Introduction to Genome Science - BISC 499

Introduction to Genome Science - BISC 499

Syllabus - 2014 Spring Semester

Basic Information

Course: Introduction to Genome Science, BISC 499, 4 credits

Textbook: Greg Gibson and Spencer V. Muse. A Primer of Genome Science (3rd Edition). Sinauer Associates, Inc.

Place and Time: Monday and Wednesday: 9:30 am - 10:50 am

Location: To be determined
Faculty: Dr. Ian Ehrenreich

Assistant Professor, Molecular and Computational Biology

Office: 319A Ray I. Irani Building.

Telephone: 213-821-5349

Email:
Office Hours: Tuesday 1:00 pm – 2:00 pm or by appointment

Discussion Section: Location and time to be determined
Online Resources: USC Blackboard (blackboard.usc.edu)

Final Exam: 8-10 am on Monday, May 13th

Report Deadline: Students are expected to generate a presentation based on a topic in genomics. A report on this topic is due during finals week and must be turned in by midnight on Tuesday, May 14th at the latest.

Course Goals and Learning Objectives

Characterizing the sequence, function, and evolution of genomes is a central focus of modern biology. In this course, we will learn about the core questions and methods of genome scientists. We will discuss techniques for comprehensively examining organisms at the levels of DNA, RNA, proteins, and metabolites. We will also talk about how this information is used to determine the molecular basis of phenotypes, such as evolutionary adaptations, crop improvements, and human disease. Lastly, we will spend time on the relationship between genomics and synthetic biology, which is a field that seeks to engineer new features into existing organisms or build new organisms based on present knowledge. The goal of this course is for students to walk away conversant in modern genomics techniques and the biological problems genome researchers hope to solve. This course is best suited for students that have taken BISC325 or BISC502a, or have had equivalent prior training in genetics.

Required Materials

·  Textbook: Gibson and Muse (see above).

·  Additional readings will be provided on Blackboard throughout the course.

Classroom Policy

Any electronic communication devices (phones, blackberries, and similar) must be turned off, and no instant messenger/chat type programs are allowed in class.

Course Plan and Weekly Readings

The class will initially involve weekly lectures on the above topics, and will build to the point where students are capable of presenting on a relevant topic of their choosing. The following is the anticipated schedule for the class; however, please note this is subject to change.

Discussion Section

Attendance at section is required. In section, students and their TA will review material from recent lectures, read scientific papers, and conduct final presentations. Sections will be structured, but students will also have ample opportunity to ask questions about recent material. Each section will begin with a short quiz.

Assessment

Grades will be based on four scores: 1) midterm exam grade, which will test understanding of material from the first part of the class, 2) final exam grade, which will largely focus on material from the second part of the class but will have some cumulative material on it, 3) final presentations, and 4) section quizzes that each week will cover points from the most recent lectures or from required section readings:

8.1. Criteria for grading: The midterm and final exams will consist of a mixture of multiple choice, fill-in-the-blank, and free response questions. Some of the free response questions will ask students to formulate strategies for solving biological problems using tools from genomics. The final presentation and report will be graded according to clarity of scientific hypothesis, appropriateness of data to address that hypothesis, ability of the student to effectively communicate their strategy, and on the substance of their conclusions.

8.2. Final presentation: Students will give a 15-minute talk to the rest of their section. These presentations will occur during the final four sections. The talk should include a number of slides in which the student describes a biological problem of interest and how it could be addressed using genomics techniques. Accompanying this talk, students will be expected to provide a double spaced, 5-page paper describing their problem. The paper should be written in Arial font with a font size of 12 and 1-inch margins on each side of the page. The primary literature should be used to reference salient points, and at least 15 papers should be referenced. The report based on the final presentation must be turned in by midnight on Tuesday, May 14th.

8.3. Course grade: The course is not curved. Letter grades will follow a straight scale: 90% and above leading to A, 80-<90% leading to B, etc. Pluses and minuses are assigned by dividing each range in corresponding halves (A, A-) or thirds (B+, B, B-, C+, ...).

Policy against Cheating

All USC students are responsible for reading and following the Student Conduct Code, which appears in the Scampus and at http://www.usc.edu/dept/publications/SCAMPUS/goverance. This policy does not apply to discussion or exchange of ideas.

Statement for Students with Disabilities

Any student requesting academic accommodations based on a disability is required to register with Disability Services and Programs (DSP) each semester. A letter of verification for approved accommodations can be obtained from DSP. Please be sure the letter is delivered to me (or to TA) as early in the semester as possible. DSP is located in STU 301 and is open 8:30 a.m.–5:00 p.m., Monday through Friday. The phone number for DSP is (213) 740-0776.

Statement on Academic Integrity

USC seeks to maintain an optimal learning environment. General principles of academic honesty include the concept of respect for the intellectual property of others, the expectation that individual work will be submitted unless otherwise allowed by an instructor, and the obligations both to protect one’s own academic work from misuse by others as well as to avoid using another’s work as one’s own. All students are expected to understand and abide by these principles. Scampus, the Student Guidebook, contains the Student Conduct Code in Section 11.00, while the recommended sanctions are located in Appendix A: http://www.usc.edu/dept/publications/SCAMPUS/gov/. Students will be referred to the Office of Student Judicial Affairs and Community Standards for further review, should there be any suspicion of academic dishonesty. The Review process can be found at: http://www.usc.edu/student-affairs/SJACS/.

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