BIOL 7240

Graduate Curriculum Committee Course Proposal Form
Graduate Curriculum Committee
Course Proposal Form for
Courses Numbered 5000 and Higher
Note: Before completing this form, please carefully read the accompanying instructions.
1. Course Prefix and Number:
BIOL 7240
2. Date:
Requested Action (check only one box):
New Course
Revision of Active Course
Revision & Unbanking of a Banked Course
Renumbering of an Existing Course from
Justification (assessment or accreditation based) for new course or course revision or
course renumbering:
In the last decade genome sequencing and comparative genomics have begun 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
graduate course curricula cannot incorporate in-depth coverage of the field. Nevertheless, understanding the
fundamentals of genomics is becoming increasingly important for graduate students in the Biology program,
and for biomedical and health-related graduate students in the IDPBS and other graduate programs. Although
the current Biology curriculum includes courses in which graduate students gain experience in 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. Comparative genomics impact a wide array of
biological and biomedical research fields, from human gene therapy to plant population ecology. In addition to
its importance for the Biology Graduate Program, this course will meet a growing need for coursework in the
Interdisciplinary Doctoral Program in the Biological Sciences (IDPBS) that provide a common language and
body of biological knowledge important to the various interdisciplinary fields covered by participating faculty
mentors. As such, this course can contribute to curricula of other graduate programs, with the potential to be
incorporated into the core coursework for the IDPBS.
Course description exactly as it should appear in the next catalog:
7240. The Evolution of Genes and Genomes (3) (S) Recent advances in comparative genomics, focusing on
the evolution of more complex eukaryotic genomes. Course includes lectures and seminar discussions of
current research publications.
If this is a course revision, briefly describe the requested change:
7. Graduate Catalog Page Number from current Graduate catalog: 68
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Graduate Curriculum Committee Course Proposal Form
8. Course Credit:
Lecture Hours
Credit Hours
Weekly OR
Per Term
Weekly OR
Per Term Credit Hours
Weekly OR
Per Term Credit Hours
Weekly OR
Per Term Credit Hours
Weekly OR
Per Term Credit Hours
Other (e.g., independent study) Please explain.
Total Credit Hours
Anticipated annual student enrollment:
Affected Degrees or Academic Programs:
MS/Biology ; MS/ Molecular
Biology & Biotechnology
Catalog Page
Changes in Degree Hours
Overlapping or Duplication with Affected Units or Programs:
Not Applicable
Notification & response from affected units is attached
Approval by the Council for Teacher Education (required for courses affecting teacher
education programs):
Not Applicable
Applicable and CTE has given their approval.
Statements of Support:
a. Staff
Current staff is adequate
Additional Staff is needed (describe needs in the box below):
b. Facilities
Current facilities are adequate
Additional Facilities are needed (describe needs in the box below):
c. Library
Initial library resources are adequate
Initial resources are needed (in the box below, give a brief explanation
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Graduate Curriculum Committee Course Proposal Form
and an estimate for the cost of acquisition of required initial resources):
d. Computer resources
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):
ITCS Resources are not needed
The following ITCS resources are needed (put a check beside each need):
Mainframe computer system
Statistical services
Network connections
Computer lab for students
Approval from the Director of ITCS attached
Course information: see Instructions for Completing the Graduate Curriculum
Committee Course Proposal Form for more detail
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
 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
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.
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Graduate Curriculum Committee Course Proposal Form
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
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)
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
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
Gene family evolution
a) Mechanisms for gene duplication
b) Why do duplicated copies remain active or disappear?
i) Neofunctionalization
ii) Subfunctionalization
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
Evolution of the genetic code
a) Origin of “universal” code
b) Evolutionary variation in the genetic code
i) Organelle genomes
ii) Nuclear genomes
Ecological genomics
a) Microarray analyses variations in gene expression
b) Ecological effects on genomes
i) Genome size
ii) Nucleotide and amino acid content
Computational models and empirical observations
a) Phylogenomics
i) Methodologies
ii) Shifting models of global evolution
b) Problems and technical challenges
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Graduate Curriculum Committee Course Proposal Form
i) Sequence biases and computational artifacts
ii) Comparative genomics and evolutionary pattern
c) Microevolution, macroevolution and genome change
D) Course assignments and grading plan
% of grade
1 midterm exams
1 final exam
Seminar participation
Short essay assignments
Term paper
Grading scale
A = 90 – 100%
B = 80 – 89%
C = 70 – 79%
F  69%
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