Graduate Curriculum Committee Course Proposal Form
Note: Before completing this form, please carefully read the accompanying instructions.
3. Requested Action (check only one box) :
X New Course
Revision of Active Course
Revision & Unbanking of a Banked Course
Renumbering of an Existing Course from
from # to #
4. 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.
5. 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.
6. 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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8. Course Credit:
Graduate Curriculum Committee Course Proposal Form
Lecture Hours
Lab
Studio
Practicum
Internship
3
Weekly OR
Weekly OR
Weekly OR
Weekly OR
Weekly OR
Per Term Credit Hours
Per Term Credit Hours
Per Term Credit Hours
Per Term Credit Hours
Per Term Credit Hours
Other (e.g., independent study) Please explain.
3
Total Credit Hours 3 s.h. s.h.
s.h.
s.h.
s.h.
s.h.
9. Anticipated annual student enrollment:
10
10. Affected Degrees or Academic Programs:
Degree(s)/Course(s)
MS/Biology ; MS/ Molecular
Biology & Biotechnology
PhD / IDBPS
Current
Catalog Page
63
Changes in Degree Hours
263-64
11. Overlapping or Duplication with Affected Units or Programs:
X Not Applicable
Notification & response from affected units is attached
12. Approval by the Council for Teacher Education (required for courses affecting teacher education programs):
X Not Applicable
Applicable and CTE has given their approval.
13. Statements of Support: a. Staff
X Current staff is adequate
Additional Staff is needed (describe needs in the box below): b. Facilities
X Current facilities are adequate
Additional Facilities are needed (describe needs in the box below): c
.
Library
X 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
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
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
14. 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 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.
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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
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) Ecological genomics a) Microarray analyses variations in gene expression b) Ecological effects on genomes i) Genome size ii) Nucleotide and amino acid content
11) 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
Assignment % 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%
25
25
10
10
30
100
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