University Curriculum Committee
Course Proposal Form
for Courses Numbered 0001 – 4999
(Faculty Senate Resolution #04–18, April 2004)
(editorially revised 02-21-07)
Note: Before completing this form, please carefully read the accompanying instructions.
BIOL 4240
1.
Course Prefix and Number:
2.
Date:
3.
Requested Action (check only one box):
X
08/07/07
New Course
Revision of Active Course
Revision & Unbanking of a Banked Course
Renumbering of Existing Course
from:
4.
#
to
#
Justification for new course or course revision or renumbering:
In the last decade genome sequencing and comparative genomics have begun to
revolutionize the biological sciences, producing a large and ever-growing body of
new data on how biological information is stored and expressed. This, in turn, has
had profound impacts on how biologists understand the organization and evolution
of genetic blueprints controlling cell function and development. Because of its rapid
development of comparative genomics, and the enormous amount of new
information that has emerged, standing Biology course curricula cannot incorporate
in-depth coverage of the field. Nevertheless, understanding the fundamentals of
genomics is becoming increasingly important for graduates of the Biology program,
and for many medical and health-related majors who populate our elective courses.
Although the current Biology curriculum includes courses in which students learn
the basic methodologies employed in comparative genetics and genomics, as yet
we offer no courses that synthesize new research results into a cohesive learning
experience for our undergraduates.
The results of our past four years of program assessment have shown that
graduating Biology majors are not meeting projected goals in the assessment
indicator subcategories of Molecular Biology/Molecular Genetics and Population
Genetics and Evolution (Our criterion: 50%, Results: four year averages of 42.2%
and 43.8% respectively). This course would contribute to both of these areas of
Biology.
5.
Course description exactly as it should appear in the next catalog:
4240. Genome Evolution (3) (S) P: BIOL 2300, or consent of
instructor. Recent advances in comparative genomics, focusing on the
evolution of more complex eukaryotic genomes. Course includes
lectures and seminar discussions of current research publications.
6.
If this is a course revision, briefly describe the requested change:
7.
Page Number from current undergraduate catalog:
8.
The Writing Across the Curriculum Committee must approve Writing
Intensive (WI) Credit for all courses prior to their consideration by the UCC.
If WI credit is requested, has this course been approved for Writing
Intensive (WI) credit (yes/no)?
no
If Yes, will all sections be Writing Intensive (yes/no)?
9.
The Academic Standards Committee must approve Foundations
Curriculum Credit for all courses prior to their consideration by the UCC. If
FC credit has been approved by the ASC, then check the appropriate box
(check at most one):
English (EN)
Science (SC)
10.
338
Humanities (HU)
Social Science (SO)
Fine Arts (FA)
Mathematics (MA)
Health (HL)
Exercise (EX)
Course Credit:
Lecture Hours
3
3
Weekly or
Per Term
Credit Hours
s.h.
Lab
Weekly or
Per Term
Credit Hours
s.h.
Studio
Weekly or
Per Term
Credit Hours
s.h.
Practicum
Weekly or
Per Term
Credit Hours
s.h.
Internship
Weekly or
Per Term
Credit Hours
s.h.
Other (e.g., independent study):
Total Credit Hours
11.
Anticipated yearly student enrollment:
12.
Affected Degrees or Academic Programs:
20
3
s.h.
Degree(s)/Course(s)
13.
Catalog Page
Change in Degree Hours
Overlapping or Duplication with Affected Units or Programs:
X
Not Applicable
Applicable (Notification and/or Response from Units Attached)
14.
Approval by the Council for Teacher Education (required for courses
affecting teacher education programs):
X
Not Applicable
Applicable (CTE has given their approval)
15.
Instructional Format: please identify the appropriate instructional format(s):
X
16.
Lecture
Internship
Lab
Student Teaching
Correspondence
Studio
Clinical
Honors
Seminar
Colloquia
Practica
Other
Statements of Support:
X
Current staff is adequate
Additional Staff is needed (describe needs in the box below):
X
Current facilities are adequate
Additional Facilities are needed (describe needs in the box below):
X
Initial library resources are adequate
Initial resources are needed (in the box below, give a brief explanation
and estimate for cost of acquisition of required resources):
X
Unit computer resources are adequate
Additional unit computer resources are needed (in the box below,
give a brief explanation and an estimate for the cost of acquisition):
X
ITCS Resources are not needed
Following ITCS resources are needed (put a check beside each need):
Mainframe computer system
Statistical services
Network connections
Computer lab for students
Describe any computer or networking requirements of this program
that are not currently fully supported for existing programs (Includes
use of classroom, laboratory, or other facilities that are not currently used
in the capacity being requested).
Approval from the Director of ITCS attached
17.
Syllabus – please insert course syllabus below. Do not submit course
syllabus as a separate file. You must include (a) the name of the textbook
chosen for the course, (b) the course objectives, (c) the course content
outline, and (d) the course assignments and grading plan.
A) Textbook
The Evolution of the Genome, T. Ryan Gregory, (Ed.) 2005. Elsevier Inc, Oxford, UK.
ISBN: 0-12-310463-8.
B) Course objectives
Students taking this course will:

demonstrate knowledge of basic genome characteristics and how they
evolve through time.

explain major developments in comparative genomics and interpret how
they relate to other biological subjects.

employ library research collections and on-line resources to uncover and
examine the most recent literature in comparative genome evolution.

organize and synthesize ongoing research developments in comparative
genomics and translate this research to their student peers.

gain proficiency in interpreting and presenting results of modern genomic
research, and in explaining in both written and oral formats.
C) Course content outline
The following subjects form the core of the initial curriculum. Topics will be updated
through time based on new and important results in comparative genomics. The
major subjects will be presented in two hours of lecture per week. The third hour is
reserved for seminar/discussion sessions, led by students, on recent primary
literature and review papers.
1) Genome Structure
a) How are genomes organized?
i) Prokaryotic genomes
ii) Eukaryotic genomes
iii) How structure impacts evolutionary change
2) Genome Size Variation
a) Range of sizes and consequences
i) How genomes vary in size among organisms.
ii) Mechanisms for changes in genome size.
iii) Genome size and developmental complexity.
iv) C-value paradox
3) How individual sequences change through time
a) Sources of variation
i) Mutations; causes and rates.
ii) External mutational agents
iii) Intrinsic mutation rates
b) Variation in rates of mutation
i) Coding versus non-coding DNA
ii) Among genes and proteins
iii) Among organisms
c) Causes of rates in variation
i) Mechanisms to prevent and repair mutations
ii) Relationship between mutation rate and substitution rate.
iii) What governs substitution rate of a given sequence?
iv) Variation in evolutionary rates among genes and other sequences
4) Acquisition of new genes through Horizontal Transfer (HGT)
a) Comparative bacterial genomics
i) Rates of transfer
ii) Consequences of transfer
b) Eukaryotic HGT
c) Effects of endosymbiosis on genomes
i) Organelle genes moving to nucleus
ii) Whole gene replacements
iii) Additional contributions (mitochondrial and chloroplast insertions)
5) Major changes in genome content
a) Genome duplications
i) Important events in genome evolution
ii) Mechanism of genome duplication
iii) Consequences of genome duplication
b) Role of mobile genetic elements
c) Repetitive DNA
d) Relative impacts of horizontal gene transfer
6) Chromosome evolution
a) Changes in ploidy
i) Plant polyploidy
ii) Animal polyploidy
b) Chromosomal rearrangements
c) Evolution of sex chromosomes
i) In animals
ii) In plants
7) Gene family evolution
a) Mechanisms for gene duplication
b) Why do duplicated copies remain active or disappear?
i) Neofunctionalization
ii) Subfunctionalization
8) Evolution of introns
a) Ancient and self-splicing introns
b) Origin and spread of spliceosomal introns
c) Patterns of intron gain and loss through eukaryotic evolution
9) Evolution of the genetic code
a) Origin of “universal” code
b) Evolutionary variation in the genetic code
i) Organelle genomes
ii) Nuclear genomes
10) Computational models and empirical observations
a) Phylogenomics
i) Methodologies
ii) Shifting models of global evolution
b) Problems and technical challenges
i) Sequence biases and computational artifacts
ii) Comparative genomics and evolutionary pattern
c) Microevolution, macroevolution and genome change
D) Course assignments and grading plan
Assignment
2 midterm exams
Seminar participation
Short essay assignments
Final exam
% of grade
50
10
10
30
100
Grading scale
A = 90 – 100%
B = 80 – 89%
C = 70 – 79%
D = 60 – 69%
F  59%