University of Toronto at Mississauga
Department of Biology

BIO 304H5S - Physiology of Neural Systems

Cricket interneuron


NOTE: this course uses Blackboard to post lecture notes, assignments and for the Discussion Forum.
This web page describes the course content in general, for details you must be enrolled in the course to access Blackboard.

Students who wish to enroll in this course must have either BIO 204 or an equivalent
course in introductory physiology that includes components of neurophysiology.
This is a limited enrollment course and priority is automatically given to students with the pre-requisites.
If you believe you have an equivalent course and have been placed as "interim" by ROSI you must email
the professor by November 15 with an explanation as to why you feel you are prepared for the course.
In your email please attach a copy of of your transcripts as a scanned JPG of your official ROSI form.
Students who are interim and do not contact the professor will not be able to enroll once classes begin.

There are no deadline extensions for term work assignments for students who miss the first lectures.  
It is your responsibility to acquire all notes and assignments from other students if you miss classes.
If you are waiting to be enrolled in the course you should attend all lectures and submit the assignments on time.

BIO 304 uses computer-based neural simulations and students who want to do well will spend at least three hours a week
 on these simulations so this course should be considered as time-intensive as one with a practical lab period.

THE PEOPLE WHO TEACH THIS COURSE
COURSE DESCRIPTION
PLAGIARISM WARNING (PLEASE READ THIS)
LECTURE SCHEDULE
TUTORIALS


THE PEOPLE WHO TEACH THIS COURSE

PROFESSOR

Professor James Fullard
email: james.fullard@utoronto.ca

COURSE DESCRIPTION
BIO 304S is a study of the mechanisms that operate in neural, sensory and neuromuscular systems. The strategy will be to provide a solid background in each of the general areas in the course and an introduction to some of the newer topics in this subject. In the advanced physiology courses (BIO 409S, 403S, 407S, 410F), this background knowledge is used to focus on several more specific areas.

In place of traditional neural lab exercises, BIO 304 uses a sophisticated computer simulation programme called NEURON to reproduce the activity of nerve cells in controlled environments.  This programme allows the student to manipulate a large number of biological variables to see how neurons respond to changes in ionic concentrations, electrical stimulation and synaptic interactions to name a few.  NEURON permits the undergraduate student to study how nerve cells operate in a detail that they would never be able to obtain in a normal laboratory setting.  The theoretical principles that students learn from these computer simulations can be used to perform examinations with living nervous tissue in advanced courses in neurobiology (e.g., BIO 409).

LECTURES
Lectures are one hour and 50 minutes long and held once a week (time and room determined by Registrar's office).  Students should read the material from the text to be prepared for the lectures.  Material in lectures will centre on the required readings but will go beyond these readings, therefore it is important to attend lectures and to use other texts in order to understand the material covered.

Mid-way through the course there is a term test. The final exam will be held during the exam period; approximately 1/3 of the marks on the final exam will be from the first half of the course with the rest from the remainder of the course. The questions on the mid-term test and final exam will come from the material presented during both lectures and tutorials and will include practical questions based upon the computer neural simulations.  Students are also responsible for material from assigned readings.

Note: there is no make-up mid-term test.  If you miss the mid-term test because of a medical excuse the final exam will be worth 50% of your course mark.
Click here for the only acceptable medical certificate for this course.

TUTORIALS
Tutorials are 50 minutes long and held once a week (time and room determined by Registrar's office).  These times are used to expand upon material introduced during lectures, answer questions arising from that material and to introduce the current week's computer neural simulation.  Attendence in tutorials is mandatory and students are responsible for any material covered during them for tests and exams. Students who intend to pass the course will spend at least three hours a week on the neural simulations so BIO 304 should be considered as time-intensive as one with a practical lab period.  There will be three tests based on these simulations conducted during the tutorials.  There are no make-ups for these tests; students who miss a test with a medical excuse will have their grade determined by the other two tests, sudents who miss a second test will receive the same mark as the test they wrote.

TEXTS
The required texts for this course are:
1. Animal Physiology 5th edition (Randall, D., Burggren, W. and French, K.) (available either from the UTM bookstore (usually the best price) or online from either Chapters.Indigo.ca (Canadian company) or Amazon.ca).
2. Neurons in Action. Tutorials and Simulations Using NEURON  (Version 2.0).  Moore, J.W. and Stuart, A.E. (Sinauer Associates, 2007) from either the UTM bookstore or Amazon.ca (be sure you buy version 2.0; publication date: 2007).  Go here to read more about this programme.

Important:  While I recommend page readings from these texts students are responsible for all material covered during lectures and tutorials whether or not this material appears in the readings.  Test and quiz questions may arise that are not covered in the recommended readings and additional texts will have to be used, such as books that are on reserve in the library, many of which cover both lecture and tutorial material.

MARKS
 The final mark for this course is based on the following:
       A. Lecture component:
            1. Mid-term test - 20%
            2. Final exam - 30%
       B. Tutorial component:
            3. Assignments - 20%
            4. Tests - 30%

World Wide Web sites to visit that have additional information on neurobiology:

Electrophysiology and The Molecular Basis of Excitability: An excellent interactive teaching site that provides animations and explanations of the concepts we cover in BIO 304.

The Fly Brain: Researchers from North America and Europe have combined their works to show you how an insect brain is put together.

Society for Neuroscience: One of the largest scientific organizations in the world, this site will lead you to information about current research and job opportunities in neurobiology.
Neurosciences on the Internet This is a library of Web sites that deal with current events, research, job opportunities, etc. in the neurosciences.

Trends in Neurosciences  A review journal with relatively easy to read articles on neurobiology including new directions in research and job opportunities.

PLAGIARISM

PLEASE READ THIS

In this course, the following are considered to be examples of plagiarism:

  1. Submitting a report wholly or in part copied from one done in a previous year. Each year the tutorial assignments are changed and reports that appear to be based on previous year's formats will considered to be plagiarised.
  2. Copying sentences from published works (e.g., scientific journals) and not enclosing them in quotation marks with a complete citation.
  3. Copying the analyses of other people's work in the computer simulation assignments.  While it is a good idea to go over the simulations with your friends all subsequent analyses and interpretations must be done by each student individually.
According to university policy, T.A.s must notify the professor of any case of suspected plagiarism who will talk to the student(s) involved and then, if the situation warrants, pass the material on to the dean of sciences. Students found guilty of wilful plagiarism face penalties ranging from severe mark deductions to dismissal from the course. These penalties can have permanent effects on a student's post-graduate opportunities and can prevent them from entering professional faculties (e.g., medical school). If you have any questions about the validity of your work please ask your T.A. or your professor.

LECTURE SCHEDULE

Students are responsible for what is covered in lectures and tutorials whether or not this material appears in the suggested readings.

A. Introduction
Readings: Animal Physiology (5th ed): pp. 49-51

1. Discussion of syllabus and course objectives, introduction to bioelectricity .

2. Concepts in DC electricity. Electron versus ionic electricity.  Computing and measuring potential, the digital oscilloscope.


    B. Passive electrical properties of cells
Readings: Animal Physiology (5th ed): pp. 114-132, 157-159.

3. Electrical model of cell membrane (1): the electrochemical basis of resting membrane potential, the Nernst and Goldman equations.

4. Electrical model of cell membrane (2): charged particle behaviour, secondary potentials, capacitance, time constant.

5. Electrical model of cell membrane (3): applied current and resultant potentials: intracellular stimulation and recording, resistance in small versus large spherical cells, parallel resistance. 

6. Electrical model of cell membrane (4): current and resistance in long cells: cable properties, series resistance, length constant.


    C. Active electrical properties of cells

    Readings: Animal Physiology (5th ed.): 132-153, 159-166.

7. Action potentials (1) Mechanisms: the "how" of APs; Na+ influx / K+ efflux, voltage-gated channels, threshold

8. Action potentials (2) Mechanisms: refractory periods, channel blockers, Na+ channel currents/kinetics.

9. Action potentials (3) Functions: the "why" of APs; coding properties: phasic/tonic responses; input/output relationships.

10. Action potentials (4) Currents and pumps: voltage clamping, whole-cell and patch clamping, voltage/current relationships.

11. Action potentials (5) Propagation: conduction velocity, spatial attributes of channel activation, saltatory conduction, myelination.

12. Action potentials (6) Extracellular action potentials, multi-cell recordings, compound action potentials.


    D. Synapses

    Readings: Animal Physiology (5th ed.): pp. 166-198.

13. Synapses (1): Electrical synapses, gap junctions, coupling ratio, synaptic delay, bidirectionality.  Chemical synapses: general anatomy, pre-synaptic mechanisms, calcium currents, vesicle morphology and regeneration, synthesis of neurotransmitters (e.g., acetylcholine).
 
14. Synapses (2): Chemical synapses: post-synaptic mechanisms, agonists and antagonists, fast and slow neurotransmission, neuromodulators.
 
15. Synapses (3): postsynaptic currents, m.e.p.p. to EPPs, EPSP versus IPSP, reversal potential, synaptic modulation, summation, facilitation.
 

    E. Synaptic integration and behaviour

    Readings:Animal Physiology (5th ed.): pp. 198-209, 425-468.

16. Synaptic modulation and integration (1): temporal and spatial summation, homo- and heterosynaptic modulation.

17. Synaptic modulation and learning in Aplysia and mammals
 

    F. Sensory systems

    Readings: Animal Physiology (5th ed.): pp. 215-276.

18. Sensory physiology (1): classification of sensory modalities, PST histograms. Mechanoreception: tactile spines in the cockroach as model for sensory processes.

19. Sensory physiology (2): The receptor cell: receptor potentials, transduction processes, extrinsic versus intrinsic mechanisms of adaptation.

20. Sensory physiology (3): Vertebrate photoreception:  molecular basis for photoreception, rhodopsin, the enzyme cascade, hyperpolarizing receptor potentials, the non-spiking secondary sensory cell.

21. Sensory physiology (4): Invertebrate photoreception: depolarizing photoreceptor potentials, polarized light reception, compound eyes in insects and crustacea, the eyes of Limulus, lateral inhibition, edge enhancement.

22. Sensory physiology (5): Visual processing in vertebrates: retinal information flow, lateral inhibition and edge enhancement.


G. Muscles

Readings: Animal Physiology (5th ed.): pp. 361-397, 411-413.

23. Muscles: structure and ultrastructure of striated muscles, electrical properties of muscle cells; excitation-contraction coupling, T-tubules, sarcoplasmic reticula and calcium regulation, temporal versus spatial summation, tetanus, neural control of muscles, motor units, multiterminal/mutineuronal neuromuscular junctions.



24. Guest Lecture - TBA
 
25. Review Session
 


TUTORIALS

The purpose of the tutorials is to introduce the computer simulation for that week and to answer any questions that arise from the lectures.  Attendance in these tutorials is mandatory since you are responsible for any material covered during them for term tests and the final exam.  After the tutorial the assignment for the computer simulation will be posted on Blackboard.  Assignments will be in the form of question sheets that are answered with numerical values, attached graphs and short answers and will require the reading of research papers.

There are nine assignments during the course that come in two forms. Some assignments are full-mark hand-ins that will have all of the answers graded by the TAs and the others are part-mark hand-ins that will be graded as "complete", "partially complete" or "missing".  Students will not know in advance what the assignments are worth.  Following the week that hand-ins are due, an answer sheet will be posted on Blackboard.  Both types of assignments will receive equal weighting on the term tests and final exam during the course.

Do not hand in copied assignments!
Assignments are mainly intended to assist students in understanding the computer simulations and are worth relatively little of the course's final mark (20%).
Students who copy assignments will not understand the simulations and will fail the tutorial tests and sections of the mid-term and final exam (approximately 50% of your final mark).
Do the math! 

Asssignments are marked as follows:

Full-mark hand-ins:
1.  Numerical values = 0.1 - 0.5 marks each.  Note: values with decimal point accuracy other than that requested will be marked as incorrect.
2.  Attached graphs = 2.0 marks each.  Note: graphs not pasted in the boxes provided will not be marked.
3.  Short answers = 3.0 - 6.0 marks each

Part-mark hand-ins:
1. Missing = 0
2. Partially complete = 0.5
3. Fully complete with all tables and questions answered = 1.0

Marks:
Four full-mark assignments X 3.5 marks each = 14 marks
Five part-mark assignments X 1.2 marks each = 6 marks
Three tests based upon computer simulations X 10 marks each = 30 marks. There are no medical exemptions for these tests, students who miss a test will have their total grade determined by the other two tests.
Total tutorial mark for the course = 50 marks

Assignments are due by 6 PM, usually of the Wednesday before tutorial and must be dropped off in the collection box outside of Room B4071. There are no extensions allowed for these assignments but students can hand in their assignments any time before the deadline.
Late assignments will not be accepted and will receive zero.


TUTORIALS AND ASSIGNMENTS

1. Introduction to "Neurons in Action".  Read "Introduction to Neurons in Action" (pp. 1-7)  to prepare for tutorial.
    Tutorial #1: The Membrane (pp. 9-15).
                                 
2. Tutorial #2: Equilibrium Potentials (pp. 17-21)

3. Tutorial #3: The Passive Axon (pp. 73-79)

4. Tutorial #4: The Na Action Potential (pp. 23-28) / Threshold: To Fire or Not to Fire (pp. 29-34)
 
5. First test based on computer simulations - covers up to and including tutorial #3  
 
6. Tutorial #5: Unmyelinated Axon (pp. 79-84) / Myelinated Axon  (pp. 85-88)

7. Tutorial #6:  Partial Demyelination (pp. 89-93)
 
8. Tutorial #7: The Neuromuscular Junction (pp. 57-62)
 
9. Second test based on computer simulations - covers up to and including assignment #6 - approximately 2/3 of this test will be on material covered since the first test.

10. Tutorial #8: Postsynaptic Inhibition (pp. 63-66) / Interactions of Synaptic Potentials (pp.67-71)

11. Tutorial #9: Site of Impulse Initiation (pp. 123-126)

12. Third test based on computer simulations - covers up to and including assignment #9 - approximately 3/4 of this test will be on material covered since the second test.