Welcome to Bioc 415


Course activities


On-line resources

Introductory lab manual (Bioc 211)
Bioc 311 resources

Bioc 415 manual (pdf)

Bioc 415 appendixes (pdf)

NOTE: Web pages are undergoing extensive editing - pages beyond this syllabus are outdated.

Instructor and office hours

Instructor:  David R. Caprette, Ph.D.
Teaching Professor, BioSciences
Office and contact information:  ABL 327, caprette@rice.edu, x3498
Hours variable (see HERE for a current schedule)

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. Each study begins with a student-led discussion of principles/concepts, questions to be asked and to be addressed experimentally, available methodology, ides for analyzing data, and experimental strategies. We will follow each study with discussion of the data collected by the teams, possible conclusions and/or changes to our plans for data analysis, and what information we might draw from 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:

  • Apply the strategies for learning difficult concepts that you have acquired from your prior course work and/or other experiences toward an understanding of the concepts behind membrane resting potentials, generation and propagation of nerve action potentials, and the electrical and mechanical properties of muscle
  • Be prepared to lead a class discussion of any of the concepts, including specific questions that have been posed to the class
  • Be prepared at any time for a quiz to assess your preparation for class and/or ability to apply concepts and principles that we have discussed in a prior class
  • Take a goal-oriented approach to the laboratory work by developing hypotheses and experimental protocols with which to test them
  • Collect, record, share, and analyze data using the best practices that you have acquired in previous lab courses and/or independent study
  • Apply best practices for writing text and preparing figures in order to present your findings in publishable form (Results)
  • Write up interpretations that address the questions that we explored through experimentation and explain the findings in terms of physical/molecular mechanisms (Discussions)
  • Adhere to the spirit, not just the letter, of the honor code

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, experimental protocols, laboratory work, 40%

All items count equally toward the average score for this part. Expect about four quizzes total, some to be unannounced. Criteria for scoring experimental protocols will include: all elements included; well stated objective (testable hypothesis or question); clear and accurate description of how the plan will accomplish the objective; plans for data analysis and for collecting data should accomplish the objective. The quality of laboratory work will be assessed in part by the quality of data collected. Were you able to complete the work? Do the data collected reflect a complete and accurate understanding of the background concepts and goals of the study? Will you and members of other teams be able to use your data to address the study's objectives?

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

Each of the two Results sections and two Discussion sections will count toward 15% of the final grade.

Criteria for grading results and discussions will be similar to criteria employed in Bioc 211 and 311. Papers are to 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, and makeup labs are not possible. Some class meetings will begin with an unannounced quiz with a time limit. Missed quizzes cannot be made up. The class and instructor will decide on the due date for the second research paper. Once the due date is set 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 converation 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.

Meeting schedule

The table immediately below this paragraph is an abbreviated schedule. Please see the Detailed Schedule (next section below) for an itemized list of reading assignments and activities, including assignments and documents to consult as you prepare for class. Note that there will be a quiz on the first day. Remaining quizzes will be unannounced. All classes will begin at 1 pm unless otherwise noted.

Day/date/time/place Topic
Mon Aug 21, 1 PM, ABL 329 then on to ABL 1xx Course introduction, quiz, student-led discussions of background material, software tutorial
Weds Aug 23, 1 PM, ABL 329 then on to ABL 1xx First membrane potential lab
Mon Aug 28, 1 PM, ABL 329 then on to ABL 1xx Second membrane potential lab
Weds Aug 30, 1 PM, ABL 329 Followup on membrane labs
Monday Sep 4, LABOR DAY HOLIDAY
Weds Sep 6, 1 PM, ABL 329 then on to ABL 1xx Introduction to nerve recording and software tutorial (Scope)
Mon Sep 11, 1 PM, ABL 1xx Nerve lab 1
Weds Sep 13, 1 PM, ABL 329 then on to ABL 1xx Nerve lab 2 
Monday Sep 18, 1 PM, ABL 329 Follow up nerve labs
Weds Sep 20, 1 PM, ABL 329 then on to ABL 1xx Introduction to nerve/muscle studies
Mon Sep 25, 1 PM, ABL 1xx Muscle lab 1
Weds Sep 27, 1 PM, ABL 329 then on to ABL 1xx Muscle lab 2
Mon Oct 2, 1 PM, ABL 329 Follow up muscle labs

Detailed schedule for fall 2017

In the Files section you will find guides to preparing for class, a laboratory manual, a set of Appendixes, materials on basic electricity, PowerPoint notes pages on selected topics, and a list of questions to be addressed in class. I will also post class data sets as you generate the data in lab. All data are the property of the entire class and should be used, selectively, for your final papers. Each assignment is to be uploaded to Canvas by the date & time due.

Day/time/place/topics Activities

Day 1

Monday Aug 21, 1 PM

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

ABL 329 (discussions)

ABL 1xx (learn the software)

 

Preparation (in advance of the first class meeting)?

  • Review the materials described in the document Day1prep.pdf, posted in Files and be prepared for a 20 question closed notes quiz

Introduction and quiz (ABL 329)

  • Introductions - names, majors, why you are taking the course
  • Decide on team assignments
  • Quiz on preparation for day 1
  • Review quiz answers
  • Course introduction including lab studies, assignments, grading

Student-led discussion

  • Discuss equilibrium potentials (Equilibrium_potential.pdf)
  • Discuss the electrogenic property of the sodium pump (Discovering.pdf)
  • Discuss the use of microelectrodes for measuring membrane potentials (Microelectrodes.pdf)
  • Plan the laboratory work to study the electrogenic contribution of the sodium pump in crayfish extensor muscle

Guided discussions

  • A/D recording, data to be recorded, transducers, calibrating and using an IC probe
  • Preparing an experimental protocol

Learn the data acquisition software (ABL 1xx)

  • Self-paced tutorial on using the AD Instruments Chart software
  • Learn to calibrate an IC probe and measure electrode tip resistance

Day 2

Wednesday Aug 23, 1:00 PM

First membrane potential lab

ABL 329 (discussion)

ABL 1xx (lab work)

Preparation

  • Review the documents Learning_physiology and Em_study_prep (prep guides folder in Resources) and prepare for Day 2 as suggested

Student-led discussion (ABL 329)

  • Briefly discuss the questions posed for today, starting promptly at 1:00 pm; identify any concepts needing clarification

Laboratory (ABL 1xx)

  • Demonstration of crayfish dissection, measuring a membrane potential
  • Precautions when using microelectrodes and holders
  • Troubleshooting suggestions
  • Students: measure control Em values and short term effect of ouabain on Em

Followup

  • Email today's results (raw data) to the instructor by the end of the day

Day 3

Monday Aug 28, 1 PM

Second membrane potential lab

ABL 329 (discussion)

ABL 1xx (lab work)

Preparation

  • Again review the document Em_study_prep in the prep guides folder in Resources and prepare for class as advised in the Day 3 section

Student-led discussions (ABL 329)

  • Address today's questions – conclusion from the ouabain study, conducting today's experiments

Laboratory (ABL 1xx)

  • Dissect crayfish, measure Em in variable K+ and Na+ solutions

Followup

  • Compile your data and send to the instructor by the end of the day

Day 4

Wednesday Aug 30, 1 PM

Discuss findings from the membrane labs and their interpretation

ABL 329

Preparation

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

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 – for suggestions please see the document Writing_papers in the prep guides folder.

Monday Sep 4
LABOR DAY HOLIDAY

Day 5

Wednesday Sep 6, 1 PM

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

ABL 329 (discussion)

ABL 1xx (learn the software)

Preparation

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

Student-led discussions (ABL 329)

  • Initiation and propagation of action potentials
  • Differences between a compound action potential and a single action potential
  • Introduce the recruitment study; what will you be doing and why?
  • Introduce the strength-duration experiment and its rationale

Guided discussion

  • Why was it necessary to abandon the equilibrium potential model?
  • Recording a compound action potential

Learn the data acquisition software (ABL 1xx)

  • Complete the self paced tutorial on using the Scope software

Day 6

Monday Sep 11, 1 PM

Nerve lab 1

ABL 1xx

Preparation

Upload complete results section from the membrane studies into your Drop Box before the start of class

  • Prepare for class as recommended in the document Nerve_lab_prep, guidelines for 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 13, 1 PM

Nerve lab 2

ABL 329 (discussion)

ABL 1xx (lab work)

Preparation

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

Student-led discussions (ABL 329)

  • 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 (ABL 1xx)

  • 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 18, 1 PM

Follow up the nerve labs

ABL 329

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 20, 1 PM

ABL 329 (discussion)

ABL 1xx (calibration)

 

Preparation

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

Student-led discussion (ABL 329)

  • 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 (ABL 1xx)

  • Calibrate force transducers and set up Units Conversion (volts to grams) for the nerve/muscle lab; an instruction sheet will be provided so that you can proceed on your own

Day 10

Monday Sep 25, 1 PM

Muscle lab 1

ABL 1xx

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 27, 1 PM

ABL 329 (discussion)

ABL 1xx (lab work)

Preparation

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

Student-led discussion (ABL 329)

  • Principles of length-tension relationships

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 2, ABL 329

Follow up muscle labs

Preparation

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

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

Created by David R. Caprette (caprette@rice.edu), Rice University 30 May 1997
Updated 3 May 2017
Copyright and Intended Use