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COURSE SYLLABUS - BIOL 404 - FA 2013
CELLULAR MECHANISMS IN VERTEBRATE PHYSIOLOGY

 

INSTRUCTOR: Richard Ordway (rwo4@psu.edu)

216 Life Sciences

Office hours:  Thursdays 10:30-12:30

 

 

I.  COURSE INTRODUCTION

01. Tu, AUG 27 - INTRODUCTION TO COURSE 

02. Th, AUG 29 - OVERVIEW OF SIGNALING IN CELLULAR PHYSIOLOGY

- STUDENT INTRODUCTIONS

 

II.  INTRODUCTION TO ELECTRICAL PROPERTIES OF EXCITABLE CELLS

03. Tu, SEP 03 - MEMBRANE POTENTIAL

04. Th, SEP 05 - INTRODUCTION TO ION CHANNELS

05. Tu, SEP 10 - THE ACTION POTENTIAL

06. Th, SEP 12 - PROPERTIES OF VOLTAGE-GATED ION CHANNELS

III. EXPERIMENTAL APPROACHES

07. Tu, SEP 17 - MOLECULAR METHODS IN CELLULAR PHYSIOLOGY

08. Th, SEP 19 - IMAGING METHODS IN CELLULAR PHYSIOLOGY

      Th, SEP 19 6:00 OPTIONAL REVIEW SESSION 

09. Tu, SEP 24 EXAM 1

 

IV.  VOLTAGE-GATED ION CHANNEL STRUCTURE-FUNCTION

10. Th, SEP 26 - MOLECULAR STRUCTURE OF VOLTAGE-GATED ION CHANNELS

11. Tu, OCT 01 - MOLECULAR MECHANISMS OF VOLTAGE-GATED ION CHANNEL

  FUNCTION 1: VOLTAGE-DEPENDENT GATING

12. Th, OCT 03 - MOLECULAR MECHANISMS OF VOLTAGE-GATED ION

CHANNEL FUNCTION 2: ION PERMEATION AND SELECTIVITY

13. Tu, OCT 08 - DISORDERS OF VOLTAGE-GATED ION CHANNELS 

14. Th, OCT 10 - STUDENT PRESENTATIONS

15. Tu, OCT 15 - STUDENT PRESENTATIONS

 

V. CHEMICAL SYNAPTIC TRANSMISSION

16. Th, OCT 17 - INTRODUCTION TO CHEMICAL SYNAPTIC TRANSMISSION

17. Tu, OCT 22 - SYNAPTIC VESICLE TRAFFICKING AND NEUROTRANSMITTER

  RELEASE

18. Th, OCT 24 - SYNAPTIC PLASTICITY

19. Tu, OCT 29 - NEUROLOGICAL DISORDERS OF SYNAPTIC FUNCTION

20. Th, OCT 31 - STUDENT PRESENTATIONS (no tricks)

21. Tu, NOV 05 - STUDENT PRESENTATIONS

      Tu, NOV 05 6:00 OPTIONAL REVIEW SESSION 

22. Th, NOV 07 EXAM 2

 

VI. NEURONAL INTEGRATION AND DOWNSTREAM EFFECTOR MECHANISMS

      IN A SIMPLE NEURAL CIRCUIT

23. Tu, NOV 12 - SYNAPTIC TRANSMISSION AND NEURONAL INTEGRATION IN

 THE CENTRAL NERVOUS SYSTEM.

24. Th, NOV 14 - INTRODUCTION TO SKELETAL MUSCLE

25. Tu, NOV 19 - MECHANISMS OF MUSCLE CONTRACTION

26. Th, NOV 21 - EXCITATION-CONTRACTION COUPLING

 

Tu, NOV 26 THANKSGIVING BREAK!


Th, NOV 28 THANKSGIVING BREAK!

 

27. Tu, DEC 03 - DISORDERS OF EXCITATION-CONTRACTION COUPLING

28. Th, DEC 05 - STUDENT PRESENTATIONS

29. Tu, DEC 10 - STUDENT PRESENTATIONS

30. Th, DEC 12 - Smartypants! Use What You’ve Learned to Understand Cardiac

   Pacemaker Mechanisms.

      Th, DEC 12 6:00 OPTIONAL REVIEW SESSION 

Finals week EXAM 3

 

 

REQUIREMENTS AND GRADING:

 

*There will three exams of equal weight, the last of which will be given during the final exam period.  The exams will have a mixed format of multiple choice and essay questions. Each exam is worth 24 % of the final grade for a total of 72 %.

 

*Students will complete one project worth 24% of the final grade.  This will involve part of an oral group presentation as well as an individual writing assignment focused on the same content. The project is intended to further develop critical thinking about primary research in molecular and cellular physiology as well as oral presentation and scientific writing skills.  Specific information and guidelines are provided at the end of this syllabus under “Student Project”.  Please be sure to review this material carefully.

*Participation in class discussions will be worth 4% of the final grade.

*Attendance is REQUIRED. 2% will be subtracted from the final grade for each unexcused absence.

*Optional review sessions will be held prior to each exam (see course schedule).

 

COLLEGE OF SCIENCE ACADEMIC INTEGRITY STATEMENT:

  Each student is responsible for completing his or her own work except when directed otherwise by the instructor.  Appropriate citations for work derived from the published literature must be included in papers.  Plagiarism from other students, published books, articles or web pages (excessive use, or use or quotation without citation to the source) is unethical and will not be tolerated.  Failure to comply will lead to sanctions against the student in accordance with the Policy on Academic Integrity (http://www.science.psu.edu/academic/Integrity/Policy.html).

 

TEXTBOOK:

Title: Cellular Physiology of Nerve and Muscle

Edition: Fourth Edition (2003)

Author: Gary G. Matthews

Publisher: Blackwell Publishing

ISBN: 1-40510-330-2

I will abbreviate “CPNM”.

 

 

SUPPLEMENTARY READING MATERIALS (2 books):

Molecular Biology of the Cell, 4th Edition (Silver Cover); Alberts, et. al (2002).

I will abbreviate “MBC”.  Two ways to use this book:

1) The hardcover book is available by request at the Life Sciences Library Reference Desk.

2) The contents of this book are also freely accessible on-line though the National Institutes of Health Bookshelf.  For required or recommended reading, specific links are provided to help you find the relevant content:

 

Principles of Neural Science, 4th Edition; Kandel, Schwartz, and Jessell (2000).

This book is available by request at the Life Sciences Library Reference Desk. There will be no required reading from this book.

 

READING ASSIGNMENTS:

Readings are listed as either Required or Recommended.  Recommended reading is entirely optional but may help to better understand the material. Students will not be responsible for material included only in the recommended reading. 

 

- SECTION I: COURSE INTRODUCTION

Required - none

Recommended -

You may wish to browse the following sections of MBC Chapter 15 Cell Communication

Introduction to Chapter 15 (http://www.ncbi.nlm.nih.gov/books/NBK21059/)

Ch. 15 General Principles (http://www.ncbi.nlm.nih.gov/books/NBK26813/)

Ch.15 Signaling Through G-Protein-Linked Cell Surface Receptors (http://www.ncbi.nlm.nih.gov/books/NBK26912/)

 

- SECTION II: INTRO. TO ELECTRICAL PROPERTIES OF EXCITABLE CELLS

Required - The following contents of CPNM:

Ch. 1

Ch. 2 pages 09-14 (through 1st paragraph)

Ch. 5 pages 47 (start at 3rd paragraph)-54

Ch. 6 pages 55-78 (through 2nd paragraph)

 

- SECTION III: EXPERIMENTAL APPROACHES

Required – The following contents of MBC Chapter 9 Visualizing Cells (using microscopy)

Introduction to Chapter 9 (http://www.ncbi.nlm.nih.gov/books/NBK21048/)

Ch. 9 Looking at Cells in the Microscope (http://www.ncbi.nlm.nih.gov/books/NBK26880/)

Ch. 9 Visualing Molecules in Living Cells (http://www.ncbi.nlm.nih.gov/books/NBK26893/)

 

Recommended - The following contents of MBC Chapter 8, Manip. Proteins, DNA and RNA:

Introduction to Chapter 8 (http://www.ncbi.nlm.nih.gov/books/NBK21058/)

Ch. 8 Fractionation of Cells (http://www.ncbi.nlm.nih.gov/books/NBK26936/)

Ch. 8 Isolating, Cloning and Sequencing DNA (http://www.ncbi.nlm.nih.gov/books/NBK26837/)

Ch. 8 Studying Gene Expression and Function (http://www.ncbi.nlm.nih.gov/books/NBK26818/)

 

- SECTION IV. VOLTAGE-GATED ION CHANNEL STRUCTURE-FUNCTION

No additional reading

 

- SECTION V: CHEMICAL SYNAPTIC TRANSMISSION

Required – CPNM Ch. 8 and Ch. 9 pages 130-144 (through 2nd paragraph)

 

Recommended – CPNM Ch. 9 pages 144-159

 

- SECTION VI. NEURONAL INTEGRATION AND DOWNSTREAM EFFECTOR
  MECHANISMS IN A SIMPLE NEURAL CIRCUIT

Required – Ch. 10 and Ch. 11 (see also Ch. 9 reading from Section V).

 

 

______________________________________________________________________________

 

 

STUDENTS WITH DISABILITIES: 

Penn State welcomes students with disabilities into the University's educational programs. If you have a disability-related need for reasonable academic adjustments in this course, contact the Office for Disability Services (ODS) at 814-863-1807 (V/TTY). For further information regarding ODS, please visit the Office for Disability Services Web site at http://equity.psu.edu/ods/.

 

In order to receive consideration for course accommodations, you must contact ODS and provide documentation (see the documentation guidelines at http://equity.psu.edu/ods/guidelines/documentation-guidelines). If the documentation supports the need for academic adjustments, ODS will provide a letter identifying appropriate academic adjustments. Please share this letter and discuss the adjustments with your instructor as early in the course as possible. You must contact ODS and request academic adjustment letters at the beginning of each semester.

 

 

BIOL 404 – FALL 2013
STUDENT PROJECT

 

SUMMARY

The student project will focus on a primary research article related to the topic covered in the corresponding section of the course.  This project includes a group assignment, for which each student will participate in one group oral presentation, as well as an individual assignment for which each student will independently provide a written description of the same content covered in his/her oral presentation. The research articles will be selected by the professor and assigned to students at random. An effort has been made to select research articles which build on the material covered in the corresponding section of the course by illustrating important concepts and experimental approaches in a way that is accessible to students. This will include a mix of older articles reporting key findings in the field as well as recent work. 

 

 

SPECIFIC REQUIREMENTS AND GRADING

As described below under PROJECT GUIDELINES, each Group Oral Presentation will address four aspects of the research article and each aspect will be presented by one of four students in the group.  Students will be graded on their individual performance in the oral presentation rather than the effectiveness of the entire group, although a well-organized and integrated group presentation will be highly appreciated.  The individual written assignment will be worth 70% of the project grade and each student’s portion of the group oral presentation will be worth the remaining 30%. This balance will encourage every group member to make a substantive contribution and will also provide students with valuable practical experience in writing about scientific research. Written assignments are due within 48 hours following the oral presentation.

 

 

PROJECT GUIDELINES

 

This project will address four aspects of each research article:

1) Background and Significance

2) Methodology

3) Results

4) Interpretation, Conclusions and Impact

 

Each group will focus on a single primary research article and one student will address each of the preceding four aspects [which aspect you present will be determined by your student number (i.e. the student with the lowest number will present (1) Background and Significance, the student with the next number will present (2) Experimental Approaches, etc…)].  Specific guidelines for each aspect of the project follow.

 

1) Background and Significance (Why was this work done?)

 

Review the context of the work.

- What is the importance of the problem?

- What is the relationship of the project to previous work?

- What contribution did the authors hope to make?

 

Specific requirements for (1) Background and Significance:

 

A) From the Introduction to the article, choose one citation (reference) to read through and mention in your presentation (you may want to have a quick look at 2 or 3 articles before choosing).

 

Note that most scientific publications fall into one of two categories: those reporting original research (primary Research Articles) and those summarizing previous work already published in a primary Research Article (Review Articles). In case you have trouble distinguishing these article types, note that the PubMed [National Center for Biotechnology Information (www.ncbi.nlm.nih.gov/pubmed)] entry for each Review Article carries the designation “Review” as shown in the example below.

 

The use of the patch clamp technique to study second messenger-mediated cellular events.

Neher E.

Neuroscience. 1988 Sep;26(3):727-34. Review. No abstract available. 

PMID: 2462183 [PubMed - indexed for MEDLINE] 

 

Although you may choose any citation from the Introduction to read and include in your presentation, a Review Article (if you can find one you like) may be more helpful in understanding the broader context of the study. If you have trouble obtaining an article on-line, let me know and I’ll try to help.  In some cases, the journal which publishes the Research Article also includes a very short summary of the study for a general audience (as part of a highlights or news section). In those cases, I will provide these summaries as separate pdfs.  You may find them helpful but they cannot be used to fulfill the requirement to discuss one citation from the Introduction to your Research Article. 

 

B) Plan to present at least three Powerpoint slides including a short outline (of your section of the presentation) and at least one visual slide (e.g. a drawing, diagram, cartoon, data figure, etc...).  Material for the visual slide(s) may be taken from the course textbooks, materials available on-line, short highlights or news summaries, other articles, etc… but should include something from the citation you chose as described in the preceding section (A). Be sure to cite the source material in your slide.

 

C) Prepare an individual writing assignment. This should include the same content covered in your presentation and should be 2-3 pages in length.  The writing of this assignment MUST be done independently by each student but the content may reflect insights gained in discussing your part of the presentation with others in your group. At the end of the written assignment, be sure to list citations including the assigned article and other sources (if any) you have drawn material from. Written assignments are due within 48 hours following the oral presentation.  

 

 

2) Methodology (How was the work done?)

 

Review the basic experimental approach.

- Why did they choose this experimental system and/or approach?

- Does it seem like a good choice? 

- Were proper control experiments performed?

 

Specific requirements for (2) Methodology:

 

A) From the description of Methods/Experimental Approaches in the article, plan to discuss the experimental system used (the preparation, organism, cell/tissue culture or in vitro system in which most experiments were carried out) as well as one specific method used.  Note that some primary research articles (especially newer ones) do not contain very much information about the methods used but rather refer the reader to on-line supplementary information (published by the journal for each article) and/or to citations of previous work.  To investigate the experimental system and one specific method, you will need to read some of this material and include it in your presentation.  You will also find useful information about Experimental Approaches in the course textbooks. Within your group, discuss to what extent the Methods you will present were used to generate the data to be discussed in the Results section [although it is not critical that they were, it is an interesting question and may lead to a productive exchange of ideas]. 

 

B) Plan to present at least three Powerpoint slides including a short outline (of your section of the presentation) and at least one visual slide (e.g. a drawing, diagram, cartoon, etc...).  Material for the visual slide(s) may be taken from the course textbooks, supplementary information for this research article, general materials available on-line, other research articles, etc... Be sure to cite the source material in your slide. 

 

C) Prepare an individual writing assignment. This should include the same content covered in your presentation and should be 2-3 pages in length.  The writing of this assignment MUST be done independently by each student but the content may reflect insights gained in discussing your part of the presentation with others in your group. At the end of the written assignment, be sure to list citations including the assigned article and other sources (if any) you have drawn material from. Written assignments are due within 48 hours following the oral presentation.  

 

 

3) Results (What did they find?)

 

Review the findings.

- What were the key observations of the study?

- How were the results presented?

 

Specific requirements for (3) Results:

 

A) From the description of results in the article, plan to discuss two key findings.  These may correspond to two whole data figures in the results section or two parts of figures (in some cases, multiple different experiments and findings are included in one figure). In selecting these findings, try to see what observations are most important to the conclusions of the study. Of course it may be difficult for you to understand the data in detail.  Do the best you can through discussion with members of your group and using other resources (course textbooks, on-line materials, previous studies, and your professor).  Within your group, discuss to what extent the data you will present were obtained using the Methods to be discussed in the Methodology section [although it is not critical that they (the data) were, it is an interesting question and may lead to a productive exchange of ideas]. 

 

B) Plan to present at least three Powerpoint slides including a short outline (of your section of the presentation) and at least two slides including original data from the research article. When presenting data, point out what was measured and the units of measure, identify the axes in graphs, emphasize important trends in the data (which may be important in later discussion of the study), if there are photographs of tissue samples, identify the structure and orientation of what is shown.  Always include scale bars and the units they represent.  

 

C) Prepare an individual writing assignment. This should include the same content covered in your presentation and should be 2-3 pages in length.  The writing of this assignment MUST be done independently by each student but the content may reflect insights gained in discussing your part of the presentation with others in your group. At the end of the written assignment, be sure to list citations including the assigned article and other sources (if any) you have drawn material from. Written assignments are due within 48 hours following the oral presentation.  

 

4) Interpretations, Conclusions and Impact (So what?)

 

Review the conclusions of the Research Article.

- Did the authors address the issues they raised in the Introduction?

- What has their work contributed?

- What would be a reasonable next step? 

- Are there broader implications of this study for human health, society, scientific research?

 - Report on your group’s discussion of the following points:

* Are the conclusions of the study strongly supported by the data?

* What is the quality of the presentation with respect to clarity of the writing as well

   as the logical arrangement and labeling of the data figures?

 

Specific requirements for (4) Discussion:

 

A) From the conclusions presented in the article Discussion, plan to address three key points.  These may include direct interpretations of the data, larger conclusions of the study, discussion of technical limitations, discussion of alternative conclusions and why they were not favored, etc…  Note that for some articles, additional figures including models developed from the reported results may be found in on-line supplementary information published by the journal for each article.  Finally, plan to include material from one additional source (any source) related to the implications of this study.  This material may be related to human health, society, future scientific research, etc…

 

B) Plan to present at least three Powerpoint slides including a short outline (of your section of the presentation) and at least one visual slide (e.g. a drawing, diagram, cartoon, etc...).  Material for the visual slide(s) may be taken from the course textbooks, supplementary information for this research article, general materials available on-line, etc... Be sure to cite the source material in your slide.  Following the presentation of your own slides, you will lead your group in a classroom discussion of your impressions with regard to the merits of this Research Article. 

 

C) Prepare an individual writing assignment. This should include the same content covered in your presentation and should be 2-3 pages in length.  The writing of this assignment MUST be done independently by each student but the content may reflect insights gained in discussing your part of the presentation with others in your group. At the end of the written assignment, be sure to list citations including the assigned article and other sources (if any) you have drawn material from. Written assignments are due within 48 hours following the oral presentation.