the
course (I grade) is only granted under extreme extenuating circumstances to a student with
satisfactory progress (minimum test average of C) in the course, and a plan for coursework
remediation must be approved by the instructor and the department head.
ACADEMIC HONESTY POLICY
All aspects of coursework in BIOL 421 must be the exclusive, independent, and original
scholarship of the student. Although the student can seek assistance from sources available
to all students, including but not limited to seeking assistance from extramural experts and
intramural writing laboratories, the student is responsible for maintaining the originality of
the coursework. Any improprieties, including but not limited to plagiarism and ghostwriting,
Genome Biology, Spr 04  Page 6
will result in a failing grade in the course, potential dismissal from the University, and
possible criminal prosecution. Improprieties during examinations will result in immediate
dismissal from the course, a grade of F in the course, and possible dismissal from the
University in accordance with the Code of Student Conduct of Nicholls State University.
ATTENDANCE POLICY
Students are expected to:
 attend class regularly. In accordance with University policy, attendance must be recorded.
Toward this end, the instructor may conceive a seating arrangement, and students are
expected to sit in an assigned seat for all lectures during the duration of the semester. In
addition, and according to University policy, four or more unexcused absences will result in a
grade of FEA (Failure—Excessive Absences).
 arrive to lecture on time and neither leave nor prepare to leave before dismissal by the
instructor. Students late for the beginning of a lecture are encouraged to attend, but they
must enter quietly, without creating disruption, and through the rear door of the classroom. If
a seating arrangement is enforced, late students must sit in the rear of the classroom (and not
in assigned seats) to avoid disruption.
 perform work during lectures and laboratories exclusively on material directly relating to the
current course topic.
 refrain from the use of all electronic communication devices (including telephones, pagers,
and wireless Internet devices) while in lecture and laboratory sessions. “Use” includes
keeping devices in active or audible modes. All devices must be turned off during lecture
and laboratory.
 conduct themselves during lectures and laboratory sessions with consideration and respect
and without disruption toward both the instructor and fellow students enrolled in the course.
Deviation from this conduct constitutes grounds for dismissal from the course and possibly
the University in accordance with the Code of Student Conduct of Nicholls State University.
ASSISTANCE WITH WRITTEN ASSIGNEMENTS
On occasion, assignments in BIOL 421 may require a written component. Students needing
assistance in developing such assignments are encouraged to visit the Writing Across the
Curriculum (WAC) Laboratory on the first floor in the Ellender Memorial Library. Writing
assistants are available for students seeking help in word-processing and creating good
presentation graphics. The hours of availability of this assistance are published on a semester
basis at the WAC Lab and on the University website.
SPECIAL NOTICE FOR STUDENTS WITH DISABILITIES
If you have a documented disability that requires assistance, you will need to register with
the Office of Disability Services for coordination of your academic accommodations. The
Office of Disability Services is located in Peltier Hall, Room 100-A. The phone number is
(985) 448-4430 (TDD449-7002).
Genome Biology, Spr 04  Page 7
IMPORTANT SEMESTER DATES (SUMMER 2004)
Monday, 07 Jun 
First day of class
Friday, 18 Jun 
University Closed
Monday, 21 Jun 
Mid-semester exams begin
Tuesday, 22 Jun 
Mid-Semester Exams end
Monday, 05 Jul 
No classes; University closed
Wednesday, 07 Jul 
Final date for automatic W when dropping a course
Friday, 16 Jul 
Last day of classes
Monday, 19 Jul 
Final Exams begin
Tuesday, 20 Jul 
Final Exams end
IMPORTANT AND USEFUL WEBSITES
http://www.nicholls.edu/biol-med/doucet/genetics
The BIOL 421 course download site. On occasion, supplementary course materials will be
available to the student from this website. In the Address box of any Internet browser, type in
the course web address, <http://www.nicholls.edu/biol-med/doucet/genetics>, followed by a
slash mark and the name of the file you are trying to download. For instance, this syllabus is
available for download at the site. The file name of the course syllabus is <syllabus.doc>. To
download a copy of the syllabus, the following should be typed into the Address box of the
Internet browser:
http://www.nicholls.edu/biol-med/doucet/genomics/syllabus.doc
The syllabus, as well as all other text files that will be available for the course, will be written in
MS Word format, and computers running MS Word will automatically open your downloaded
document. Slides and other graphics from the lectures will be created in MS Powerpoint format,
and, for this reason, to download slides you need access to a computer with Powerpoint software
installed.
http://www.ncbi.nlm.nih.gov/
The National Center for Biotechnology Information (NCBI). The NCBI is a component and
service of the National Institutes of Health. The NCBI website is a window to a multitude of the
world's finest and most useful databases and search engines. In this course, the most useful
component of the website will be PubMed, the world's premiere search engine for biomedical
literature. The mother website, http://www.nih.gov/, may also contain useful information.
http://www.ncbi.nlm.nih.gov/Omim/
OMIM: Online Mendelian Inheritance in Man. This database is a catalog of human genes and
genetic disorders authored and edited by Dr. Victor A. McKusick and his colleagues at Johns
Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center
for Biotechnology Information. The database contains textual information, pictures, and
reference information. It also contains links to NCBI's Entrez database of MEDLINE articles and
sequence information.
http://www.graylab.ac.uk/omd/index.html
The On-Line Medical Dictionary (OMD). OMD is a searchable dictionary created by Dr
Graham Dark and contains terms relating to biochemistry, cell biology, chemistry, medicine,
Genome Biology, Spr 04  Page 8
molecular biology, physics, plant biology, radiobiology, science and technology. It includes
acronyms, jargon, theory, conventions, standards, institutions, projects, eponyms, and history
relating to medicine or science.
http://www.nicholls.edu/ellender/ellender.htm
The Ellender Memorial Library Homepage. This is the University library’s homepage, and it
contains multiple search engines for its own holdings as well as those of the statewide LOUIS
system of academic libraries. Access to the University’s electronic subscriptions is also
available here.
http://illiad.louis.lsu.edu.illiad/Ins/logon.html
ILLiad. This is the University’s and the LOUIS system’s new electronic interlibrary loan
system. Fast and highly reliable.
http://www.lsuhsc.edu/no/centers/genetics/LAfamilies
Genetics and Louisiana Families. Genetics and Louisiana Families is an anthology of genetics
information written and designed specifically for a rural, non-medical and general audience.
Through excellent writing and superb, careful editing, it serves as a prime example of how
technical scientific topics that profoundly affect the well being of families can be conveyed in
clear, understandable, and educational forms.
http://www.nhgri.nih.gov/
NHGRI: National Human Genome Research Institute. This is the home page for the Human
Genome Project, which began in 1989 and moves onward in this new millennium. On this site
you can check the research and institutes involved, the current progress and related news, link to
countless informative sites, and even use a comprehensive on-line genetics glossary. This site is
filled with very important and very relevant information for students of genetics.