FraidyRat: A Virtual Module Examining the Neural Circuitry Underlying Fear Conditioning.

FraidyRat is a teaching tool that allows students to investigate the neural basis of fear conditioning and extinction using a virtual rat with a virtual brain. FraidyRat models well-known phenomena at both a behavioral and neural level. Students use virtual versions of tract tracing, systemic and intracerebrally infused drugs, neural recording, and electrical stimulation to understand the neural substrates underlying the observed behavior. This module helps students develop critical thinking skills in order to deduce immediate cause and effect as well as inductive reasoning to grasp the broader scheme. This module utilizes scaffolded instruction and formative assessment to shape the thinking of students as they unfold and discover the neural mechanisms responsible for fear conditioning and extinction in FraidyRat, which largely reflect what is found in real rats. Experience with this three-week module resulted in students showing significant gains in content knowledge as well as a trend toward gains in critical thinking. An attitudinal questionnaire showed that students had an overall positive experience. This module can be replicated at any institution with just a computer. All materials are available at: https://mdcune.psych.ucla.edu/modules/fraidy-rat.

Brain Volume Fractions in Mammals in Relation to Behavior in Carnivores, Primates, Ungulates, and Rodents.

The volume fraction (VF) of a given brain region, or the proper mass, ought to reflect the importance of that region in the life of a given species. This study sought to examine the VF of various brain regions across 61 different species of mammals to discern if there were regularities or differences among mammalian orders. We examined the brains of carnivores (n = 17), ungulates (n = 8), rodents (n = 7), primates (n = 11), and other mammals (n = 18) from the online collections at the National Museum of Health and Medicine. We measured and obtained the VF of several brain regions: the striatum, thalamus, neocortex, cerebellum, hippocampus, and piriform area. We refined our analyses by using phylogenetic size correction, yielding the corrected (c)VF. Our groups showed marked differences in gross brain architecture. Primates and carnivores were divergent in some measures, particularly the cVF of the striatum, even though their overall brain size range was roughly the same. Rodents predictably had relatively large cVFs of subcortical structures due to the fact that their neocortical cVF was smaller, particularly when compared to primates. Not so predictably, rodents had the largest cerebellar cVF, and there were marked discrepancies in cerebellar data across groups. Ungulates had a larger piriform area than primates, perhaps due to their olfactory processing abilities. We provide interpretations of our results in the light of the comparative behavioral and neuroanatomical literature.

Using Online Images to Teach Quantitative Skills via Comparative Neuroanatomy: Applying the Directives of Vision and Change.

Vision and Change calls for increasing the quantitative skills of biology majors, which includes neuroscience majors. Accordingly, we have devised a module to give students practice at regression analyses, covariance, and ANOVA. This module consists of a quantitative comparative neuroanatomy lab in which students explore the size of the hippocampus relative to the brain in 62 different mammalian species-from an anteater to a zebu. We utilize a digital image library (with appropriate metadata) allowing students to quantify the size of the hippocampus as well as obtain an index of the size of the brain in these various species. Students then answer the following questions: (1) Do brains scale with body size? (2) Does the hippocampus scale with brain size? (3) If we control for body size, does the hippocampus still scale with brain size? (4) How does the hippocampus change as a proportion of brain size? (5) Is the proportional scaling of the hippocampus different among primates, carnivores, and other mammals? (6) Do the data provide evidence for mosaic or concerted evolution? Measures of the pedagogical efficacy showed clear and significant gains on a PreTest vs PostTest assessment of material related to the module. An open ended qualitative measure revealed students' perception of the purposes of the module, which were consistent with the learning goals. This module utilizes open access digital resources and can be performed at any institution. All the materials or links to online resources can be found at https://mdcune.psych.ucla.edu/modules/cna.

Gel Scramble: An E-Tool for Teaching Molecular Neuroscience.

In this completely digital teaching module, students interpret the results of two separate procedures: a restriction endonuclease digestion, and a polymerase chain reaction (PCR). The first consists of matching restriction endonuclease digest protocols with images obtained from stained agarose gels. Students are given the sequence of six plasmid cDNAs, characteristics of the plasmid vector, and the endonuclease digest protocols, which specify the enzyme(s) used. Students calculate the expected lengths of digestion products using this information and free tools available on the web. Students learn how to read gels and then match their predicted fragment lengths to the digital images obtained from the gel electrophoresis of the cDNA digest. In the PCR experiment, students are given six cDNA sequences and six sets of primers. By querying NCBI BLAST, students can match the PCR fragments to the lengths of the predicted in silico PCR products. The ruse posed to students is that the gels were inadvertently mislabeled during processing. Although students know the experimental details, they do not know which gel goes with a given restriction endonuclease digest or PCR-they must deduce the answers. Because the gel images are from actual students' experiments, the data sometimes result from mishandling/mislabeling or faulty protocol execution. The most challenging part of the exercise is to explain these errors. This latter aspect requires students to use critical thinking skills to explain aberrant outcomes. This entire exercise is available in a digital format and downloadable for free at http://mdcune.psych.ucla.edu/modules/gel.

Teaching neuroinformatics with an emphasis on quantitative locus analysis.

Although powerful bioinformatics tools are available for free on the web and are used by neuroscience professionals on a daily basis, neuroscience students are largely ignorant of them. This Neuroinformatics module weaves together several bioinformatics tools to make a comprehensive unit. This unit encompasses quantifying a phenotype through a Quantitative Trait Locus (QTL) analysis, which links phenotype to loci on chromosomes that likely had an impact on the phenotype. Students then are able to sift through a list of genes in the region(s) of the chromosome identified by the QTL analysis and find a candidate gene that has relatively high expression in the brain region of interest. Once such a candidate gene is identified, students can find out more information about the gene, including the cells/layers in which it is expressed, the sequence of the gene, and an article about the gene. All of the resources employed are available at no cost via the internet. Didactic elements of this instructional module include genetics, neuroanatomy, Quantitative Trait Locus analysis, molecular techniques in neuroscience, and statistics-including multiple regression, ANOVA, and a bootstrap technique. This module was presented at the Faculty for Undergraduate Neuroscience (FUN) 2011 Workshop at Pomona College and can be accessed at http://mdcune.psych.ucla.edu/modules/bioinformatics.

Using digital images of the zebra finch song system as a tool to teach organizational effects of steroid hormones: a free downloadable module.

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 (analysis of variance and post hoc tests). We have provided free access to these digital tools at the following website: http://mdcune.psych.ucla.edu/modules/birdsong.

Teaching bioinformatics and neuroinformatics by using free web-based tools.

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. Students integrate 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, National Center for Biotechnology Information's Entrez Gene, and the Allen Brain Atlas), and information resources (PubMed). Instructors can use these various websites in concert to teach genetics from the phenotypic level to the molecular level, aspects of neuroanatomy and histology, statistics, quantitative trait locus analysis, and molecular biology (including in situ hybridization and microarray analysis), and to introduce bioinformatic resources. Students use these resources to discover 1) the region(s) of chromosome(s) influencing the phenotypic 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 student/instructor's manual, PowerPoints, sample exams, and links to free Web resources can be found at http://mdcune.psych.ucla.edu/modules/bioinformatics.

SWIMMY: Free Software for Teaching Neurophysiology of Neuronal Circuits.

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.