BIOC 415: EXPERIMENTAL PHYSIOLOGY, FALL 2018

This course requires a significant amount of pre-class preparation and there will be a quiz on the first day. If you plan to take the course in fall 2018 then you will need access to resources in Canvas. If you plan to take the course and have not yet enrolled, then please contact the instructor (caprette@rice.edu), provide your netID, and ask to be added to the course site in Canvas.

Course Learning Goals and Intended Learning Outcomes

“A good physiological experiment like a good physical one requires that it should present anywhere, at any time, under identical conditions, the same certain and unequivocal phenomena that can always be confirmed.”

(Johannes Peter Müller, 1801-1858)

Overall learning goals

Specific goals and outcomes

Goal: Learn the mechanisms that underlie the functions of excitable cells

Learning outcomes

Goal: Learn to test explanations of physiological phenomena by posing hypotheses and developing strategies for testing them

Learning outcomes

Goal: Learn to collect meaningful data and to distinguish useful from flawed or insufficient data

Learning outcomes

Goal:  Learn to contribute effectively to both narrow and broader goals as part of a team effort

Learning outcomes

Goal: Apply and advance previously acquired skills for analyzing and interpreting data and reporting findings and interpretation

Learning outcomes

Course Details

Details are subject to change at the instructor's discretion.

Instructor and office hours

Instructor:  David R. Caprette, Ph.D.
Teaching Professor, BioSciences
Office and contact information:  ABL 327, caprette@rice.edu, x3498
See HERE for a schedule of office hours

Brief description

In BIOC 415 (Experimental Physiology), teams of students explore the properties of excitable cells and the mechanisms behind those properties. Experimental studies focus on the origin of membrane potentials, generation/propagation of action potentials and properties of nerves, and mechanisms for controlling muscle contractile strength. For each study we will discuss theoretical principles, methodology, questions to address experimentally, ideas for analyzing data, and experimental strategies. We will follow the laboratory work with discussions of data collected by the teams and how we might interpret the data.

Expectations

NOTE: This course begins with a significant amount of pre-class preparation and a quiz on the first day. To help you prepare, please read the file "Day1prep.pdf" in the prep guides folder in Files.

BIOC 415 is a "capstone" laboratory course, meaning that students are expected to apply previously learned skills to new studies. As a student in BIOC 415 you are expected to:

Course grade

Each assignment will receive a score on a percent scale, to be recorded in the Gradebook. After weighting and averaging all scores I will assign letter grades as described in the table below.

A+, ≥ 97
A, 93-97
A-, 90-93

B+, 87-90
B, 83-87
B-, 80-83

C+, 77-80
C, 73-77
C-, 70-73

D+, 67-70
D, 63-67
D-, 60-63
F, ≤ 60

Assignments will contribute to the final course grade in the following proportions. See the detailed meeting schedule for assignments and due dates.

Quizzes, 20%

The in-class quiz on the first day is designed to assess your preparation for the course, outlined in the Day 1 prep guide. Remaining quizzes will assess your preparedness for discussions and lab work and your grasp of the concepts and experimental rationale from previous discussions and lab work. All in-class quizzes and the material they cover will be announced. Al quizzes, including the on-line tutorials and HW assignments, will count equally toward your average quiz score.

Protocols, data & critiques, and participation, 20%

Criteria for scoring experimental protocols will include: completeness; well stated objective (testable hypothesis or question); plans for data analysis; plan for collecting data and complete rationale (how the plan will help accomplish the objective). The quality of laboratory work will be assessed in part by the quality of data collected. Do the data collected and your assessment of the value of your teams data reflect a complete and accurate understanding of the background concepts and goals of the study? The participation component includes your participation in class discussions (included in the score for the relevant protocol).

Two research papers (results and discussion only), 60%

The score on each Results section and each Discussion will comprise 15% of the final grade.

Criteria for grading results and discussions are similar to criteria employed in Bioc 211 and 311. Papers are to be prepared as text documents (e.g., Microsoft Word), properly formatted, saved as PDFs, and uploaded into Canvas. To permit anonymous grading, please use only your student ID (S0.....) to identify yourself - do not put your name anywhere on the paper. If it is no trouble, it would be best to include your student ID in the header so that it shows up on all pages.

Attendance and due date policies

On time attendance is required, makeup labs are not possible, and missed quizzes cannot be made up. See the detailed schedule for due dates for all assignments, including the research papers, and the usual late policy applies. The grade for any late assignment will be reduced by 10% for each day or part of day past the original due date and time. For example, if the paper is due at 1 pm in class and is uploaded that evening, the grade will be reduced by 10%. If it is uploaded after 1 pm the following day the deduction will be 20%. Saturdays, Sundays, and holidays count. Please notify the instructor promptly if you encounter any issues attempting to upload your paper.

Honor code policy

The Rice honor code applies to all assignments in this course. Students will work together to plan and conduct experiments and to compile raw data. In class we will discuss how to analyze the data and interpret the findings, and you are free to continue such discussions outside of class. You may want to share ideas on how to convert raw data to a presentable form, what statistics or visual elements (e.g., graphs) to employ, what the findings mean, mechanisms that explain the findings, etc. You may share ideas in conversation only – no form of written collaboration is permitted.  Aside from sharing your ideas, the final work must be your own work, in entirety. There is to be no co-writing of experimental designs or papers, paraphrasing of other students' work, or sharing of figures or tables. Students are not to allow access by other students to any of their work whether it is in preparation or in final form.

Students with disabilities

Any student with a documented disability needing adjustments or accommodations is requested to speak with Dr. Caprette during the first two weeks of class. All discussions will remain confidential. Such students should also contact Disability Support Services in the Ley Student Center.

Resources

In addition to the tutorials posted in Quizzes. you will find the following resources in Files.

All data are the property of the entire class and should be used, selectively, for your final papers.

Detailed schedule for fall 2018

Day/time/place/topics Activities

Day 1

Monday Aug 20

Course introduction, prepare for studies on the origin of the membrane potential

 

Preparation (in advance of the first class meeting)‚Äč

  • Review the materials described under "Preparing for the first class meeting" in the document Day1prep.pdf, posted in Files (in folder Prep guides); be prepared for a 20 question closed notes quiz

Day 1 activities

  • Introductions and quiz
  • Discussions, as outlined in the Day 1 prep guide
  • Self paced tutorial on using the data acquisition software, calibrating an intracellular probe

Day 2

Wednesday Aug 22

First membrane potential lab

Preparation

  • Review the introduction and the materials described under "Day 2 – First membrane potential lab" in the document Em_study_prep.pdf, posted in Files (in folder Prep guides)

Day 2 activities

  • Briefly discuss the questions posed for today, starting promptly at 1:00 pm; identify any concepts needing clarification
  • Instructor will demonstrate a crayfish dissection and how to measure a membrane potential, and discuss p recautions when using microelectrodes and holders along with suggestions for troubleshooting the preparation
  • Conduct the experiment to measure the Em of crayfish extensor muscles and to study the short term effect of ouabain on Em

Followup

  • Email today's results (raw data) to the instructor by the end of the day
  • Provide a critique of your team's data before the next class (assignment: Em data pt. 1)

Day 3

Monday Aug 27

Second membrane potential lab

Preparation

  • Review the document Em_study_prep in the prep guides folder in Files and prepare for class as advised in the Day 3 section

Day 3 activities

  • We will begin with a quiz to assess your preparation for today and to follow up the first Em lab
  • Discuss the questions for today including conclusions from the ouabain study
  • Discuss plans for today's experiments
  • Dissect crayfish, conduct experiments to measure Em in variable K+ and Na+ solutions

Followup

  • Compile your data and send to the instructor by the end of the day
  • Provide a critique of your team's data before the next class (assignment: Em data pt. 2)

Day 4

Wednesday Aug 29

Discuss findings from the membrane labs and their interpretation

Preparation

  • Review the relevant parts of Em_study_prep with emphasis on Day 4 and be prepared for the discussions

Student-led discussion

  • Share ideas for analyzing, presenting, and interpreting the data from the experiments with membrane potentials
  • Discuss the questions posed for today

Your first results section will be due in one week, at the start of class

Monday Sep 3, LABOR DAY HOLIDAY

Day 5

Wednesday Sep 5

Learning to use the Scope software; introduction to the nerve studies

Preparation

Upload your results section from the membrane studies into Canvas before the start of clas

  • For a good start toward learning properties of vertebrate nerves, prepare for class as recommended in the document Nerve_lab_prep, Day 5

Discussions

  • We will go over HW1&2 and initiation and propagation of action potentials, differences between a compound action potential and a single action potential, rationale behind the recruitment and the strength-duration studies

Laboratory

  • Complete the self paced tutorial on using the Scope software

Day 6

Monday Sep 10

Nerve Lab 1

 

Preparation

  • Prepare for class as recommended in the document Nerve_lab_prep, Day 6

Laboratory

  • Instructor demonstration: dissection, chamber preparation, recording a CAP
  • Prepare nerve, collect recruitment and S-D data
  • Time permitting, explore nerve properties, including velocity, refractory period, start planning data collection for next time

Followup

  • Send raw data to the instructor within 24 hours

Day 7

Wednesday Sep 12

Nerve lab 2

Preparation

  • Prepare for class as recommended in the document Nerve_lab_prep, guidelines for Day 7

Student-led discussions

  • Share your plans for analyzing the recruitment and strength-duration data
  • Discuss the function of a myelin sheath, saltatory conduction, and why some axons conduct faster than others
  • Discuss the rationale behind absolute and relative refractory periods
  • Share plans for the studies on conduction velocity and estimating a refractory period

Laboratory

  • Estimate conduction velocities using alternative methods
  • Conduct two series of refractory period experiments, one with threshold stimulus, one with suprathreshold stimulus
  • Explore changes in properties of the compound action potential with the nerve partly blocked with lildocaine

Followup

  • Send raw data to the instructor within 24 hours
  • Prepare a preliminary analysis of all of the nerve study data

Day 8

Monday Sep 17

Follow up the nerve labs

Preparation

  • Prepare for class as recommended in the document Nerve_lab_prep, guidelines for Day 8

Student-led discussion

  • Share your findings, explanations, mechanisms, and significance, one experiment at a time
  • Share your ideas for the best ways of presenting the findings in text and as figures

Your discussion of the membrane lab findings will be due in one week

Day 9

Wednesday Sep 19


 

Preparation

  • Prepare for class as recommended in the document Muscle_lab_prep, guidelines for Day 9

Student-led discussion

  • Discuss motor units and the relationship between tension and compound action potential
  • Review excitation/contraction coupling in muscle
  • Discuss the role of calcium in mediating frequency dependent changes in contraction strength
  • Plan the studies on recruitment and effects of frequency

Calibration

  • Calibrate force transducers and set up Units Conversion (volts to grams) for the nerve/muscle lab as explained on the instruction sheet

Day 10

Monday Sep 24

Muscle lab 1

Remember to upload your membrane lab discussion before the start of class

Preparation

  • Prepare for class as recommended in the document Muscle_lab_prep, guidelines for Day 10

Laboratory

  • Instructor demonstration: nerve/muscle preparation; recording data in "windows"
  • Prepare nerve & muscle for recording data
  • Collect data for Treppe, recruitment of motor units, frequency-dependent contractile force (tetanus)

Followup

  • Send raw data to the instructor within 24 hours

Day 11

Wednesday Sep 26

Muscle lab 2

Preparation

  • Prepare for class as recommended in the document Muscle_lab_prep, guidelines for Day 11

Laboratory

  • Prepare nerve/muscle for recording data
  • Collect data on isotonic, isometric length-tension relationships and design experiment on fatigue

Followup

  • Send raw data to the instructor within 24 hours

Day 12

Monday Oct 1

Follow up muscle labs

Preparation

  • Prepare for class as recommended in the document Muscle_lab_prep, guidelines for Day 12

Student-led discussion

  • Discuss ideas for analyzing and interpreting the recruitment and frequency data
  • Discuss how to analyze and interpret the length-tension data
  • [with instructor] Set separate due dates for the second and last results and discussion sections; write up either the nerve studies or the nerve-muscle studies – each individual chooses

Last updated 3 Aug 2018