NSC 230: Experimental Methods in Neuroscience, Fall 2004


Instructor:  Adam Hall: x3467, Sabin Reed 337, ahall@science.smith.edu
Office Hours: Tu 9-10A, F 4-5P, or by appointment.
Teaching Assistants: Wing Yee-Yeung ( wyeung@smith.edu ) and Jeanne McKeon (jmckeon@smith.edu)

Overview:

The goal of this course is to acquaint you with tools you will use to conduct certain types of neuroscience research. You will learn to assess journal articles describing research conducted by other scientists, design and conduct your own experiments, analyze the results both graphically and statistically, and present your findings via written papers and PowerPoint presentations. You will be busy! The good news is that you have two experienced TAs, dedicated to getting you up to speed on all these skills. This is a required course for the Neuroscience major.

The following syllabus is detailed; below there is an overview of the entire course. The precise timing of this schedule may change depending on how our experiments progress.

a. Introduction. (Week 1-2)

Intro to Philosophy of Science. Ethics of Animal Use,

b. Measurement of Behavior (Weeks 2-4)

Techniques to quantify mouse behavior; comparing different mouse strains.

Scales of Measurement, Descriptive statistics, Measures of Inter-rater reliability

Graphic presentation of data, Writing Methods and Results sections

c. Two Groups, Between subjects design (Weeks 5–6)

Compare 2 strains of mice in several behavioral assays

Inferential statistics for 2 group designs: t-tests.

Writing Introduction/Reference Lists/Discussion. Library Orientation.

d. Scientific Presentation (Week 7-8)

Scientific Writing and powerpoint presentation. Fraud in science.

e. Histology (Week 9)

Humane treatment of animals. Anesthesia/analgesia

Cutting frozen sections, Nissl staining.

Compare size of brain areas in mice strains

f. Inferential Statistics-ANOVAs and factorial design (Weeks 10)

g. Neurochemistry (Weeks 11)

Enzyme assays on brain homogenates.

Studying inhibition of acetylcholinesterase by Tacrine HCl.

h. Independent Research Projects - Factorial design (Weeks 12-14)

Finding previously published research on a selected topic

Designing and conducting an experiment

Analyzing the results: Analysis of Variance, Post-hoc tests

Final paper and poster presentation

Syllabus:

Week 1 – Sept 8

Wed: Introduction to syllabus. Complete Health forms.

Week 2 – Sept 13, 15

Ethics of Animal Use. Philosophy of Science.

Mon: Discuss Philosophy of Science readings. 2.45-3.30pm Orientation to animal quarters, Dr. Joanne Huyler, Director of the Smith Animal Care Facility.

Wed : Discuss ethical issues related to animal use.

Readings:

• In course reader: Chapter 14 “Very abstract questions: The philosophy of science” in What Science is and how it works, by GN Derry, 1999.
• In course reader: Read pages 233-266 from “Ethical Issues in Scientific Research: An Anthology” (and on reserve). Come to class prepared to summarize the main points of the essays and give your opinion.
• In “Design of Experiments in Neuroscience” Chapter 1 and Chapter 2, p24-34.
• In course reader: Seeking alternatives, from “Animal Experimentation: A guide to the issues” V. Manamy.

Week 3 – Sept 20, 22

Techniques to quantify mouse behavior; comparing different mouse strains.

Scales of Measurement. Inter-rater reliability.

Mon: Scoring behavior of a mouse in an open field. Inter-rater reliability. Present protocol for open field test. Discuss readings. Conduct open field test.

Wed : Conduct open field test (cont.) Continue to discuss readings. Analyze data from open field tests.

Readings:

• In course reader: Ch 4 Crawley “What’s wrong with my mouse?”
• In course reader: Ch 5 “Laboratory Notebooks” from At the Bench: A Laboratory Navigator, by K. Barker, 1998.
• In “Design of Experiments in Neuroscience” Chapter 3.

Week 4 – Sep 27, 29

Descriptive statistics, exploratory data analysis. Graphic Presentation of data

Correlations. Writing Methods and Results sections of experimental reports

Mon: Descriptive stats and graphics. Writing Methods/Results.

3.00pm Dr. Betty McGuire, guest lecture discussing methods for conducting studies in the field. Rotarod tests – discuss protocol, demonstrate. Begin rotarod testing.

Wed:Complete rotarod testing. Discuss correlations in context of rotarod to open field measures. Elevated plus maze – discuss protocol.

Readings:

• In “Design of Experiments in Neuroscience” Appendix A pp120-125
• In “Design of Experiments in Neuroscience” Chapter 7.
• In “Design of Experiments in Neuroscience” Appendix B.
• Handout: article to critique in-class (Darwish et al., 2001)
• In course reader: Ch 10 Crawley “What’s wrong with my mouse?” (Section on elevated maze).

Due : Open field/rotarod report (Methods and Results only) : Fri Oct 1, 5.00pm.

Week 5 – Oct 4, Oct 6

Techniques to quantify mouse behavior; comparing different mouse strains.

Graphic Presentation of data.

Writing Introduction and Reference List sections of experimental reports

Mon: Elevated plus maze testing. Further discuss descriptive stats and graphics. Discuss article critique, Darwish et al., 2001.

Wed: Discuss writing an introduction/reference list using published articles.Draft elevated plus maze reports. 2-3pm Young Science Library orientation, Rocco Piccinino.

Due : Elevated plus report draft (Intro, Methods, Results only): 5pm Fri Oct 8th.

Week 6 - Autumn recess:Oct 11, Oct 13

Learning and memory behavioral research techniques

Wed: Discuss draft reports, discuss ‘What is an Experiment? and Controlling variables. Introduce inferential stats. Barnes maze protocol and demonstration.

Readings:

• In “Design of Experiments in Neuroscience” Chapter 4 and 5
• In “Design of Experiments in Neuroscience” Appendix A pp125-128.
• Handout: First assessed article critique (Lund and Lephart, 1998)

Elevated plus maze final report (Intro, Methods and Results only) due: Oct 15.

Week 7–Oct 18, Class Oct 20

Writing a Discussion. Ethical issues in scientific research: fraud and deception.

Due : First article critique – due Oct 20

Mon class: Discuss elevated maze reports. Writing Discussion section.

Wed class : Discuss readings relating to fraud in science. Second article.

Readings:

• In course reader: Pages 65-109 in “Ethical Issues in Scientific Research”
• In “Design of Experiments in Neuroscience” Chapter 2, p21-24.
• Handout: Second assessed article critique (McClay, 1998)

Week 8 – Oct 25, 27

AH away at Soc. Neurosci meeting, San Diego CA.

Scientific presentations.

Mon class : Presentation on the Smith College microscopy facility by Judith Wopereis.

Wed class : Effective Use of Powerpoint in scientific presentations. Design presentation in PowerPoint of chosen articles.

Readings:

• Hand-out: A paper relevant to behavioral lab work (binder provided of papers to choose from, or find your own).
• In course reader: Ch 16 “The Light Microscope” from At the Bench: A Laboratory Navigator, by K. Barker, 1998. (up to p. 417)

Week 9 – Nov 1, 3

Histology.

Mon : Presentations of chosen articles. Highlights of SFN conference. Humane treatment of animals. Discuss readings. Techniques for image analysis and quantification.

Due : Second article critique –in class Nov 1.

Wed: Cut brain sections. Mount sections on slides. Anesthesia and analgesia. Discuss readings. Compare size of brain areas in mice strains.

Readings:

• In course reader: “Mouse and rat anesthesia and analgesia” from Current Protocols in Neuroscience, 2001.

Week 10 – Nov 8, 10

Histology (continued). Inferential Statistics. Factorial design and ANOVAs.

Mon : Coating slides, staining and visualizing with the light microscope. ANOVAs.

Wed: Factorial design.

Due: Histology lab write-up, 5.00pm Fri Nov 5 th.

Readings

• Handout: Third assessed article critique (Chapillon and Debouzie, 2000)
• In “Design of Experiments in Neuroscience” Chapter 6 and Appendix A, pp 128-130.

Week 11 – Nov 15, 17

An Introduction to Neurochemistry.

Mon class: Assay acetylcholinesterase activity in different mouse brain strains/regions.

Due : Third article critique –Nov 15 at beginning of class.

Wed class: Effect of Tacrine HCl on enzyme activity. Calculating the rate of the enzyme reaction. Graphing data and writing reports.

Week 12 – Nov 22,Thanksgiving Recess: Nov 24

Experimental design.

Mon: Design your experiments in light of previous research. Behavioral experiments must be a 2 x 2 factorial design.

Due:Neurochemistry lab write-up, in class

Due: end of class : 1 page summary of your experimental design, analysis and relevant references.

Week 13 – Nov 29, Dec 1

Independent Research Projects.

Mon: Performing your experiment.

Wed: Performing your experiment.

Week 13 – Dec 6, 8

Independent Research Projects. Final Review session

Mon: Conducting an experiment

Wed: Analyzing the results. Review session.

Due Dec. 8: First draft of final paper.

Readings

• In “Design of Experiments in Neuroscience” Chapter 8 and Appendix D.

Week 14 – Dec 13

Prepare PPT presentation.

Mon class: Powerpoint presentations in class.

Final independent project report, due Tues Dec14 by 5.00pm:

Assignments:

25% of your grade: critical reading of original articles, and short answer questions

Article Critique 1: 5%

Article Critique 2: 5%

Article Critique 3: 5%

Final exam: 10% (consists of one article critique and 10 short answer questions on any topic covered throughout the semester)

60% of your grade: writing scientific articles, designing and interpreting an experiment

Experimental Report 1 (Open Field/Rotarod): 5%

Experimental Report 2 (Elevated maze): 15%

Experimental Report 3: (Histology): 5%

Experimental Report 4: (Neurochemistry): 10%

Experimental Report 5: (Independent Research Project): 25%

10% of your grade: Oral presentations

Article presentation: 5%

Final Project Presentation: 5%

5% Class Involvement : for general participation in the discussion of required readings and for in-class write-ups.

5% Extra credit. Critique of “The Making of Memory: from Molecules to Mind” by Steven Rose.

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