NORTH CAROLINA STATE UNIVERSITY
GRADUATE COURSE ACTION FORM
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TYPE OF PROPOSAL
DEPARTMENT/PROGRAM
Biotechnology
COURSE PREFIX/NUMBER
BIT465/465L/565/565L
New Course
Drop Course
Course Revision
Dual-Level Course
REVISION
Content
Prefix/Number
Title
Abbreviated Title
Credit Hours
Contact Hours
Grading Method
Pre-Corequisites
Restrictive Statement
Description
Scheduling
PREVIOUS PREFIX/NUMBER
DATE OF LAST ACTION
COURSE TITLE
Real-time PCR Techniques
ABBREVIATED TITLE
REAL-TIME PCR
SCHEDULING
Fall
Spring X
Alt. Year Odd
COURSE OFFERED
CREDIT HOURS
CONTACT HOURS
Studio
Summer
Every Year X
Alt. Year Even
Other
BY DISTANCE EDUCATION ONLY
ON CAMPUS ONLY
BOTH ON CAMPUS AND BY DISTANCE EDUCATION
X
2
Lecture/Recitation 2 Seminar
Independent Study/Research
X
Laboratory 5 Problem
Internship/Practicum/Field Work
GRADING
ABCDF
INSTRUCTOR (NAME/RANK)
Chris Ashwell, Assistant Professor
Graduate Faculty Status Associate X
X
X
S/U
ANTICIPATED ENROLLMENT
Per semester 16
PREREQUISITE(S)
BIT410 or BIT510
Max.Section 1
Full
Multiple sections Yes
No X
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 __________________________
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
CATALOG DESCRIPTION (limit to 80 words):
course.
1
RECOMMENDED BY:
DOCUMENTATION AS REQUIRED
Please number all document pages
_______________________________________________________________________
Department Head/Director of Graduate Programs
Date
Course Justification
X
Proposed Revision(s) with
Justification
Student Learning Objectives
X
ENDORSED BY:
X
Enrollment for Last 5 Years
X
_______________________________________________________________________
Chair, College Graduate Studies Committee
Date
New Resources Statement
X
Consultation with other Departments
Syllabus (Old and New)
X
Explanation of differences in
requirements of dual-level courses
X
________________________________________________________________________
College Dean(s)
Date
APPROVED:
_______________________________________________________________________
Dean of the Graduate School

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.
2
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
chris_ashwell@ncsu.edu
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
3
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
4
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
Wednesday
Lecture
Monday
Lab
Week 2
Wednesday
Lecture- quiz
Monday
Lab
Week 3
Wednesday
Lecture- quiz
Monday
Lab
Week 4
Wednesday
Lecture
Monday
Lab
Week 5
Wednesday
Lecture- quiz
Week 1
• Discuss syllabus, lab policy, organize groups
• Intro to real-time PCR and the enemy RNAse
• RNA extraction and characterization
• Gene Expression with qPCR, alternatives,
programming the MyiQ instrument
• Oligo design, homework
• 2-step real-time PCR- SYBR green, optimization
• Instrumentation options
• Design of TaqMan probes, homework
• Real-time PCR using SYBR
• Guest Lecturer from Instrumentation supplier
• DNA extraction from food samples and
characterize
• Analysis of Real-time PCR data, homework
5
Monday
Lab
Week 6
Wednesday
Lecture- quiz
Monday
Lab
Week 7
Wednesday
Lecture-quiz
Monday
Lab
Week 8
Wednesday
Lecture
Wednesday
Lab
•Run TaqMan experiment to detect Salmonella
• Using Real-time PCR to detect organisms,
homework
• Extract genomic DNA and characterize
• SNP detection using real-time PCR
• BIT565 students turn in project proposal
• SNP detection
• Review, wrap up, course evaluations
• Final Exam
• Report results- Turn in lab notebooks
6
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
chris_ashwell@ncsu.edu
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
7
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
Grading: 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 that will be consists of 15 multiple choice
questions and 3 short answer/word problems. These questions will be similar 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. It is recommended to wear a lab coat and advised to wear safety
goggles.
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
8
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)
Course outline
Wednesday
Lecture
Monday
Lab
Week 2
Wednesday
Lecture- quiz
Monday
Lab
Week 3
Wednesday
Lecture- quiz
Monday
Lab
Week 1
• Discuss syllabus, lab policy, organize groups
• Intro to real-time PCR and the enemy RNAse
• RNA extraction and characterization
• Gene Expression with qPCR, alternatives,
programming the MyiQ instrument
• Oligo design, homework
• 2-step real-time PCR- SYBR green, optimization
• Instrumentation options
• Design of TaqMan probes, homework
• Real-time PCR using SYBR
Week 4
Wednesday
Lecture
Monday
Lab
• Guest Lecturer from Instrumentation supplier
Week 5
Wednesday
Lecture- quiz
Monday
Lab
• Analysis of Real-time PCR data, homework
Week 6
Wednesday
Lecture- quiz
Monday
Lab
• DNA extraction from food samples and
characterize
•Run TaqMan experiment to detect Salmonella
• Using Real-time PCR to detect organisms,
homework
• Extract genomic DNA and characterize
Week 7
Wednesday
Lecture-quiz
Monday
Lab
• SNP detection using real-time PCR
Week 8
Wednesday
Lecture
Wednesday
Lab
• Review, wrap up, course evaluations
• SNP detection
• Final Exam
• Report results- Turn in lab notebooks
9