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Abstract To understand the relative importance of cis and trans effects on regulation, we crossed multi-parent recombinant-inbred-lines (RILs) to a common tester and measured allele specific gene expression in the offspring. Testing difference of allelic imbalance between two RIL x Tester crosses is a test of cis or trans depending on the RIL alleles compared. The study design also enables to separate two sources of trans variation, genetic and environmental, detected via interactions with cis effects. We demonstrate the effectiveness of this approach in a long-read RNA-seq experiment in female abdominal tissue at two time points in Drosophila melanogaster. Among the 40% of all loci that show evidence of genetic variation in cis, trans effects due to environment are detectable in 31% of loci and trans effects due to genetic background in 19%, with little overlap in sources of trans variation. The genes identified in this study are associated with genes previously reported to exhibit genetic variation in gene expression. Eleven genes in a QTL for thermotolerance, previously shown to differ in expression based on temperature, have evidence for regulation of gene expression regardless of the environment, including the cuticular protein Cpr67B, suggesting a functional role for standing variation in gene expression. This study provides a blueprint for identifying regulatory variation in gene expression, as the tester design maximizes cis variation and enables the efficient assessment of all pairs of RIL alleles relative to the tester, a much smaller study compared to the pairwise direct assessment. 

Racial biases, which harm marginalized and excluded communities, may be combatted by clarifying misconceptions about race during biology lessons. We developed a human genetics laboratory activity that challenges the misconception that race is biological (biological essentialism). We assessed the relationship between this activity and student outcomes using a survey of students’ attitudes about biological essentialism and color-evasive ideology and a concept inventory about phylogeny and human diversity. Students in the human genetics laboratory activity showed a significant decrease in their acceptance of biological essentialism compared with a control group, but did not show changes in color-evasive ideology. Students in both groups exhibited increased knowledge in both areas of the concept inventory, but the gains were larger in the human genetics laboratory. In the second iteration of this activity, we found that only white students’ decreases in biological essentialist beliefs were significant and the activity failed to decrease color-evasive ideologies for all students. Concept inventory gains were similar and significant for both white and non-white students in this iteration. Our findings underscore the effectiveness of addressing misconceptions about the biological origins of race and encourage more research on ways to effectively change damaging student attitudes about race in undergraduate genetics education. 

Abstract Evolutionary perspectives on the deployment of immune factors following infection have been shaped by studies on a limited number of biomedical model systems with a heavy emphasis on vertebrate species. Although their contributions to contemporary immunology cannot be understated, a broader phylogenetic perspective is needed to understand the evolution of immune systems across Metazoa. In our study, we leverage differential gene expression analyses to identify genes implicated in the antiviral immune response of the acorn worm hemichordate, Saccoglossus kowalevskii, and place them in the context of immunity evolution within deuterostomes—the animal clade composed of chordates, hemichordates, and echinoderms. Following acute exposure to the synthetic viral double-stranded RNA analog, poly(I:C), we show that S. kowalevskii responds by regulating the transcription of genes associated with canonical innate immunity signaling pathways (e.g., nuclear factor κB and interferon regulatory factor signaling) and metabolic processes (e.g., lipid metabolism), as well as many genes without clear evidence of orthology with those of model species. Aggregated across all experimental time point contrasts, we identify 423 genes that are differentially expressed in response to poly(I:C). We also identify 147 genes with altered temporal patterns of expression in response to immune challenge. By characterizing the molecular toolkit involved in hemichordate antiviral immunity, our findings provide vital evolutionary context for understanding the origins of immune systems within Deuterostomia. 

Abstract Objectives Arachnids have fascinating and unique biology, particularly for questions on sex differences and behavior, creating the potential for development of powerful emerging models in this group. Recent advances in genomic techniques have paved the way for a significant increase in the breadth of genomic studies in non-model organisms. One growing area of research is comparative transcriptomics. When phylogenetic relationships to model organisms are known, comparative genomic studies provide context for analysis of homologous genes and pathways. The goal of this study was to lay the groundwork for comparative transcriptomics of sex differences in the brain of wolf spiders, a non-model organism of the pyhlum Euarthropoda, by generating transcriptomes and analyzing gene expression. Data description To examine sex-differential gene expression, short read transcript sequencing and de novo transcriptome assembly were performed. Messenger RNA was isolated from brain tissue of male and female subadult and mature wolf spiders ( Schizocosa ocreata ). The raw data consist of sequences for the two different life stages in each sex. Computational analyses on these data include de novo transcriptome assembly and differential expression analyses. Sample-specific and combined transcriptomes, gene annotations, and differential expression results are described in this data note and are available from publicly-available databases. 

Synopsis  Early exposure to course-based undergraduate research experiences (CUREs) in introductory biology courses can promote positive student outcomes such as increased confidence, critical thinking, and views of applicability in lower-level courses, but it is unknown if these same impacts are achieved by upper-level courses. Upper-level courses differ from introductory courses in several ways, and one difference that could impact these positive student outcomes is the importance of balancing structure with independence in upper-level CUREs where students typically have more autonomy and greater complexity in their research projects. Here we compare and discuss two formats of upper-level biology CUREs (Guided and Autonomous) that vary along a continuum between structure and independence. We share our experiences teaching an upper-level CURE in two different formats and contrast those formats through student reported perceptions of confidence, professional applicability, and CURE format. Results indicate that the Guided Format (i.e., a more even balance between structure and independence) led to more positive impacts on student outcomes than the Autonomous Format (less structure and increased independence). We review the benefits and drawbacks of each approach while considering the unique elements of upper-level courses relative to lower-level courses. We conclude with a discussion of how implementing structured skill-building can assist instructors in adapting CUREs to their courses.