BIO325 Neurophysiology
Spring 2020
Course Syllabus
Instructor: Dr. Barry K. Rhoades
106 Munroe Science Center
Office Phone: 757-5238
Home Phone: 747-5348
Office hours: Monday 9:00 - 10:00 AM
Tuesday 3:00 - 4:00 PM
Wednesday 9:00 - 10:00 AM
Thursday 3:00 - 4:00 PM
Friday 9:00 - 10:00 AM
or by appointment
(I will be in my office during these times. Feel free to drop in to my office any other time from 9:00 to 5:00 weekdays. When I am not in my office, I am often in my lab space in Munroe 101/103. If I can meet with you at that time I will, otherwise I will make an appointment for a future time.)
Textbooks: REQUIRED:
(multiple copies intalled on lab computers)
Moore, J.W. (2008) Neurons in Action 2: Tutorials and Simulations Using Neuron.
Sinauer. ISBN #087893537X
(on loan for semester)
Reichert, H. (1992) Introduction to Neuroscience Thieme/Oxford. ISBN #0195210107
RECOMMENDED:
(available to read in lab room)
Byrne, J.H. & Roberts, J.L. (2009) From Molecules to Networks: An Introduction
to Cellular and Molecular Neuroscience. Academic Press. ISBN #0123741327
Matthews, G.G. (1999) 11th Hour: Introduction to Neuroscience.
Wiley-Blackwell. ISBN #9780632044146
Wyttenbach, R.A., Johnson, B.R., & Hoy, R.R. (1999) Crawdad: A CD-ROM Lab
Manual for Neurophysiology (Student Version). Sinauer. ISBN #0878939474
On-line Course Materials:
homepage: http://pierce.wesleyancollege.edu/faculty/brhoades/courses/Bio325manual
syllabus: http://pierce.wesleyancollege.edu/faculty/brhoades/courses/Bio325manual/syllabus.html
lab manual: http://pierce.wesleyancollege.edu/faculty/brhoades/courses/Bio325manual/labguide.html
Class Meetings: Period 4 (MWF 11:00 AM - 12:00 PM)
Lab Meetings: Periods7-9 Wednesday (2:30 - 5:20ish PM)
Note: Please be prepared for some labs to run a bit long.
Prerequisites: BIO 103 or BIO 110
BIO 203 or PSY 230
PSY/NSC 207 or consent of instructor
Note: This 300-level course moves fairly rapidly through intermediate-level topics in fundamental cellular and systems neuroscience. It is also laboratory intensive and requires students to learn challenging techniques and relate them to a consistent conceptual framework. It is essential that all students come into the course with previous course exposure to core cell biology, the fundamentals of how nerve cells work, and basic life science experimental practice. The prerequisuites are neither punative nor arbitrary; they are intended to insure that all students have a reasonable opportunity to keep up with the content of the course.
Schedules of Topics, Readings, Laboratory Exercises, Exams, and Sssignments: Complete schedules for the course are listed at the end of this syllabus. These are tentative schedules and are subject to revision. One or more exercises may be eliminated or substituted due to time constraints or unavailability of materials.
Course Description and Objectives: Neurophysiology is a lab-centered course which covers both practical and theoretical aspects of neurobiology from the cellular to the systems levels. The focus of this course is on basic electrophysiological methods and analysis, and how these support neurobiological theory.
Course Design and Content: The approach of this course is "learning by doing". As much as possible, techniques will be introduced in hands-on exercises. The core of this course is a unique interweaving of exercises adapted from three primary sources.
The first source is Crawdad, an NSF-sponsored effort at Cornell University to develop a set of laboratory exercises which clearly illustrate central aspects of neurobiology. As the name suggests, these laboratories focus primarily on a single well-studied animal preparation, the crayfish abdominal nerve cord. Through these exercises you can learn general microsurgical, microfabrication, and micromanipulation techniques, the colplexities of electrophysiological recording, and practical aspects of computer-based data processing and display. Mastering the most challenging of these exercises will require a good bit of patience and practice; common requirements for all worthwhile science.
The second source is the Do-it-Yourself Neuron (DIYN), a set of electronic hardware realizations of the equivalent circuit model, developed at Wesleyan, and designed to help you understand the electrical properties of nerve cells and the utility of electronic models. DIYN simulations are also a good way to practice and learn electronic recording and display methods without the additional complexities and frustrations of microsurgical preparation, electrode manufacture, signal acquisition, noise control, etc. inherent in recording from living tissue.
The third source is Neurons in Action 2 (NIA) by J.H.Moore & A.E. Stuart (Sinauer, c2008). This set of computer simulations are designed to clarify particular theoretical and practical aspects of neurophysiology. They are based on three fundamental models of neuronal and synaptic function - the :equivalent circuit (membranes), the Hodgin-Huxley equations (action potentials), and the alpha synapse (synapses). The degree to which you can understand, explain, and predict results from NIA will be a good indicator of how well you really understand basic neuroscience theory.
Wesleyan College Statement on Accessibility: Wesleyan College is committed to equal education, full participation and access to facilities for all students. Any student who requires reasonable academic accommodations, use of auxiliary aids or facility access for a class must first register with Disability Resources by contacting Jill Amos, lamos@wesleyancollege.edu or (478) 757-5219. If reasonable accommodations are established, students should request Accommodation Letters from Disability Resources then schedule an appointment to meet with the professor to determine how the accommodations will be implemented for each class as early in the semester as possible. Accommodations require advance notice to implement and will not be retroactively administered for the semester. Accommodations that decrease the integrity of a course will not be approved.
Wesleyan College Department of Biology Policy on the Honor Code: The Honor Code is the foundation upon which life in the Wesleyan College community is built. Academic violations of the Honor Code include, but are not limited to: cheating, plagiarism, unauthorized collaboration, inventing or falsifying information, turning in work for more than one class without authorization, or helping someone else violate the Honor Code. Students must self-report academic violations of the Honor Code to the faculty member teaching the class. If a student knows of an academic violation of the Honor Code by another student, she must report that violation to the faculty member if the student does not self-report.
In this class, cheating (giving or receiving any unauthorized information or supplying information from any source other than your memory) on any exam will result in a course semester grade of F. Plagiarism and/or improper citation on any assignment will be dealt with on a case by case basis, but also may result in an F grade for the assignment or the course. If a student is unclear about violation of the Honor Code for any assignment, she should contact the instructor before handing in the assignment. . All academic violations of the Honor Code will also be reported to the Provost, who may impose additional penalties for repeat offenders, including expulsion from school. Repeat offenders will be sent to Honor Council by the Provost, who may impose additional social penalties. For more information on how the Honor Code works, including the appeals process, refer to The Wesleyanne: Student Handbook
Students further agree that by taking this course all required papers may be subject to submission for textual similarity review to Turnitin.com for the detection of plagiarism. All submitted papers will be included as source documents in the Turnitin.com reference database solely for the purpose of detecting plagiarism of such papers. Use of the Turnitin.com service is subject to the Usage Policy posted on the Turnitin.com site
Attendance: You are expected to attend classes regularly. Any absence is potentially problematic, in that it compromises both your work and that of your laboratory partner(s). Excessive unexcused absences (more than 4) from class will be reported to the Dean in accordance with college policy and may result in a penalty of one full grade point.
Class Preparation and Participation: It is essential that you come to class each day having carefully read through the assigned text readings, including lab preparatory readings and manual guides. If at all possible, you should also at least step through each Neurons in Action simulation before the scheduled class period. "Lecture" sessions time will focus on "dry" laboratory exercises (electronic DIYN and computer NIA simulations), as well as directed discussions. The questions which you develop from your readings, the home simulations, and the laboratory exercises will form the basis for the bulk of these class discussions. The more preparation you bring into class, the more we will have to discuss. The weekly "lab" sessions will focus on the "wet" labs involving crayfish and other live animal preparations. 10% of your grade will be based on you holding up your end of the discussions and doing your part in your lab group.
Time Expenditure: There is a general expectation at Wesleyan that you will spend at least two-three hours working outside of class for every hour you spend in class. The course materials and course room are available to you precisely so that you can spend much of this time working directly with them to prepare for the exams and complete the worksheets.
Some lab exercises WILL require more time to complete than scheduled class period(s). The lab room will be accessible to you weekdays from 6AM to 10PM, whenever the single other class (BIO 211) is not meeting. You should count on spending at least one additional 2-3 hour session in the lab most weeks. It would be best to schedule this time with at least one laboratory partner. .
Neurons in Action 2 (NIA) will be installed on multiple computers in the lab. I will try to also facilitate installation on your personal computer, but I cannot guarantee success. We will run through each exercise in class, but you should count on rerunning each exercise in more detail and saving/printing the results your own time, outside of class/lab times.
Wesleyan College Statement on Civility in the Classroom: Students, faculty, and staff are expected to treat each other with respect in all interactions. Int the classroom, rude, disruptive, and/or disrespectful behaviors as determined by the faculty member interfere other students’ rights and with the instructor’s ability to teach. Therefore, anyone exhibiting unacceptable behaviors during the class will be asked to leave and will be counted absent for that class period. Failure to cooperate with this process will result in disciplinary action that may include withdrawal from the class or dismissal from the College. Violations will be reproted to the Provost.
Cell Phones: Please do your classmates the courtesy of turning off your cell phones during class and lab periods. If you must answer your cell phone, please leave the room to do so. If you leave the room, please do not come back. If you feel that you must monitor your cell phone during class or lab, please get permission from the instructor.
Wesleyan College Statement on Educational Privacy: In order to promote an environment in which ideas may be freely expressed, the interior office and classroom spaces at Wesleyan are private spaces. The unauthorized creation of photographic images, audio recordings, and/or video recordings of students or faculty in these spaces is considered to be disruptive behavior which may result in a student's removal from class according to the instructor’s discretion. The distribution of any such recordings of students or faculty without the express written permission of the College is strictly prohibited and is subject to disciplinary action by the Provost of the College.
All novel materials developed and presented in this course are the academic and intellectual property of the course instructor, course students, and/or Wesleyan College. Unauthorized photography, recording, electronic monitoring, and/or web dissemination of any portions of class or laboratory materials or sessions potentially violates the legitimate expectations of privacy of your classmates and the course instructor. Please obtain the explicit permission of the instructor before making any video or audio recordings in this course. Please do not, under any circumstances, post recordings or images from this class to electronic or social media.
Laboratory Data Sheets: You will turn in the results of the laboratory exercises and NIA simulations in the form of Data Sheets. Each sheet will corresponds to the "meat" of a full scale lab write-up, without any of the "trimmings". It will consist primarily of properly labeled and annotated graphs, tables, computer printouts, and calculation results based on the data which you have gathered during the experiment, along with answers to specific questions. Instructions for what to include in each data sheet will be provided with each laboratory guide.
The due date for each data sheet will be two weeks after the scheduled ending date for that exercise. Late work may have a deduction of up to a full grade point for each part of a week the assignment is late. You will be graded on a total of eight data sheets - four from exercises labeled "A" (biological preparations) in the course schedule, two from exercises labeled "B" (electronic hardware simulations) and two from exercises labeled “C” (NIA computer simulations). Each Data Sheet will be worth 5% of your final grade, for a total of 40%. All written work is due by 5:00PM on Thursday, May 7th.
Exams: There will be three written exams given in this course, as indicated in the schedule. Each exam will draw on materials from both the laboratory exercises and the class readings.
The verbal final exam will be a 20-minute verbal exam, scheduled for a personal time slot during the final two weeks of the course. The purpose of this exam is simply to allow me to assess how well you understand the theoretical and practical aspects of the laboratory exercises. This exam will count as 5% of your grade.
Grading: The semester grade will be computed on the following basis:
Classroom Discussion Participation 10% 90% + A Laboratory Data Sheets 40% 80% + B Midterm Exam I 10% 70% + C Midterm Exam II 15% 60% + D Class Final Exam 20% 59% - F Verbal Lab Final Exam 5% Total 100%
Course Schedule:
READING ASSIGNMENTS AND DISCUSSIONS Week Date Topic
Texts - B = Byrne & Roberts
M= Matthews
R = Reichert
1
Jan 13-17
Course Overview, Neurons
B1 [1-4;skim 7-13]
M I
R1
2
Jan 20-24 Bioelectric Circuits and Recording
B2 [19-23; skim 24-42;42-47]
R2 [18-26]
preview NIA simulation environment
3
Jan 27-31
Ion Channels, EPs, the RP
B6 [159-164] B5 [133-139; Box 5.1; Box 5.2]
R2 [26-30]
4
Feb 3-7
The Equivalent Circuit Model
B4 [111-113]
R2 [13-17]
5
Feb 10-14
Cable Properties
B4 [113-121]
M II 3
R2 [25-26]
6
Feb 17-21
MIDTERM EXAM I
Intro to Action Potentials
B5 [139-143; Box 5-3] 7
Feb 24-28
The Voltage Clamp Experiment
The Hodgkin-Huxley Model
R2 [17-25]
B7 [181-199]
8
March 2-6
Neural Activity Patterns
March 9-13 Spring Break
9
March 16-20
Action Potential Initiation and Propagation
On Beyond H-H
B5 [143, skim 147-154]
B6 [164-176]; B7 [208-211]
R2 [42-50]
10
March 23-27
Electrical Vs. Chemical Synapses
B15 [445-454; skim 454-462]
B8 [217-228; skim 228-242]
11
March 30
- April 3
Postsynaptic Summation and Integration
M III 5; R2 [43-53]
12
April 6-10 MIDTERM EXAM II
Neurotransmitters, Neuromodulators, Neurocytoarchitecture
Ch 9
B11 [321-343]; Ch 16 [469-482]
13
April 13-17 Neuroplasticity
B4 [121-128]; B17 [skim];
14
April 20-24 Sensory Coding and Processing
B8 [255-257]; B19
M III; R3
Article - Miller et al.
R4
15
April 27
- May 1Sensorimotor Coordination
M IV
R5
16
May 4-6
Catchup
Scheduled VERBAL LAB FINAL
May 7
May 8-12
Reading Day - all written work due
FINAL EXAM - Date and Time TBA
TENTATIVE LABORATORY SCHEDULE
CLASS/LAB EXERCISES AND DISCUSSIONS W
Date
Monday
Wednesday
Wednesday
LabFriday
1
Jan 13-17
Course Intro
Neurons
Lab 1 - Electrophys Instrumentation
Lab 2a - PowerLab Tutorial
2
Jan 20-24
MLK Holiday
Lab 2b - PowerLab Tutorial
Lab 3- Electric Fish [A]
Electric Circuits
3
Jan 27-31
Lab 5a - DIYN RC Circuits
Lab 5b - DIYN RC Circuits Lab 4 - Crayfish IIIs [A]
Membrane Potentials
& Currents
4
Feb 3-7
Estimates of the Resting Potential
Equivalent Circuit
- CompartmentLab 4 - Crayfish IIIs [A]
Lab 6a - NIA Resting Potentials [C]
5 Feb 10-14
Equivalent Circuit
- Distributed
Lab 6b - NIA passive Spread [C] Lab 7 - Crayfish Muscle RPs [A]
Lab 8a - DIYN Cable Properties [B]
6
Feb 17-21
Lab 8b - DIYN Cable Properites [B]
Review/Catchup Midterm I
Action Potentials
7 Feb 24-28
Lab 9a - DIYN AP Simulation [B]
Lab 9b - DIYN AP Simulation [B] Lab 7 - Crayfish Muscle RPs [A]
AP Mechanism
H-H Voltage Clamp
8
March 2-6
Lab 10a - NIA Voltage Clamp [C]
Lab 10b - NIA Voltage Clamp [C] Lab 12 - Snail Brain Recording [A]
Lab 11a - NIA Action Potentials [C]
March 9-13 Spring Break Spring Break Spring Break
Spring Break
9
March 16-20
Lab 11b - NIA Action Potentials [C]
On Beyond H-H Lab 12 - Snail Brain Recording [A]
Action Potential Propagation Mechanism
10
March 23-27
Lab 13a - NIA AP Propagation [C]
Lab 13b - NIA AP Propagation [C] Lab 16 - Crayfish NMJ [A]
Synapses - Chemical vs. Electrical
11
March 30
- April 3
Lab 14a - NIA PSPs [C]
Lab 15b - DIYN Elect Synapses [B] Lab 16/17 - Crayfish NMJ/Neuroplast [A]
Lab 15b - DIYN Elect Synapses [B]
12
April 6-10
Summation & Neuronal Integration
Review/Catchup Midterm II
Easter Break
13
April 13-17
Lab 14b - NIA PSP Integration [C]
Neuroplasticity Mechanisms Lab 17 - Crayfish Neuroplasticity [A]
Spike Train Analysis
14
April 20-24
Sensory Coding
Student Scholarship Day Student Scholarship Day
Sensory Processing
15
April 27
- May 1
Field Potentials
Sensorimotor Integration Lab 18 - Crayfish Stretch Receptor [A]
Review/Catchup
16 May 4-6
Review/Catchup
Review/Catchup Lab 19 - Fly ERG [A]
Finals Week May 7
May 8-12
Thursday Reading Day
Final Exam DATE and TIME TBD*
LAB WRITEUPS:
[A] - 4 of 8
[B] - 2 of 3
[C] - 2 of 5
*The lab portion of the FInal Exam is a 1 on 1 verbal final to be scheduled with the instructor during the final week of class. It will focus on laboratory instrumentation and methods.