NORTH CAROLINA STATE UNIVERSITY

GRADUATE COURSE ACTION FORM

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Department/Program / Biotechnology
Course Prefix/Number / BIT465/465L/565/565L
Previous Prefix/Number
Date of Last Action
Course Title / Real-time PCR Techniques
Abbreviated Title / Real-time PCR
Scheduling Fall Spring X Summer Every Year X
Alt. Year Odd Alt. Year Even Other
Course Offered / By Distance Education Only On Campus Only X
Both On Campus and by Distance Education
Credit Hours 2
Contact Hours Lecture/Recitation 2 Seminar Laboratory 5 Problem
Studio Independent Study/Research Internship/Practicum/Field Work
Grading / ABCDF X S/U
Instructor (Name/Rank) / Chris Ashwell, Assistant Professor
Graduate Faculty Status Associate X Full
TYPE OF PROPOSAL
New Course
Drop Course / X
Course Revision
Dual-Level Course / X
REVISION
Content
Prefix/Number
Title
Abbreviated Title
Credit Hours
Contact Hours
Grading Method
Pre-Corequisites
Restrictive Statement
Description
Scheduling
Anticipated Enrollment / Per semester 16 Max.Section 1 Multiple sections Yes No X
Prerequisite(s) / BIT410 or BIT510
Corequisite(s)
Pre/Corequisite for
Restrictive Statement / Students must register for both the lecture and lab sections
Curricula/Minors
Required
Qualified Elective / BIT
Proposed effective date / 08/01/2006 / Approved effective date ______
Catalog Description (limit to 80 words): Real-time PCR is an evolving technique with its basis in the dynamic properties of the polymerase chain reaction and fluorescent detection. We will review current real-time theory, techniques, machinery, troubleshooting, tools, and advanced protocols for sequence detection including SYBR green, TaqMan, Beacons, multiplexing, and single nucleotide polymorphism analysis. Students will have the opportunity to utilize skills learned during lecture in a laboratory environment. At the conclusion of this course, students should feel comfortable with real-time experimental design, its tools, and analysis of generated data. This is a half-semester course.
DOCUMENTATION AS REQUIRED
Please number all document pages
Course Justification
/
X
Proposed Revision(s) with Justification
/
X
Student Learning Objectives
/
X
Enrollment for Last 5 Years
/
X
New Resources Statement
/
X
Consultation with other Departments
/
Syllabus (Old and New)
/
X
Explanation of differences in requirements of dual-level courses
/
X

Recommended by:

______

Department Head/Director of Graduate Programs Date

Endorsed by:

_________

Chair, College Graduate Studies Committee Date

______

College Dean(s) Date

Approved:

______

Dean of the Graduate School Date

·  Course Justification – Methodology is constantly changing in the Biotechnology field. Students in this area need the ability to evaluate new technologies, design, execute, and analyze appropriate experiments. This course will provide students with knowledge, skills, and abilities to perform experiments using real-time PCR, a technique which has replace many classic molecular biology methods over the last few years.

·  Enrollment for Last 5 Years – This course is being taught as BIT595R/595S. Enrollment is expected to continue at 16 students per semester. Spring 2006 – 14 students. We expect enrollment to continue at 16 students for BIT 465/565 combined.

·  New Resources Statement – No new resources are needed for the course. Sufficient resources are currently provided through the Biotechnology Minor Program

·  Consultation with other Departments -- none

·  Syllabus (Old and New) – Follows on page 3 with the addition of the requirements for students registered for the 500 level.

·  Explanation of differences in requirements of dual-level courses – Details describing the difference in expectations from students registered for the 500 level of this course are described in the syllabus. In brief, the 500 level students are required to write a project proposal incorporating all of the information covered in the course to address an experimental problem preferably one related to the students specific research interests. This assignment results in a difference in grading from the 400 level students which is also described in the syllabus.

1

NEW SYLLABUS

BIT465/565 : Real-time PCR techniques
An introduction to real-time PCR technologies including methods to measure gene expression, enumerate organisms, and genotype single nucleotide polymorphisms.
Instructor / Dr. Chris Ashwell
Email /
Phone / 513-7335
Office hours / 134E Scott Hall, Wed 2:30-3:00pm
Location / Lectures in 6117 Jordan Hall, with laboratory in 158 Scott Hall
Prerequisite / BIT 410 or BIT 510
Textbook / None
Teaching assistant

Course Overview: Real-time PCR is an evolving technique with its basis in the dynamic properties of the polymerase chain reaction and fluorescent detection. We will review current real-time theory, techniques, machinery, troubleshooting, tools, and advanced protocols for sequence detection including SYBR green, TaqMan, Beacons, multiplexing, and SNP analysis. Students will have the opportunity to utilize skills learned during lecture in a laboratory environment. At the conclusion of this course, students should feel comfortable with real-time experimental design, its tools, and analysis of generated data.

Student Learning Outcomes:

After completion of this course students will be able to:

·  Explain the theory behind real-time PCR.

·  Evaluate and determine suitable real-time PCR methodologies.

·  Design experiments using real-time PCR techniques.

·  Analyze real-time PCR data and make analytical or qualitative conclusions

Attendance policy: Students will be working in groups of two for the duration of the semester. It is your responsibility to read the laboratory protocol before class and to attend each session. Failure to do so will place an undue burden on your lab partner. Attendance at ALL laboratories is mandatory. Missing a lecture period during which lab exercises are to be performed will greatly affect your class participation grade. Attendance for both sessions is critical to your success in this course. We do understand that circumstances might arise beyond your control. If you are unable to attend, it is your responsibility to contact the course instructor immediately. We will do our best to accommodate individuals that have extenuating circumstances. University approved excused absences can be found at: http://www.ncsu.edu/policies/academic_affairs/courses_undergrad/REG02.20.3.php

Grading for BIT465: 20% attendance and lab participation, 20% lab notebooks, 20% homework assignments, 20% quizzes, 20% final exam

A+ ≥ 98%, A ≥ 92%, A- ≥ 90%, B+ ≥ 88%, B ≥ 82%, B- ≥ 80%, C+ ≥ 78%, C ≥ 72%, C- ≥ 70%, D+ ≥ 68%, D ≥ 62%, D- ≥ 60%, F < 60%

Audits: Students auditing the course must complete all assignments unless previous arrangements have been made with the instructor.

Lab protocols: All lab protocols will be provided at the lecture preceding the laboratory. They must be read BEFORE coming to lab, and must be brought to the laboratory.

Lab notebooks: Each lab session must be documented and include the protocol as well as results. You must write out protocols and incorporate them into your lab notebook before coming to class. Your TA or instructor must sign your notebook before you leave the lab.

Take home exercises: Take home exercises must be typed. They are due at the beginning of lecture period on the due date. One letter grade will be dropped for each class meeting lecture or lab it is late. Students are encouraged to form study groups to work on these assignments, but copying is not permitted and each student must understand and write the answers in their own words. Begin working on these as early as possible-they are more time-consuming than they appear at first glance. *Note that no help will be given on take home assignments the day that they are due by the instructor or TA.

Academic integrity: University regulations require that every course syllabus remind students that the Code of Student Conduct defines a university policy on academic integrity already pledged by each student. Instructors assume that the students' names on their submitted work imply compliance with this policy. http://www.ncsu.edu/policies/student_services/student_discipline/POL11.35.1.php

Lab participation: Students will be working in groups of two people. Each person will have the opportunity to perform various tasks in the laboratory. Demonstrations will be provided for the advanced equipment.

Quizzes: Students will be assessed for their comprehension of the prior week’s lecture and lab assignments at the beginning of each lecture. Each quiz (5 total) will consist of 5 multiple choice questions which will be graded in class and the answers reviewed immediately following.

Final Exam: Students will be given a cumulative final exam. The questions will be similar in structure to the quiz questions and the homework assignments.

Laboratory safety: General lab safety will be discussed during the first lab period. You will be working with a variety of chemicals and some general precautions should be made. We expect that you do not wear open-toed shoes. Lab coat and safety goggles are required.

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/provost/offices/affirm_action/dss/ For more information on NC State's policy on students with disabilities, please see the Academic Accommodations for Students with Disabilities Regulation at: (http://www.ncsu.edu/policies/academic_affairs/courses_undergrad/REG02.20.1.php)

Behavior is also addressed under the Code of Student Conduct: (http://www.ncsu.edu/policies/student_services/student_discipline/POL11.35.1.php) Harassment of any kind will not be tolerated and includes behavior that is directed toward a particular person (or persons), is unwelcome and severe or pervasive, and violates criminal law, civil rights law, the NCSU Administrative Regulation on harassment, or that unreasonably interferes with the target person's employment, academic pursuits, or participation in University-sponsored activities. Additional information can be found at: http://www.ncsu.edu/provost/offices/affirm_action/policies.html

Students registered for BIT565: Students registered for BIT565 will complete an additional project above and beyond the course requirements for BIT465 outlined in this syllabus. Students registered for BIT565 will prepare a proposal that will incorporate an aspect of real-time PCR analysis into the experimental design. The function of this exercise is to develop independent thinking skills in planning experiments involving real-time PCR techniques. It is preferred that this project proposal be focused on the individual students personal research area but is not required. The subject of a student’s proposal should be discussed with the instructor and determined by Week 3 of the course. The proposal should include a brief background on the problem to be addressed, experimental design, sample collection, assay design (custom or commercial), analysis methods, potential pitfalls, and a proposed budget. These proposals will be submitted during week 7 of the course at the beginning of the lecture period. These proposals will be included in the assessment of grades as follows.

Grading for BIT565: 10% attendance and lab participation, 10% lab notebooks, 20 % project proposal, 20% homework assignments, 20% quizzes, 20% final exam

A+ ≥ 98%, A ≥ 92%, A- ≥ 90%, B+ ≥ 88%, B ≥ 82%, B- ≥ 80%, C+ ≥ 78%, C ≥ 72%, C- ≥ 70%, D+ ≥ 68%, D ≥ 62%, D- ≥ 60%, F < 60%

Course outline Week 1
Wednesday
Lecture / • Discuss syllabus, lab policy, organize groups
• Intro to real-time PCR and the enemy RNAse
Monday
Lab / • RNA extraction and characterization
Week 2
Wednesday
Lecture- quiz / • Gene Expression with qPCR, alternatives, programming the MyiQ instrument
• Oligo design, homework
Monday
Lab / • 2-step real-time PCR- SYBR green, optimization
Week 3
Wednesday
Lecture- quiz / • Instrumentation options
• Design of TaqMan probes, homework
Monday
Lab / • Real-time PCR using SYBR
Week 4
Wednesday
Lecture / • Guest Lecturer from Instrumentation supplier
Monday
Lab / • DNA extraction from food samples and characterize
Week 5
Wednesday
Lecture- quiz / • Analysis of Real-time PCR data, homework
Monday
Lab / •Run TaqMan experiment to detect Salmonella
Week 6
Wednesday
Lecture- quiz / • Using Real-time PCR to detect organisms, homework
Monday
Lab / • Extract genomic DNA and characterize
Week 7
Wednesday
Lecture-quiz / • SNP detection using real-time PCR
• BIT565 students turn in project proposal
Monday
Lab / • SNP detection
Week 8
Wednesday
Lecture / • Review, wrap up, course evaluations
Wednesday
Lab / • Final Exam
• Report results- Turn in lab notebooks


OLD SYLLABUS

BIT595R/595S : Real-time PCR techniques
An introduction to real-time PCR technologies including methods to measure gene expression, enumerate organisms, and genotype single nucleotide polymorphisms.
Instructor / Dr. Chris Ashwell
Email /
Phone / 513-7335
Office hours / 134E Scott Hall, Wed 2:30-3:00pm
Location / Lectures in 6117 Jordan Hall, with laboratory in 158 Scott Hall
Prerequisite / BIT 410 or BIT 510
Textbook / None
Teaching assistant

Course Overview: Real-time PCR is an evolving technique with its basis in the dynamic properties of the polymerase chain reaction and fluorescent detection. We will review current real-time theory, techniques, machinery, troubleshooting, tools, and advanced protocols for sequence detection including SYBR green, TaqMan, Beacons, multiplexing, and SNP analysis. Students will have the opportunity to utilize skills learned during lecture in a laboratory environment. At the conclusion of this course, students should feel comfortable with real-time experimental design, its tools, and analysis of generated data.

Student Learning Outcomes:

After completion of this course students will be able to:

·  Explain the theory behind real-time PCR.

·  Evaluate and determine suitable real-time PCR methodologies.

·  Design experiments using real-time PCR techniques.

·  Analyze real-time PCR data and make analytical or qualitative conclusions

Attendance policy: Students will be working in groups of two for the duration of the semester. It is your responsibility to read the laboratory protocol before class and to attend each session. Failure to do so will place an undue burden on your lab partner. Attendance at ALL laboratories is mandatory. Missing a lecture period during which lab exercises are to be performed will greatly affect your class participation grade (up to 5% of your final grade). Attendance for both sessions is critical to your success in this course. We do understand that circumstances might arise beyond your control. If you are unable to attend, it is your responsibility to contact the course instructor immediately. We will do our best to accommodate individuals that have extenuating circumstances. University approved excused absences can be found at: http://www.ncsu.edu/policies/academic_affairs/courses_undergrad/REG02.20.3.php