AFNS 575
Advanced Functional Genomics in Agricultural, Food and Nutritional Science
Fall 2017
1. Department: Department of Agricultural, Food and Nutritional Science 2. Coordinator: Dr. Leluo Guan
4-16F Ag/For Centre
Email: [email protected], phone: 780-492-2480 Office hours: by appointment only
3. Instructors: Dr. Leluo Guan
Dr. Urmila Basu, Email: [email protected], phone: 780-492-8712
4. Lecture and Lab time/places - Lectures (410C or 318J Ag/For Centre), Lab (4-32 Ag/For Centre). The time frame for each module will be developed once the students are registered and the coordinator receives their time schedule. The modules (including optional modules) will be run sequentially in September, October and November, respectively in Fall semester, 2017.
5. Course objective: In this course, the graduate students will be introduced to basic and advanced functional genomics methodologies for studying gene expression and gene networks. Admission to this course is by consent of the course coordinator. Three modules must be completed to obtain credit in the course. There are three “core” modules for AFNS 575 and advanced molecular technology modules may be available through AFNS 575 as well as several modules concurrently offered through AFNS 570 (Coordinator: Dr. Spencer Proctor). A student can choose the most appropriate optional modules based on consultation with the course coordinator.
6. Method of Student Evaluation: For each module
10% - Lab Notes/Notebooks – The marking will be given based on the precise recording on what you have done in the lab and what are the main results.
These will be collected after each module completed.
10% - Participation - This component includes many factors such as attending the lectures, organizational skills, and how carefully the exercises in the lab are carried out. Missing lecture and lab section without proper notifications will lead to the reduction of marks.
60% (20%X3) Module papers - This should be submitted to the instructor by the defined due date for each module. The topic of the written assessment will be determined by the instructor and will focus on a summary of the various techniques, a discussion of problem solving, strategies for these techniques, as well as consideration of the potential application of these techniques in the student’s own future research. Each paper will be marked out of 100. All
assignments must be handed in for marking. If a student does not complete an assignment and submit on the day it is due, penalized reduction of 10%
per day will be implemented. Late assignments (handed in more than 1 week late) will not be considered for marking.
20% Oral presentation Students will choose and prepare a 15~20 min Power Point presentation based on the relevant research that applies the methods / technologies learned in the modules. Students will prepare a Power Point presentation and be expected to demonstrate an understanding of the key findings of their assigned papers, particularly with regards to the application of the methodology. Students will then participate in a group discussion. The marking assessment will be posted during the first week of the class.
100% Total
Raw marks will be assigned to reflect performance on each component of the course. Letter grades will be assigned only to the final distribution of mark totals.
7. Recommended or optional learning resources: Lab manuals, protocols, hand-out for lectures, and research papers will be provided by the instructors.
8. Course Content:
Fall Semester (2017)
Course introduction: September 7, 2017
Module 1: Approaches to isolate, quantify, and manipulate genetic material
(Instructor: Drs. Leluo Guan) (Week of September 11, 2017, report due September 24, 2017)
Aseptic cell culture – Requirements and Practices
DNA/RNA (mRNA) extraction from tissues
Quantification isolated DNA/RNA
Qualification of DNA/RNA by electrophoresis
mRNA/miRNA and protein isolation and applications -lecture
Module 2: Gene amplification technologies, Sequencing and annotation (Instructor:
Dr. Guan) (Week of Oct 2, 2017, report due October 15, 2017)
Introduction and searching public database for nucleotide and protein Sequences, PCR Primer design principles
PCR and Trouble shooting
Introduction to Next generation Sequencing and its Applications -lecture
Sequence analysis and annotation using databases (gene identification, microbial profile analysis, transcriptome analysis)
Gene Amplification and Editing -lecture
Module 3: Real Time Quantitative PCR and Droplet Digital PCR– Measuring Gene Expression
(Instructor: Dr. Urmila Basu) (Week of October 30, 2017, report due November 12, 2017)
Primer and probe designing using primer express software, review of the Sequence detection software
Quantitation of RNA and DNA (isolated in previous module) for real time module, DNase treatment, and first-strand cDNA synthesis (RT)
Real Time PCR from cDNA and DNA (Sybr Green Technology)
Droplet Digital PCR from DNA samples
Data extraction and data analysis from real time PCR and DDPCR
Oral presentation: November 22 and 23, 2017
Presentation topic: how the techniques/knowledge learnt in the course can be applied in your research field and your research project. Presentation will be 20 min for each student, which includes 15 min of presentation and 5 min of questions. All presentation files need to be submitted to Course Instructors by 5 pm, November 20 (Monday). Penalized reduction of 10% per day will be considered for late submission.
9. Required Course Text:
Readings will be assigned and will be available via the Internet.
Information in the readings and course notes will NOT necessarily be covered in the lectures of the course but it is expected that students will know this information for answering questions in the midterm and final examinations.
10. Academic Integrity
“The University of Alberta is committed to the highest standards of academic integrity and honesty.
Students are expected to be familiar with these standards regarding academic honesty and to uphold the policies of the University in this respect. Students are particularly urged to familiarize
themselves with the provisions of the Code of Student Behavior
(www.ualberta.ca/secretariat/appeals.htm) and avoid any behavior which could potentially result in suspicions of cheating, plagiarism, misrepresentation of facts and/or participation in an offence.
Academic dishonesty is a serious offence and can result in suspension or expulsion from the University.” (GFC 2003)
11. Code of Student Behavior
“All students at the University of Alberta are subject to the Code of Student Behavior, as outlined at http://www.ualberta.ca/~unisecr/policy/sec30.html. Please familiarize yourself with it and ensure that you do not participate in any inappropriate behavior as defined by the Code. Key components of the code include the following statements.
30.3.2(1) Plagiarism
No Student shall submit the words, ideas, images or data of another person as the Student’s own in any academic writing, essay, thesis, project, assignment, presentation or poster in a course or program of study.
30.3.2(2) Cheating
30.3.2(2) a No Student shall in the course of an examination or other similar activity, obtain or attempt to obtain information from another Student or other unauthorized source, give or attempt to give information to another Student, or use, attempt to use or possess for the purposes of use any unauthorized material.
30.3.2(2) b No Student shall represent or attempt to represent him or herself as another or have or attempt to have himself or herself represented by another in the taking of an examination,
preparation of a paper or other similar activity. See also misrepresentation in 30.3.6(4).
30.3.2(2) c No Student shall represent another’s substantial editorial or compositional assistance on an assignment as the Student’s own work.
30.3.2(2) d No Student shall submit in any course or program of study, without the written approval of the course Instructor, all or a substantial portion of any academic writing, essay, thesis, research report, project, assignment, presentation or poster for which credit has previously been obtained by the Student or which has been or is being submitted by the Student in another course or program of study in the University or elsewhere.
30.3.2(2) e No Student shall submit in any course or program of study any academic writing, essay, thesis, report, project, assignment, presentation or poster containing a statement of fact known by the Student to be false or a reference to a source the Student knows to contain fabricated claims (unless acknowledged by the Student), or a fabricated reference to a source.