Cell & Systems Biology

UNIVERSITY OF TORONTO

CSB346 Neurobiology of Respiration

Winter 2024

COURSE SYLLABUS
Course Number: CSB346H1S Term: Winter 2024
Course Title: Neurobiology of Respiration Office Questions will be addressed
Hours during breaks and before or
and after class, or by making an
location: appointment with Dr. Fraigne by
email.
Course Day/Time: Tues 3-5 (tutorials Thurs 5) Location: MP202
Instructor: Jimmy Fraigne Email: [email protected]
Teaching See below Email: See below
Assistant:
Course Nalini M Dominique-Guyah Email: [email protected]
Administrator:

Teaching Assistants:
Name email
Anita [email protected]
Irina [email protected]
Anthony [email protected]
Matthew [email protected]

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Course Description
The primary aim of the course is to highlight how breathing is generated and regulated by both
the central and peripheral nervous systems. We will discuss these topics from molecular, cellular
and systems levels. An emphasis will be placed on the control of breathing during both health and
disease. For example, we will discuss how sleep disorders impact respiratory control.
Understanding how the brain controls breathing is an important and exciting area of scientific and
clinical study.

The secondary aim of the course is to focus on describing the scientific method, and how to read
and criticize scientific publications. This is an appropriate course for students who are interested
in aspects of neuroscience and clinical pathophysiology.

Lecture Topics:
1. Overview of the respiratory system – anatomy of the lungs and airways
2. Overview of the respiratory system – neuro-anatomy
3. Cellular and systems approaches to studying respiratory neurobiology
4. Mechanics of breathing
5. Work of breathing
6. The brain and breathing – what’s the link?
7. Peripheral mechanisms of respiratory control
8. Central mechanisms of respiratory control
9. Genetics and breathing (e.g., Central congenital hypoventilation syndrome)
10. Respiratory disorders (e.g., Sleep apnea)

Learning Outcomes
By the end of this course, students will understand the neuronal mechanism implicated in
the control of breathing. They will know the anatomy, physiology and neural mechanism
of breathing. Students will also develop skills to read, dissect and criticize primary
research articles.

Course Requirements
Prerequisites: BIO270&271/PSL300 & 301

Communication and Quercus

This course will be delivered in person in MP202 (Lecture: Tuesday 3-5pm & Tutorial: Thursday
5-6pm) and recording will be available online after each lecture and tutorial, the timing of upload
cannot be guaranteed. The upload of the recording is to help students. The course is delivered
in-person. All testing will be in-person. Weekly quizzes will be on-line via Quercus.

Please use the Discussion forum on Quercus to ask any course-related questions or content-
related questions. We will not be answering individual questions about course content
through email.

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Please note- the expectation for this course will be to use Quercus Discussion board or in-class
discussion wherever possible for course and content-related questions. If you have questions
that you feel are more private, then please email Dr. Fraigne at [email protected]. I will
try to get back to you as quickly as possible.

For all matters regarding course administration, please contact the Course Administrator, Nalini
Dominique-Guyah at [email protected]. This includes missed term tests (medical
notes, scheduling, etc…), and any additional questions or concerns you may have regarding the
course. For any emails to Nalini, please ensure that you put “CSB346” in the subject line.

Office Hours: I will answer questions about course material before, after and during the break of
each class. If you require meeting with me outside of class time, please email me your request
and I will arrange a time to meet.

Notice of Video Recording

To provide you with recordings of the in-person lecture and tutorial, I will use the University’s
Opencast Content Capture System (OCCS). This course content (PowerPoint slides) and my
voice will be recorded on video and will be available to students in the course for viewing
remotely and after each session.

Course videos and materials belong to the instructor, the University, and/or other source
depending on the specific facts of each situation, and are protected by copyright. In this course,
you are permitted to download session videos and materials for your own academic use, but you
should not copy, share, or use them for any other purpose without the explicit permission of the
instructor.

For questions about recording and use of videos please contact your instructor.

Required Course Material

Evaluations in this course are all based on lecture material and primary research articles
that are open publications (i.e. no cost to use). There is no required textbook and all
primary articles used in the course will be provided for you in PDF format on the course
website.

Relevant Dates
Please visit the Arts and Science website for a list of academic dates and deadlines:
https://www.artsci.utoronto.ca/current/dates-deadlines/academic-dates

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Topics (tentative – subject to change)

Lecture Week Start Date Topic
Week 1 January 9 Lecture 1: Introduction to neurobiology of respiration
Week 2 January 16 Lecture 2: Respiratory physiology
January 18 Tutorial introduction and research
Week 3 January 23 Lecture 3: Neural control of breathing
January 25 Tutorial example paper
Week 4 January 30 Lecture 4: Respiratory rhythm generation/Paper: Defining
February 1 PreBotzinger complex rhythm and pattern-generating
neuro-microcircuit in vivo
Tutorial review Assignment 1
Week 5 February 6 Assignment test 1
Week 6 February 13 Lecture 5: Central chemoreception/Paper: Nalcn is a
“leak” sodium channel that regulates excitability of
brainstem chemosensory neurons and breathing
Reading Week February 20 (no classes – reading week February 19-23)
Week 7 February 27 Term test
February 29 Return Assignment test 1
Week 8 March 5 Lecture 6: Oxygen sensing
March 7 Tutorial review Assignment 2
Week 9 March 12 Assignment test 2
Week 10 March 19 Lecture 7: Airway and pulmonary reflexes/Paper: Vagal
sensory neuron subtypes that differentially control
breathing.
March 21
Tutorial return Term test
Week 11 March 26 Lecture 8: Respiratory control during sleep/Paper:
Breathing control center neurons that promote arousal in
mice
Week 12 April 2 Final class and Q/A for Final assessment
April 4 Tutorial return Assignment test 2
Final Exam April 10-30 During Faculty Final Exam Period - TBD

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Evaluation
Date Subject % of Final Grade
Weekly Quizzes Starting Jan 9 lecture material for that week 10%
Assignment Test 1 Feb. 6 Assignment 1 15%
Term Test Feb. 27 Lecture 1-4 30%
Assignment Test 2 Mar. 12 Assignment 2 15%
Final Assessment TBD Lecture 5-8 30%

The format of the midterm test, assignment tests and final assessment will consist
of Multiple Choice questions (MCQ), True/False (T/F) and long answers.

Test policy
We will be having two Assignment tests that focus on peer-reviewed scientific papers
related to the course topic, and 1 term test and 1 final exam that cover material from
lectures. These tests will be 2 hours in length and will consist of multiple-choice
questions, true/false (T/F) and long answer questions.

For the two Assignment tests, the quiz and long answer questions will require you to
understand the details of the scientific paper. You can use the paper and any notes you
may have made to write the test. The questions will only be based on the paper you are
assigned to read. You must answer in your own words, and you are not allowed to copy
answers from the paper—This will be considered plagiarism. (see below: Error!
Reference source not found.).

Missed test policy

If you miss any of the tests you must submit a Declaration of Absence on ACORN and
either designate Nalini to receive a copy directly or email her a copy. If you have already
declared an absence this semester, then you will need to have a Validation of Illness
(VOI) form completed and submitted. No matter the situation, you need to email Nalini
with the reason for missing the test and any documentation supporting your missed test.
Nalini can be reached at [email protected] Please make sure that the subject
line is “CSB346 – missed test”.

Make-up test: for the Term Test there will be a make-up test. It will cover the same
material. If you miss the make-up test (for any reason) then its value (30%) will be
shifted to the final examination. You will need to submit separate documentation for
missing the make-up test.

Assignment tests: if you miss any of the assignment tests, the value of the test (15%)
will be shifted to the final. There are no make-up tests for any of the assignment tests.

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Weekly quizzes: There are no make-ups/extensions for missed weekly quizzes.

Note: you need an acceptable and validated reason for not writing any of the tests.
Please contact Nalini Dominique-Guyah at [email protected] if you have a
general inquiry, administrative problem, or have missed any assessment. For any missed
coursework, students must complete and provide a Declaration of Absence on ACORN or
a VOI within 1 week of the test date. Here is the link to the Absence Declaration tool on
ACORN.

Please also note: Students who have two term tests scheduled at the same time
because they have enrolled in courses that conflict will not be given special consideration
under these circumstances by the Department of Cell and Systems Biology.

Lab/Tutorial Information
Tutorials are held on Thursdays in MP202. See lecture schedule for days.

TAs:

Name email
Anita [email protected]
Irina [email protected]
Anthony [email protected]
Matthew [email protected]

Health and well-being

Your health and well-being in this course are important to everyone – from the instructors,
TAs, administrative staff and the University of Toronto as a whole. The following are
suggestions and resources to make sure you have a productive and healthy semester.
The university experience can be a challenging one, there is no need to go about it alone.
If you or anyone you know could use someone to talk to (or text with), here are some
resources in addition to your instructors, program coordinators, and TAs:

 Your College Registrar: uoft.me/registrars

 UofT Health and Wellness: 700 Bay Street Toronto, ON M5G 1Z6
416-978-8030 | [email protected]

24/7 emergency counselling services:

 U of T My Student Support Program (My SSP) | 1-844-451-9700. Outside of
North America, call 001-416-380-6578.
Culturally-competent mental health and counselling services in 146 languages
for all U of T students.

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 Good2Talk Student Helpline | 1-866-925-5454
Professional counseling, information and referrals helpline for mental health,
addictions and students well-being.

Acorn Absence Declaration

You can use the Absence Declaration tool on ACORN to record any absence from
academic work, whether for medical or non-medical reasons (e.g., COVID, cold, flu and
other illnesses, injuries or family situations). You should complete the Absence
Declaration anytime you are absent from academic work, not just when you have missed
a specific course deadline. Please note that you remain responsible for meeting the
course requirements. In certain cases, you will need to submit a U of T Verification of
Student Illness or Injury form (VOI):

For complex petitions: If you are submitting a petition due to illness or injury and your
petition is complex, a VOI can help support the petition request.

For exam rewrite petitions: If you are submitting a petition to rewrite an in-person final
exam, you will need to submit the VOI form as supporting documentation.

For longer term illness: The Absence Declaration tool can be used to declare an
absence up to seven days from the current day, plus two days retroactive. For absences
that extend beyond this time limit, you will need to submit the VOI form.

The VOI must be completed by a medical practitioner and must include the day(s) of your
illness or injury. You are encouraged to speak to your College Registrar’s Office if you are
unclear about submitting a VOI.

Use of a Plagiarism Detection Tool for Course Assignments

“Normally, students will be required to submit their course essays to the University’s
plagiarism detection tool for a review of textual similarity and detection of possible
plagiarism. In doing so, students will allow their essays to be included as source
documents in the tool’s reference database, where they will be used solely for the
purpose of detecting plagiarism. The terms that apply to the University’s use of this tool
are described on the Centre for Teaching Support & Innovation web site.”
(https://uoft.me/pdt-faq).”

Academic Integrity
“Academic integrity is a foundation of our university community’s intellectual life. What
does it mean to act with academic integrity? Acting with academic integrity means not
‘cheating’ to get ahead. U of T supports the International Center for Academic Integrity’s
definition of academic integrity as acting with honesty, trust, fairness, respect,
responsibility, and courage in all academic matters.”
https://www.academicintegrity.utoronto.ca/

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“The University of Toronto treats cases of academic misconduct very seriously. Academic
integrity is a fundamental value of learning and scholarship at the U of T. Participating
honestly, respectfully, responsibly, and fairly in this academic community ensures that
your U of T degree is valued and respected as a true signifier of your individual academic
achievement.
The University of Toronto’s Code of Behaviour on Academic Matters outlines the
behaviours that constitute academic misconduct, the processes for addressing academic
offences, and the penalties that may be imposed. You are expected to be familiar with the
contents of this document. Potential offences include, but are not limited to:

In papers and assignments:

 using someone else’s ideas or words without appropriate acknowledgement
 submitting your own work in more than one course without the permission of the
instructor
 making up sources or facts
 obtaining or providing unauthorized assistance on any assignment (this includes
working in groups on assignments that are supposed to be individual work)

On tests and exams:

 using or possessing any unauthorized aid, including a cell phone
 looking at someone else’s answers
 letting someone else look at your answers
 misrepresenting your identity
 submitting an altered test for re-grading

Misrepresentation:
 falsifying or altering any documentation required by the University, including (but
not limited to) doctor’s notes
 falsifying institutional documents or grades

All suspected cases of academic misconduct will be investigated following the procedures
outlined in the Code of Behaviour on Academic Matters. If you have any questions about
what is or is not permitted in this course, please do not hesitate to contact me. If you have
questions about appropriate research and citation methods, you are expected to seek out
additional information from me or other available campus resources like the College
Writing Centres, the Academic Success Centre, or the U of T Writing Website.”

Avoiding Plagiarism
https://advice.writing.utoronto.ca/using-sources/how-not-to-plagiarize/

Accommodations
Students with Disabilities:
“Students with diverse learning styles and needs are welcome in this course. In particular,
if you have a disability or health consideration that may require accommodations, please

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feel free to approach me and/or the Accessibility Services Office as soon as possible.
The Accessibility Services staff are available by appointment to assess specific needs,
provide referrals and arrange appropriate accommodations. The sooner you let them and
me know your needs, the quicker we can assist you in achieving your learning goals in
this course.”

Accessibility Services: [email protected] or

https://studentlife.utoronto.ca/department/accessibility-services/

Religious Observances:
“The University provides reasonable accommodation of the needs of students who
observe religious holy days other than those already accommodated by ordinary
scheduling and statutory holidays. Students have a responsibility to alert members of the
teaching staff in a timely fashion to upcoming religious observances and anticipated
absences and instructors will make every reasonable effort to avoid scheduling tests,
examinations or other compulsory activities at these times.

Please reach out to your course instructor or administrator as early as possible to

communicate any anticipated absences related to religious observances, and to discuss
any possible related implications for course work.”

Family Care Responsibilities:

“The University of Toronto strives to provide a family-friendly environment. You may wish
to inform me if you are a student with family responsibilities. If you are a student parent or
have family responsibilities, you also may wish to visit the Family Care Office website
at familycare.utoronto.ca.”

Equity, Diversity and Inclusion

“The University of Toronto is committed to equity, human rights and respect for diversity.
All members of the learning environment in this course should strive to create an
atmosphere of mutual respect where all members of our community can express
themselves, engage with each other, and respect one another’s differences. U of T does
not condone discrimination or harassment against any persons or communities.”

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