MBG*4300 Plant Molecular Genetics

course node page

This course is not offered in the Fall 2021 semester. The course outline distributed to the class at the beginning of the semester describes the course content and delivery, and defines the methods and criteria to be used in establishing the final grades for the course.

This course studies the molecular genetics of plants. The topics include: plant genome diversity and synteny; Arabidopsis thaliana genome, hormonal, environmental and developmental regulation of gene expression; chloroplast and mitochondrial genomes; and gene expression and silencing in transgenics. The course will be delivered using a lecture and paper discussion format. Students will learn and use a variety of computer techniques to search and analyze plant genome databases.

 

Plants are immobile, autotrophic and multicellular: How do genes and gene regulation make immobility possible? How are plants and plant molecular genetics unique compared to animals (mobile, heterotrophic), microbes (unicellular) or fungi (immobile, heterotrophic)? In this course, you will be given weekly background lectures (one per week) in plant molecular genetics including guided tutorials using online genetics, genomics, molecular biology, proteomics and metabolomics databases. Topics will include plant proteins and proteomics, evolution of plant proteins and plant genomes, coordination of nuclear and chloroplast genomes, plant gene regulation, and the molecular genetics of primary and secondary metabolism, biotic and abiotic stress resistance and plant development. In addition, the class will be divided into small tutorial group sections which will each meet once per week with the course instructor. The purpose of the tutorial section format is to solve problems in plant molecular genetics using independent problem-based learning. In the problem-based learning component, students will learn about the practice of being a critical scientist, which involves understanding what is truly known and unknown,  designing logical experiments to test hypotheses, creating and defending grant proposals and peer reviewing of the proposals of others. The course will also include formal career mentoring.

Instructors:

Manish N. Raizada

Teaching Assistant:

Credit Weight:

0.50

Course Level:

  • Undergraduate

Academic Department (or campus):

Department of Plant Agriculture

Campus:

Guelph

Semester Offering:

  • Fall

Class Schedule and Location:

Please refer to Web Advisor for class schedule and location.

Learning outcomes:

By the end of this course, you should be able to:
  1. Gain basic background knowledge literacy in plant molecular genetics sufficient for a post-graduate career in molecular genetics or plant molecular genetics
  2. Gain basic competency in online databases used by experimental plant molecular geneticists including genomics, metabolomics, proteomics and molecular biology databases
  3. Learn to generate focused questions, generate hypotheses and design a series of logical experiments to test the hypotheses, as training for writing post-graduate scholarship proposals in molecular genetics
  4. Gain competency in verbally presenting and defending experimental proposals, as training for a career in post-graduate research in the real world including presentations at scientific conferences
  5. Critically evaluate experimental proposals in plant molecular genetics, as training for anonymous scientific peer review in the real world
  6. Learn skills that enable selecting a long-term career

Lecture Content:

Lecture topics include:
  • Introduction to Plants
    • organize sections
    • plant strategies, life cycle, anatomy
    • introduction to Arabidopsis
  • tutorial to links on plant anatomy
  • TAIR database tutorial, searching seed stocks, BLASTing, TDNA stocks
  • tutorial on using PubMed, Web of Science databases, Science Citation Impact/best journals to read
  • Molecular Methods II
  • Career Day - Part I - choosing a career (discussion, answer questions)
  • Career Day - Part 2 - practice of being a scientist: real world process of peer reviewing, publishing, grants, citation impact, careers, grad school, etc; discussion
  • how to map and isolate a gene; creating RIL lines, F2 populations, molecular marker-assisted mapping, BAC clones, complementation
  • Arabidopsis genome
  • Genomics Tutorial
  • Proteomics Tutorial
  • Metabolomics Tutorial
  • Online Molecular and Science Software Tools and answer questions on final written assignment
Labs & Seminars:
Seminar Topics
  • Brainstorm great unsolved problems in plant molecular genetics
  • Each student presents a 5min oral report of each great unsolved problem followed by questions/discussion. The group votes to focus on one problem for the remainder of the “grant cycle”. The group divides the topic into subtopics (1 subtopic/student)
  • Each student presents a 5 min oral report providing background to the subtopic, followed by defining one question/hypothesis, and a preliminary set of experiments to answer the question. The group+instructor provide feedback.
  • Each student gives a 5min oral report to present their experimental proposal, followed by questions (defence), along with handouts containing their hypothesis and a 1-2 page flow chart with their methodological details.
  • Brainstorm great unsolved problems in plant molecular genetics
  • Each student presents a 5min oral report of each great unsolved problem followed by questions/discussion. The group votes to focus on one problem for the remainder of the “grant cycle”. The group divides the topic into subtopics (1 subtopic/student)
  • Each student presents a 5 min oral report providing background to the subtopic, followed by defining one question/hypothesis, and a preliminary set of experiments to answer the question. The group+instructor provide feedback.
  • Each student gives a 5min oral report to present their experimental proposal, followed by questions (defence), along with handouts containing their hypothesis and a 1-2 page flow chart with their methodological details.
    • Students select a great unsolved problem in plant molecular genetics from previous brainstorms for Cycle C.
  • Each student presents a 5min oral report of each great unsolved problem followed by questions/discussion. The group votes to focus on one problem for the remainder of the “grant cycle”. The group divides the topic into subtopics (1 subtopic/student)
  • Each student presents a 5 min oral report providing background to the subtopic, followed by defining one question/hypothesis, and a preliminary set of experiments to answer the question. The group+instructor provide feedback.
  • Each student gives a 5min oral report to present their experimental proposal, followed by questions (defence), along with handouts containing their hypothesis and a 1-2 page flow chart with their methodological details.
  • Each student submits a 2 page written proposal to Dropbox 60 minutes before their Section (1 page background, 1 page methodology, followed by references) (with line numbers)

Course Assignments and Tests:

Discussion Brainstorm for First Cycle 1%
5 minutes oral report of great unsolved problem nomination for group vote 4%
Oral report of grant proposal background info; feedback on experimental design 6%
Oral defence with Methodology handout 13%
Discussion for next cycle 1%
5 minutes oral report of great unsolved problem nomination for group vote 4%
Oral report of grant proposal background info; feedback on experimental design 6%
Oral defence with Methodology handout; Discussion for next cycle 13%
5 minutes oral report of great unsolved problem nomination for group vote 4%
Oral report of grant proposal background info; feedback on experimental design 6%
Oral defence with Methodology handout 12%
2 Page written proposal 20%
Quizzes 10%

 

Final examination:

There is no final exam for this course.

Course Resources:

Required Texts
None
 
Recommended Texts
The course relies on the primary literature and review papers. Students are encouraged to read articles in high quality journals including but not limited to:
  • Relevant Primary Journals: Nature Plants, Plant Cell, Plant Physiology, Frontiers in Plant Science, BMC Plant Biology, etc.
  • Relevant Review Journals: Annual Review of Plant Biology, Trends in Plant Science, Current Opinion in Plant Biology
  • General Journals: Science, Nature, Cell. Genes and Development. Development, Proceedings of the National Academy of Sciences USA (PNAS), Nature Genetics, Nature Reviews Genetics, PLoS journals, Developmental Cell, Genetics, Genome Biology, etc.
Other Resources: Online plant genomics databases:

Course Policies:

Late Policy
No oral presentations are accepted late, nor can missed in-class tests be re-written, except without a medical note or extreme circumstance. For late written assignments, there will be a 20% mark deduction per day, except when a medical note or other extreme circumstance is presented
 
Time and place for submission
All written and oral submissions are due in class during the assigned tutorial section.
Grading system
Course Policy on Group Work
There is no group work in this course, though each tutorial group is encouraged to provide experimental suggestions and critical evaluation following in-class oral presentations.
Recording of Materials
Presentations which are made in relation to course work—including lectures—cannot be recorded or copied without the written permission of the presenter, whether the instructor, a classmate or guest lecturer. Material recorded with permission is restricted to use for that course unless further permission is granted.
 
Obeying Covid Protocols During Lecture and Small Group Sections
Please note that pandemic restrictions in place at the time of each lecture / tutorial must be followed by everyone according to the guidelines provided by the University and the local public health unit. The pandemic is a community problem and we all need to actively participate in a community solution. Restrictions may include but not be limited to a vaccination requirement, proper use of appropriate PPE, hand sanitation, social distancing and other measures. Failure to comply with restrictions that are in place at the time of the lecture / tutorial could result in the immediate cancelation of that lecture / tutorial. Students would still be responsible for learning the material that was to be covered in that lecture / tutorial regardless of the cancelation.

Other Course Information:

University Policies

Academic Consideration

When you find yourself unable to meet an in-course requirement because of illness or compassionate reasons, please advise the course instructor in writing, with your name, id#, and e-mail contact. See the academic calendar for information on regulations and procedures for Academic Consideration:

Academic Misconduct

The University of Guelph is committed to upholding the highest standards of academic integrity and it is the responsibility of all members of the University community, faculty, staff, and students  to be aware of what constitutes academic misconduct and to do as much as possible to prevent academic offences from occurring.

University of Guelph students have the responsibility of abiding by the University's policy on academic misconduct regardless of their location of study; faculty, staff and students have the responsibility of supporting an environment that discourages misconduct. Students need to remain aware that instructors have access to and the right to use electronic and other means of detection. Please note: Whether or not a student intended to commit academic misconduct is not relevant for a finding of guilt. Hurried or careless submission of assignments does not excuse students from responsibility for verifying the academic integrity of their work before submitting it. Students who are in any doubt as to whether an action on their part could be construed as an academic offence should consult with a faculty member or faculty advisor.

The Academic Misconduct Policy is detailed in the University Calenders:

Accessibility

The University of Guelph is committed to creating a barrier-free environment. Providing services for students is a shared responsibility among students, faculty and administrators. This relationship is based on respect of individual rights, the dignity of the individual and the University community's shared commitment to an open and supportive learning environment. Students requiring service or accommodation, whether due to an identified, ongoing disability or a short-term disability should contact the Student Accessibility Services (SAS), formerly Centre for Students with Disabilities (CSD), as soon as possible.

For more information, contact CSD at 519-824-4120 ext. 56208 or email sas@uoguelph.ca or visit the Student Accessibility Services website: http://www.uoguelph.ca/csd/.

Course Evaluation Information

Your ratings and comments are important.  Course evaluation data are used to assess and enhance the quality of teaching and student learning at the University of Guelph.  Student course ratings and comments are used as an important component in the Faculty Tenure & Promotion process, and as valuable feedback to help instructors improve their teaching effectiveness and to improve the delivery of the course.

Your responses will not affect your grade.  Course evaluation data are distributed to individual instructors after final grades have been submitted to the Registrar, following the completion of each academic semester.

Please be honest, respectful, constructive and thorough.  Instructors and review committees place great value on student course ratings and read all comments provided in course evaluations. It is helpful to provide comments on the strengths of the course, in addition to the areas for improvement.  Please refrain from personal comments unless they relate to teaching and learning.

Click here for the University of Guelph Course Evaluation System