UCLA Department of Psychology

This document contains supporting material for "Design of a neurally plausible

model of fear learning" by FB Krasne, MS Fanselow, and M Zelikowsky. The model is

referred to as FRAT (for Fraidy Rat). The first main section of this paper provides a full

mathematical description of the model. The second section presents a number of

simulations that were not included in the main paper.

Zebra finch song behavior is sexually dimorphic: males sing and females do not. The neural

system underlying this behavior is sexually dimorphic, and this sex difference is easy to quantify.

During development, the zebra finch song system can be altered by steroid hormones,

specifically estradiol, which actually masculinizes it. Because of the ease of quantification and

experimental manipulation, the zebra finch song system has great potential for use in

undergraduate labs.

Unfortunately, the underlying costs prohibit use of this system in undergraduate labs. Further, the

time required to perform a developmental study renders such undertakings unrealistic within a

single academic term.

We have overcome these barriers by creating digital tools, including an image library of song

nuclei from zebra finch brains. Students using this library replicate and extend a published

experiment examining the dose of estradiol required to masculinize the female zebra finch brain.

We have used this library for several terms, and students not only obtain significant experimental

results but also make gains in understanding content, experimental controls, and inferential

statistics (ANOVA and post-hoc tests). We have provided free access to these digital tools at

http://mdcune.psych.ucla.edu/modules/birdsong.

This document contains supporting material for "Design of a neurally plausible fear learning model" by FB Krasne, MS Fanselow, and M Zelikowsky. The model is referred to as FRAT (for Fraidy Rat). The first main section of this paper provides a full mathematical presentation of the model. The second section presents a number of simulations that were not included in the main paper.

We are providing free digital resources for teaching neuroscience labs at http://mdcune.psych.ucla.edu/. These resources will ultimately include materials for teaching laboratories in electrophysiology of neuronal circuits (SWIMMY), a Neuroinformatics/Bioinformatics module, and two modules for investigating the effects of hormones on early CNS development—one focusing on the development of the song system and one focusing on sex differences in spinal cord motor neurons. All of these modules are inquiry based—students gain from genuine experiences in doing actual studies rather than just simulations. These materials should provide instructors the ability to provide good quality laboratory experiences regardless of resource limitations. Currently, modules on sex differences in the spinal cord and virtual neural circuits (SWIMMY) are available on our website. More will be available in summer 2009 and 2010. SWIMMY was demonstrated at the Faculty for Undergraduate Neuroscience (FUN) Workshop—The Undergraduate Neuroscience Education: Interactions, interdisciplines, and curricular best practices at Macalester College in July 2008.

This completely computer-based module’s purpose is to introduce students to bioinformatics resources. We present an easy-to-adopt module that weaves together

several important bioinformatic tools so students can grasp how these tools are used in answering research questions. This module integrates information gathered from websites dealing with anatomy (Mouse Brain Library), Quantitative Trait Locus analysis

(WebQTL from GeneNetwork), bioinformatics and gene expression analyses (University of California, Santa Cruz Genome Browser, NCBI Entrez Gene, and the Allen Brain Atlas), and information resources (PubMed).

This module provides for teaching genetics from the phenotypic level to the molecular level, some neuroanatomy, some aspects of histology, statistics, Quantitaive Trait Locus analysis, molecular biology including in situ hybridization and microarray analysis in addition to introducing bioinformatic resources. Students use these resources to discover 1) the region(s) of chromosome(s) influencing the trait, 2) a list of candidate genes—narrowed by expression data, 3) the in situ pattern of a given gene in the region of

interest, 4) the nucleotide sequence of the candidate gene, and 5) articles describing the gene. Teaching materials such as a detailed instructor’s manual, powerpoints, sample exams, and links to free web resources can be found at http://mdcune.psych.ucla.edu/modules/bioinformatics.

To circumvent the many problems in teaching neurophysiology as a “wet lab,” we developed SWIMMY, a virtual fish that swims by moving its virtual tail by means of a virtual neural circuit. SWIMMY diminishes the need for expensive equipment, troubleshooting, and manual skills that require practice. Also, SWIMMY effectively replaces live preparations, which some students find objectionable.

Using SWIMMY, students (1) review the basics of neurophysiology, (2) identify the neurons in the circuit, (3) ascertain the neurons’ synaptic interconnections, (4) discover which cells generate the motor pattern of swimming, (5) discover how the rhythm is generated, and finally (6) use an animation that corresponds to the activity of the motoneurons to discover the behavioral effects produced by various lesions and explain them in terms of their neural underpinnings. SWIMMY is a genuine inquiry-based exercise producing data that requires individual thought and interpretation. It is neither a cookbook exercise nor a demonstration.

We have used SWIMMY for several terms with great success. SWIMMY solidifies students’ understanding of material learned in traditional lecture courses because they must apply the concepts. Student ratings of SWIMMY have been very positive, particularly ratings from students who have also been exposed to a “wet” neurophysiology lab.

Because SWIMMY requires only computers for implementation and makes minimal demands on instructional resources, it provides for a great deal of flexibility. Instructors could use SWIMMY as part of a traditional lab course, as a classroom exercise, in distance learning, or in blended instructional formats (internet with classroom). SWIMMY is now available for free online complete with student and instructor manuals at http://mdcune.psych.ucla.edu.

Sheep brain dissection is a mainstay of many neuroscience and biological psychology lab courses. Sheep brain dissection is relatively easy and requires only the brains, surgical gloves, and a large, sharp knife without serrations to provide a valuable learning experience. Preserved sheep brains are readily available from a variety of vendors at a reasonable cost. (Getting brains with the dura already removed is highly recommended because students tend to tear up the brain when removing the dura.) Most structures in the sheep brain are highly homologous to structures in the brains of other placental mammals, including humans. Only cortical structures, particularly sulci and gyri, which are not always homologous across mammalian orders, differ markedly between humans and sheep. Thus, specific facts learned from dissecting sheep brains can be readily generalized to other species.

A published hard-copy photographic atlas of the sheep brain is available (Vanderwolf and Cooley, 2002), but searching the internet also reveals many resources made freely available by instructors at a variety of institutions. Most of the websites are designed to be supplements for specific courses, but some are clearly designed for broader use. Many websites could serve as excellent supplements to in-lab dissections, and some could even replace in-lab dissections if resources are tight or if students have ethical objections to using animals.

This article describes a laboratory module taught at UCLA and offers digitized microscope images that will allow instructors to recreate this module at their home institutions with only a computer required. This module allows for 1) an exploration of the effects of hormones on neural development, 2) the demonstration of sex differences in the nervous system, 3) the production of robust and statistically significant data by novice undergraduates, 4) the discussion of sophisticated statistical analyses (ANOVAs with significant main effects and an interaction), and 5) the understanding of at least some of the neuroanatomy of the spinal cord. Specifically, this module both replicates and extends a previously published experiment on sexually dimorphic neurons in the spinal cord of rats (Grisham et al., 1992), which examined the effect of antiandrogen exposure (Flutamide) in utero on sexually dimorphic spinal motoneurons in male and female rats.