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.
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.
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.
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