Genomics Course: ANS 575
Title: Current Topics in Genomics and Proteomics in Animal Science
Instructor:
Dr. H. Sunny Liu (http://www4.ncsu.edu:8030/~hliu4/ )
232D Polk Hall
Phone: 515-4024
E-mail: hc_liu@ncsu.edu
Office hours: By appointment only in 232D Polk Hall
Textbook: A Primer of Genome Science, authors: Greg Gibson and Spencer Muse. Sinauer
Associates, Inc. In addition, at each class we will discuss at least two papers. I will provide a list
of suggested papers at each lecture.
Location and Time: Room 2112 Williams Hall, Tuesdays/Thursdays 10:15 AM – 11:30 AM
Attendance Policy: Attendance is expected. I appreciate being informed of likely absences.
University regulation on excused and unexcused absence can be found in
www.ncsu.edu/policies/academic_affairs/pols_regs/REG205.00.4.php or at 515-2572
Making sure your background is adequate: This course is designed for advanced students. A
thorough knowledge of basic genetic concepts and molecular genetics normally covered in an
undergraduate general genetics course (e.g., ANS 215 or GN411) is required.
Course Objectives:
1.
To obtain an integrated exposure to the major current concepts in genomics and
proteomics.
2.
To acquire knowledge of the genomic and proteomic methods at a level that will
allow you to read and comprehend articles dealing with animal genome research.
3.
To become proficient in critically evaluating and understanding current scientific
literature concerning the applications of genomic and proteomic methods in animal
research.
4.
To obtain experience in being able to professionally discuss scientific research in a
public forum.
Class format: This course is a lecture-seminar format. Background material includes the
assigned textbook and references. In discussing individual topics, I will first give an introductory
lecture and refer to different chapters in the textbook as a potential study guide. Each student will
be expected to read all the assigned research papers and to be prepared to discuss the assigned
readings in class. Each student will be assigned a date on which to lead the discussion for an
assigned topic.
Each class:
1 lecture session to introduce the next topic (40 min)
1 literature discussion session (35 min)
e.g., class 1. lecture on topic x
class 2. paper discussion on topic x, and lecture on topic y
class 3. paper discussion on topic y, and lecture on topic z
Student responsibility:
Weekly: read the appropriate chapters from the textbook and read the papers for discussion. For
selected classes, the student assigned to lead the discussion will scan through the referenced
literature and then check with instructor to gain approval of the selected 1 or 2 papers at least one
week prior to the assigned discussion date. Each student is expected to read every paper, not just
the one(s) you are assigned to present. Each student is expected to actively participate in the
discussion, and this part counts as 20% towards your final grade.
Exams: There are two exams: Mid term and Final. Both are essay format and are take home
exams. Each exam will be passed out in class and returned to my office in 232D Polk Hall or the
classroom by the next lecture at 10:15 AM. Students are expected to utilize any resource to
answer the exams, EXCEPT for discussing or copying each other’s answers.
Term paper: Students registered in ANS 590A must turn in a term paper to earn 20% credit.
The term paper will consist of an analysis or review of a particular genomic system on a
particular farm animal. The subject must be approved in advance, and the paper will be due on
the last day of class. The term paper has to be at least 10 pages in double-spaced format.
Plagiarism will not be tolerated.
Grading: It is my goal to create an opportunity for learning rather than a competitive
atmosphere. Thus, course grades will be assigned on a straight percentage scale of total points.
ANS 575
30%: Mid term
30%: Final
20%: Term paper
20%: In class paper discussion
100%: Final grades
Academic Integrity: North Carolina State University expects students to follow the university
policy on academic integrity, which can be found in the Code of Student Conduct,
http://www.ncsu.edu/policies/student_services/student_discipline/POL11.35.1.php .
Students with disabilities: Reasonable accommodations will be made for students with
verifiable disabilities. In order to take advantage of available accommodations, students must
register with Disability Services for Students at 1900 Student Health Center, Campus Box 7509,
515-7653. http://www.ncsu.edu/policies/academic_affairs/courses_undergrad/REG02.20.1.php
Note: Please turn off cell phones during class.
Lecture outline
Date
Topic
08/24/06
08/29/06
08/31/06
09/05/06
09/07/06
09/12/06
09/14/06
09/19/06
09/21/06
09/26/06
09/28/06
10/03/06
10/05/06
10/10/06
10/12/06
10/1706
10/19/06
10/24/06
10/26/06
10/31/06
11/02/06
11/07/06
11/09/06
11/14/06
11/16/06
11/21/06
11/23/06
11/28/06
11/30/06
12/05/06
12/07/06
Course overview, review of basic principles of genetics
Review of basic principles of genetics
Review of basic principles of genetics
Genes, gene families, and genomes
Genetic markers and genomic variation
SNP, QTL and genotyping
Mapping polygenic traits and disease genes
Positional cloning, mutation and diagnostic tests
Genome sequencing approaches and technology
Databases and sequence comparison technique
Phylogeny, synteny
Metabolic reconstruction and the metabolome
EST and gene discovery
Exam review-take home exam –due on 10/17/06
Fall Break ! No class !
RNA differential display
Closed platforms, such as cDNA microarrays
Microarray applications
Open platforms, such as SAGE
Gene expression and disease
Gene expression and performance trait
Genetic engineering of cells and organisms
Gene silencing, microRNA, and siRNA technologies
Introduction of proteomics
Expression proteomics
Functional proteomics
Thanksgiving Holiday ! No class !
Protein-protein interaction
Protein microarrays
Bioethics
Special topic—to be announced; take home exam—due on 12/12/06; Term
paper due!!