PLNT*6320 Metabolic Processes in Crop Plants

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The following description is for the course offering in Fall 2022 and is subject to change. It is provided for information only. 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.
 

A comprehensive examination of the metabolic mechanisms and versatility whereby autotrophic organisms sustain themselves. Emphasis will be placed on our current understanding of the regulation and integration of metabolic processes in plants, and their physiological and agricultural significance including available research methodologies.

Prerequisite: BIOC*2580

Restriction: no auditing without permission of Instructor.

This course is designed to provide a broad overview of plant metabolism with opportunities to explore specific topics in detail. It is a plant biology course that emphasizes integration of biological processes from the biochemical up to the whole plant levels. The exact topics to be covered will be dictated in part by the specific interests of students in the course. The depth of study will go beyond the level of a 4th year undergraduate course on plant biochemistry and physiology, with the goal of approaching a level of understanding that allows experimental implementation. Emphasis will be placed on understanding the regulation and interaction between metabolic processes in plants at the molecular to whole-plant levels, and their physiological and agricultural implications. Detailed aspects of carbon, nitrogen, and sulfur metabolism are examined since collectively these processes contribute ~99% of the biomass in plants. An understanding of basic biochemical principles, components of the plant cell, the plant life cycle, and basic aspects of regulation of gene expression will be assumed.

Instructors:

Barry J. Micallef

Teaching Assistant:

Credit Weight:

0.50

Course Level:

  • Graduate

Academic Department (or campus):

Department of Plant Agriculture

Campus:

Guelph

Semester Offering:

  • Fall

Class Schedule and Location:

Please refer to WebAdvisor for class schedule and location.

Learning outcomes:

By the end of the course you should be able to:

1. understand the historical development and current understanding of the field of plant metabolism such that the interactions between various plant metabolic processes can be understood and appreciated;
2. understand the field of plant metabolism at a level that allows experimental implementation, including available methodologies;
3. integrate the field of plant metabolism with other disciplines including other biological fields, chemistry, biophysics, environmental and social sciences, and agriculture to gain a greater appreciation for the potential of applying our knowledge of plant metabolism to improving humanity including global issues such as the food supply, sustainable energy, and climate change;
4. apply knowledge of plant metabolism to specific research problems associated with biological processes, agriculture, forestry, energy production, and medicine.

Lecture Content:

Topics to be covered in lectures include

Course Introduction/Introduction to Plant Metabolism

  • Discussion of the course outline, organizational aspects of the course, analysis of scientific papers.
  • Background knowledge assumed for this course.
  • Introduction to plant metabolism, including definition of sources and sinks, definition of 1o and 2o metabolic processes, interactions between metabolic and developmental processes, integration of metabolic processes and interactions between sources and sinks, consideration of flux rates, regulation in space and time, metabolic flexibility in plants.

An Introduction to Source Metabolism in Plants​

  • An examination of how the biochemical components and reactions of solar energy capture and transduction (i.e. light reactions of photosynthesis) affect the energy-use efficiency of photosynthesis, including: (1) properties of light-absorbing pigments; (2) photons absorbed by the light harvesting complex; (3) quantum efficiency of photochemistry; and (4) conversion of light energy to ATP and NADPH.
  • Relationship between structure and function for the components involved in light capture and energy transduction.                                                                                                                                                                      

An Introduction to Source Metabolism in Plants - Photosynthetic C Metabolism

  • An examination of components of photosynthetic C metabolism and their regulation, including: (1) utilization of energy in ATP & NADPH to reduce CO2 to triose-P; (2) photorespiratory CO2 loss; and (3) sucrose and starch synthesis in source tissues.

An Introduction to Source Metabolism in Plants-N & S Metabolism

  • An examination of components of N & S metabolism and their regulation, including: (1) N & S uptake; (2) nitrate assimilation; and (3) amino acid metabolism.

An Introduction to Sink Metabolism in Plants

  • An examination of the components involved in sink metabolism and their regulation, including: (1) phloem loading and unloading of sugars; (2) transport mechanisms; and (3) utilization of sugars in sink tissues.
Additional Course Information

Course Content                                                                                                                                     
This course is designed to provide a broad overview of plant metabolism with opportunities to explore specific topics in detail. It is a plant biology course that emphasizes integration of biological processes from the biochemical up to the whole plant levels. The exact topics to be covered will be dictated in part by the specific interests of students in the course.  The depth of study will go beyond the level of a 4th year undergraduate course on plant biochemistry and physiology, with the goal of approaching a level of understanding that allows experimental implementation. Emphasis will be placed on understanding the regulation and interaction between metabolic processes in plants at the molecular to whole-plant levels, and their physiological and agricultural implications. Detailed aspects of carbon, nitrogen, and sulfur metabolism are examined since collectively these processes contribute ~99% of the biomass in plants. The interaction of C, N and S metabolism with plant developmental processes will be discussed. An understanding of basic biochemical principles, components of the plant cell, the plant life cycle, and basic aspects of regulation of gene expression will be assumed. NOTE: PLNT*6320 is a full course (0.5), whereas graduate-level seminar and colloquium courses are typically half-course (.25). Thus the workload in PLNT*6320 reflects a full course.

Auditing versus Course Credit
Students are strongly encouraged to take PLNT 6320 for credit. Auditing requires written permission by B. Micallef, and non-registered attendance in the course is not allowed. Anyone auditing will be expected to give lecture presentation and lead a scientific paper discussion, provide evaluations for student presentations, and participate in class discussions.         

Method of Course Presentation
The 1st class meeting will be an introduction to the course. The next 4 weeks will involve an examination and discussion of 4 scientific papers led by B. Micallef, and these discussions will be supplemented with lecture material. There will be a question associated with each scientific paper to be answered by students for marking. During Weeks 6-8, the course will consist of student lecture presentations on topics in plant metabolism at an advanced level, and subsequently during Weeks 9-12 there will be student-led discussions of scientific papers and associated questions to be answered. An opportunity to integrate material will be provided during the presentations (see Section 5 below). Available research methodologies will be examined in detail, including genetic, biochemical, and physiological approaches to studying plant structure and function.

Details on how to present the student presentations remotely will be discussed in detail during the initial class meeting.

The first 5 weeks of the course will involve an overview of metabolic processes in autotrophic organisms by B. Micallef, including an examination of specific scientific papers and methodologies. During Weeks 6-8, the course will consist of student lecture presentations on topics in plant metabolism, and subsequently during Weeks 9-12 there will be student seminars on specific scientific papers.  An opportunity to integrate material will be provided during the presentations and written assignments. Discussion and participation will be encouraged at all times in the course (20% of grade).

 

 

Labs & Seminars:
  • Student lecture presentations - Specific topics on source and sink metabolism in plants
  • Student-led discussions of scientific papers

 

Potential Topics for the Student Lecture Presentation
The topics below are suggestions, and they do not cover all potential topics that are relevant in the course.
1) Structure and function of the electron transport chain and light harvesting complexes, including potential applications to sustainable energy production.
2) Bioenergetics of energy capture by plants.
3) Synthesis of chlorophyll and carotenoids in the chloroplast and their importance to the electron transport chain and plant function (e.g. photoinhibition, ROS).
4) Adaptations of the photosynthetic apparatus to high and low irradiance.
5) Sensing of abiotic factors (e.g., light, temperature), including signal transduction pathways (e.g., photoreceptors, circadian clock); stress tolerance in plants.
6) Photorespiration and variations in photosynthetic C reduction (e.g. C4 metabolism, CAM metabolism), influence of abiotic factors.
7) Rubisco and its regulation in plants, modification of Rubisco.
8) Sucrose and starch synthesis in source leaves, including nighttime starch degradation in chloroplasts; utilization of sucrose and starch in sink tissues.
9) Modification of carbon metabolism in plants apart from Rubisco and photorespiration.
10) Long distance transport processes in plants, including phloem loading and unloading.
11) Biosynthesis of vitamin C and its physiological roles in plants.
12) Mechanisms of cellular transport including H+/Ca2+-ATPases, co-transporters, and ion channels.
13) Uptake and transport of water in plants, including the concept of water potential and the role of membrane transporters (e.g. aquaporins), stomates.
14) Nitrogen and sulfur uptake, reduction, and assimilation, including biochemical aspects of N2 fixation.
15) Cell wall structure, function, and biogenesis, importance of cell walls in agriculture.
16) Phenylpropanoid metabolism including primary and secondary metabolites, physiological roles and agricultural and nutritional importance
17) Alkaloid compounds and their synthesis, including examples of mixed synthesis and interaction between biochemical pathways, relationship to medicine
18) Starch, protein, or lipid synthesis in sink tissues including seeds.
19) Terpenoid synthesis in sink tissues including primary and secondary terpenoids (e.g. Vit E, terpenoid-based plant growth regulators, volatiles, etc.).
20) Synthesis of N- and S-based plant growth regulators and their functions in plants.
21) Signal transduction pathways associated with plant growth regulators (e.g., regulation of plant growth and development through ubiquitin-associated SCF complexes).
22) Relationship between metabolic processes and signal transduction pathways in plants.
23) Gene expression in plant organelles and its regulation in plants.
24) The relationship between stress tolerance and plant metabolism (e.g., metabolic factors involved in temperature or drought tolerance).
25) The relationship between metabolism and plant developmental processes (e.g., sugar sensing in plants, plant growth regulators, environmental interactions).
26) Biochemical regulation of plant developmental processes (e.g., florigen protein).
27) Plant-biotic interactions including interactions with pathogenic organisms.
 

Course Assignments and Tests:

Assignment or Test Contribution to Final Grade

Lecture Presentation

20%

Preliminary outline for lecture presentation

5%

Student-led scientific paper discussion

20%

Designing and marking a question directed to the student-led scientific paper discussion

5%

Answers to questions on scientific papers (6 in total x 5% answer)

30%

Participation

20%
Additional Notes:
Lecture Presentation on a Topic in Plant Metabolism (25% of final grade)
This assignment will provide students with an opportunity to deliver an advanced 50-min participatory/active learning lecture on a topic in plant metabolism. It is worth 30% of the final grade in the course (20% for the presentation and 5% for a lecture outline). Questions can be asked by the audience anytime during the lecture, and student presenters should anticipate 10 min for questions when designing the lecture. Your lecture presentation should provide an accurate representation of our present state of knowledge for the topic. In terms of the ‘big picture’, also attempt to address the relevance of the topic to plant physiology, and the practical relevance of the topic. The complete list of references used in preparing the PowerPoint presentation should be listed at the end of your PowerPoint presentation, and these references should be cited within the lecture presentation where appropriate. Detailed guidelines for the lecture presentation including the marking scheme are provided on CourseLink.
 
 
Student-led Discussion of a Scientific Paper (25% of final grade)
This assignment will consist of two parts: (i) a 50-min lecture presentation (40-min lecture & ~10 min for questions) (20% of final grade); and (ii) a detailed outline of the lecture presentation provided no less than 2 weeks before the actual lecture presentation (5% of final grade). This assignment will provide students with an opportunity to deliver an advanced 50-min participatory/active learning lecture on a topic in plant metabolism. Questions can be asked by the audience anytime during the lecture, and student presenters should anticipate ~10 min for questions and discussion when designing the lecture. Topics must be chosen in consultation with the instructor by Sept 30 to provide a complementary selection of topics. A detailed outline of the lecture presentation must be handed into the instructor for marking no less than 2 weeks before the actual lecture presentation. The following must be provided to the instructor 4 days prior to the scheduled presentation for posting on CourseLink: (1) a final version of the PowerPoint presentation in .ppt format; and (2) pdf copies of 3 relevant review papers from the scientific literature for posting on CourseLink.
Your lecture presentation should provide an accurate representation of our present state of knowledge for that topic. In terms of the ‘big picture’, also attempt to address the relevance of the topic to plant function, and the practical relevance of the topic. The complete list of references used in preparing the PowerPoint presentation should be listed at the end of your PowerPoint presentation, and these references should be cited within the lecture presentation where appropriate.
Detailed guidelines for the lecture presentation, including the lecture outline, are provided in a separate document on CourseLink.
 
Student-led Presentation and Discussion of a Scientific Paper-Weeks 10-12 (25% of final grade)
This assignment will consist of two parts: (i) a 50-min student-led presentation and discussion of an original scientific paper (20% of final grade); and (ii) the development and marking of a question directed to the scientific paper (5% of final grade). IMPORTANT: the scientific paper chosen by each student should be directly relevant to the topic discussed by them in the previous lecture presentation. This will allow the class to have some background relevant to the scientific paper. Compared to the lecture presentation, the student-led paper discussion will require a greater emphasis on methodology, experimental design, and data analysis and interpretation, and it will be more focused overall. Detailed guidelines for the student-led scientific paper presentation including the marking scheme are provided in a separate document on CourseLink. See Section 5(a) above for the policy regarding a missed presentation.
Initially, students should provide the instructor with 2-3 original scientific papers they would like to discuss, and then in consultation with the instructor one of these papers will be selected for the student-led presentation and discussion. Scientific papers must be chosen in consultation with the course instructor by Oct 14 to provide a complementary selection of topics. A pdf of the scientific paper will be posted on CourseLink by the instructor once finalized. The selected scientific paper will provide the basis for the discussion. The discussion will consist of two parts: (1) an uninterrupted PowerPoint presentation of the scientific paper that is no more than 20-min & 15 slides in length, not including the title slide and literature cited slide(s); and (2) a ~30 min informal student-led discussion of the scientific paper. The 20-min PowerPoint presentation is to consist of the following items: (1) up to 4 introductory slides (not including the title slide) that provide the objective(s) of the paper, rationale for the experimental design, and any necessary background information; (2) a discussion of up to 5 key figures and/or tables from the scientific paper using up to 2 slides per figure or table (i.e. up to 10 slides total), such that relevant methods, and the results and conclusions are provided; (3) no more than one slide providing the main conclusion(s) from the paper and future directions; and (4) additional slide(s) providing the Literature Cited. Thus, the 20-min presentation should consist of no more than 15 well-designed slides + a title slide and slide(s) for the Literature Cited. A copy of your PowerPoint presentation in ppt format must be provided to the instructor during the class it is presented for posting on CourseLink after the presentation is complete. This PowerPoint presentation is not provided to the class beforehand, since that would defeat the purpose of the exercise.
The 30-min student-led discussion can include any aspects of the scientific paper, including data not discussed during the 20-min presentation, and potential applications to the improvement of agriculture, forestry, etc. To encourage discussion, it is recommended that each class member prepares two questions or comments directed to the scientific paper prior to class.

A question directed to the scientific paper that is being presented in the student-led paper presentation will be developed by the presenter and answered by the class for marking. The question must be provided to the instructor for posting on CourseLink no later than two weeks prior to the student-led presentation. The goal of this assignment is to encourage a detailed reading of the paper to be presented in the student-led discussion. Questions should foster an in-depth analysis of the paper and can include:

  • Queries as to the hypothesis being tested, and how the experiment(s) allowed the hypothesis to be tested including the quality of the experiment(s);
  • Explanation of a methodology and how it was critical in addressing a scientific question;
  • Design of the next critical experiments to further the research area;
  • Analysis of data and methodology to assess limitations in the study;
  • Anything you think is appropriate.

Questions will be marked by the presenting student. A scanned pdf of the marked copies of the student answers is due to the instructor by Sunday of the next week by 4 pm for final approval of the grade. The quality of both the question and the marking of the question will be assessed by the instructor for 5% of your final grade. When developing a marking scheme for marking the question, the total score should add up to at least 20 points to prevent too large a deduction per point. Detailed guidelines for developing and marking the questions, including the marking scheme, are provided in a separate document on Courselink.

Answering Questions Directed to Scientific-Paper Discussions (30% of final grade)
During Weeks 1-5 the course instructor will provide four questions directed to a scientific paper. Three of the four questions must be answered and handed in for marking. Each answer is worth 5% of the final grade for a total of 15% of the final grade. If all four questions are answered, the best 3 out of 4 marks will be used to calculate the final grade.
In addition, during Weeks 10-12 each student presenter will provide the class with one question directed to their student-led scientific paper presentation (see 5(c)), and answers will be marked by the student presenter. The best 4 marks will be used to calculate the final grade (5% each) for a total of 20% of the final grade. Thus, there is the option to answer only 2 questions or to answer more if you believe this will improve your overall grade. Each answer will have a word limit of 1 double-spaced page per question (12-font, New Times Roman, 2.5 cm margins all).
Answers to the questions provided both by the course instructor and student presenters are due to the course instructor (not the student presenter) as a hard copy in class just before the scientific paper presentation begins; they cannot be handed in at a later time. Detailed guidelines for answering the questions, including the marking scheme, are provided in a separate document on CourseLink.

Detailed guidelines for developing and marking the questions including the marking scheme are provided on CourseLink. The quality of both the question and the marking of the question will be assessed by the course instructor for a total of 5% of the final grade.

Regarding the questions marked by student presenters, a scanned version of the marked hard copies of the answers are due to the instructor by Sunday of the next week by 4 pm for final approval of the grade. The quality of both the question and the marking of the question will be assessed by the instructor for 5% of the final grade.

Class Participation (20% of final grade)
Level of class participation will be determined by the instructor through: (i) participation in class discussions; (ii) the quality of evaluation of student presentations (see Sections 5(a) and 5(b) above); (iii) conforming to instructions, including due dates; and (iv) class attendance. Each of these 4 components will constitute 5% of your final grade for a total of 20%, and participation components can overlap (e.g. if you miss a class, it will affect (i) and (vi) and it could affect (ii)). For (iv), class attendance, one % point of the final grade will be deducted for each missed class regardless of the reason.

Final examination:

There is no final exam for this course.

Course Resources:

There will be numerous handouts on CourseLink, including selected papers from the scientific literature, other selected readings, and PowerPoint presentations.
Required Texts:

Not applicable

Recommended Texts:

Not applicable

Lab Manual:

Not applicable

Other Resources:

There will be numerous handouts on CourseLink, including selected papers from the scientific literature, other selected readings, and PowerPoint presentations.

Additional Useful Sources:                                                                                                                   

There are several journals that provide original scientific articles dedicated to plant biology such as Plant Physiology, The Plant Cell, The Plant Journal, Plant Molecular Biology, Plant and Cell Physiology, Journal of Experimental Botany, Plant, Cell and Environment, etc.  Wider-audience journals such as Science, Nature, Proceedings of the National Academy of Sciences, Cell, etc. also include many original articles in plant biology.

There are also several journals that publish review articles such as Annual Reviews of Plant Physiology and Plant Molecular Biology, Annual Plant Reviews, Trends in Plant Science, Current Opinion in Plant Science, Annual Reviews of Biochemistry, etc.

Field Trips:

Not applicable

Additional Costs:

Not applicable

Course Policies:

Grading Policies
The standard penalty for late assignments will be 10% of the assignment value per working day late. Please note that these policies are binding unless academic consideration is given to an individual student. Also see Graduate Grading Procedures.
If you need to miss an exam or a lab period, the course instructor should be informed ahead of time and supporting documentation provided where appropriate. Failure to follow these rules could result in a loss of marks.
 
Conforming to Instructions
Marks will be deducted for not conforming to instructions, including not conforming to due dates, as outlined in 6. Course Evaluation either directly in an assignment or through Participation.
 
Due Dates
For the lecture presentation, topics must be chosen in consultation with the instructor to provide a complementary selection of topics. A detailed outline of the lecture presentation must be handed into the instructor for marking no less than 2 weeks before the actual lecture presentation. The following must be provided to the instructor 4 days prior to the scheduled lecture presentation for posting on CourseLink: (1) a final version of the PowerPoint presentation in .ppt format; and (2) pdf copies of 3 relevant review papers from the scientific literature.
For the student-led scientific paper presentation and discussion, scientific papers must be chosen in consultation with the course instructor to provide a complementary selection of topics. A pdf of the scientific paper must be provided to the instructor for posting on CourseLink once finalized. A copy of the PowerPoint presentation in ppt format must be provided to the instructor in class on the day of the presentation for posting on CourseLink after the presentation is complete.
For questions directed to scientific papers presented by either the course instructor or student presenters, questions will be marked by the course instructor or presenting student, respectively. The question directed to student presentations must be provided to the instructor for posting on CourseLink no later than two weeks prior to the student-led presentation. Answers are due in class as a hard copy to the course instructor before the seminar presentation occurs; they cannot be handed in at a later time.
If the lecture presentation or student-led scientific paper presentation and discussion must be missed at the scheduled date for a legitimate reason, the instructor must be told prior to class or marks will be deducted, and an attempt will be made to reschedule the lecture in class. Supporting documentation for an absence may be requested by the instructor, particularly if the instructor is not informed prior to class.

For the Lecture Presentation, topics will be chosen in consultation with the instructor by the end of Week 2 to provide a complementary selection of topics. A detailed outline of the lecture presentation is to be handed into the instructor for marking no less than 2 weeks before the actual lecture presentation. The outline will constitute one-quarter of the presentation mark. The following should be provided to the instructor 4 days prior to the scheduled presentation for posting on CourseLink: (1) a final version of the PowerPoint presentation in .ppt format; and (2) pdf copies of 3 relevant papers from the scientific literature.

Scientific papers will be chosen in consultation with the course instructor by the end of Week 4 to provide a complementary selection of topics. A pdf of the scientific paper will be posted on CourseLink by the instructor once finalized.  A copy of the PowerPoint presentation in ppt format must be  provided to the instructor in class for posting on CourseLink.

For questions directed to scientific papers presented by either the course instructor or student presenters, questions will be marked by the course instructor or presenting student, respectively. Answers are due in class as a hard copy before the seminar presentation occurs; they cannot be handed in at a later time. There will be 2 questions provided by the course instructor, and a minimum of 4 questions from student presenters must be answered and handed in for marking. Each answer will be worth proportionally the same % of the final grade (5% each) for a total of 30%. Regarding the questions marked by student presenters, the marked hard copies of the answers will be due to the instructor by Wednesday of the next week for final approval of the grade. The quality of both the question and the marking of the question will be assessed by the instructor for 5% of the final grade.

Each of the four components for Participation will constitute 5% of the final grade for a total of 20%, and participation components can overlap (e.g. if you miss a class, it will effect (i) and (iv) and it could effect (ii)).

If the lecture presentation or student-led scientific paper discussion must be missed at the scheduled date for a legitimate reason, the instructor should be told prior to class if possible, and an attempt will be made to reschedule the lecture in class at a later date. Supporting documentation for an absence may be requested by the instructor, particularly if the instructor is not informed prior to class.

Course Policy on Group Work:

Not applicable.

Course Policy regarding use of electronic devices and recording of lectures:

Electronic recording of classes is expressly forbidden without consent of the instructor, whether the instructor, a classmate or guest lecturer. When recordings are permitted they are solely for the use of the authorized student and may not be reproduced, or transmitted to others, without the express written consent of the instructor. Material recorded with permission is restricted to use for that course unless further permission is granted.

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/.

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