In this lab, students will work with messy data to try to answer the question “How do plants inherit cotyledon color?”

This authentic research experience lesson teaches the core concept of systems and the competencies of quantitative reasoning, communication, and the ability to apply science. The research is student driven, the results are unknown, and the students engage in an iterative process to gather data, collaborating with classmates.  It is designed for first-year biology majors, in a class size of 15-30 students who can work in groups of three.  Students will learn to properly design an experiment, work as teams, analyze data, evaluate conclusions, and communicate findings to others. Additionally, this lesson also incorporates self-reflection and peer assessment when students produce a poster as a summative assessment. Over a five–week period, students will explore how an abiotic factor affects growth, reproduction, and survival of Daphnia.  Students are asked to compare their results to published literature. By the end, students should have a better understanding of science as an ongoing process where results are being updated and furthering the state of knowledge.

This case describes a three-part assignment in which students discuss key processes that regulate the stability and resilience of the Earth system and our increased risk of generating large-scale abrupt or irreversible environmental changes. Here, we use the planetary boundaries concept as a case study. Students are first asked to complete a pre-reading assignment in which they illustrate their perceptions of the degree to which human activity has changed nine earth system processes (e.g., nitrogen cycling, biodiversity loss, ocean acidification). Students then read primary literature on the planetary boundaries concept and complete a reading assurance assignment in which they summarize the reading and reflect on questions generated by the reading. In class, students work together in assigned groups to create a diagram of their collective perceptions and identify processes for which there was the largest misalignment with those presented in the paper. Students then discuss and summarize the evidence used by the authors to justify where these processes stand with respect to the safe operating space for humanity. The lesson concludes with a facilitated discussion and lecture on sustainability governance. This lesson provides students with a "capstone" activity to integrate ecological concepts discussed over the course of a semester and frames a larger discussion on socio-ecological aspects of global environmental change.

Primary image: Example of a student’s illustrated perceptions prior to reading ‘A safe operating space for humanity’ (Rockström et al. 2009). The wedges represent an estimate of the extent to which humans have changed nine earth system processes.

Students require a deep understanding of the central dogma before they can understand complex topics such as evolution and biochemical disorders. However, getting undergraduate biology students to apply higher-order thinking skills to the central dogma is a challenge. Students remember and regurgitate the molecular details of transcription and translation but if asked to apply these details, such as how a DNA mutation might affect phenotype, it becomes clear that most students do not deeply understand the central dogma. This lesson is a five-week series of laboratory activities designed to help students transition from applying lower order thinking skills to the central dogma to applying higher-order thinking skills. Over five weeks, students explore the phenotype of Arabidopsis asymmetric leaves 1 (as1) and as2 mutants. Students isolate DNA from wild-type and mutant plants and determine the sequence of the AS1 and AS2 alleles. Students use the DNA sequence data to determine the mutant protein amino acid sequences. They submit the mutant and wild-type protein sequences to a free online server and obtain three-dimensional (3-D) models of the wild-type and mutant proteins. They use free software to analyze and compare the 3-D models to determine the structural differences between the wild-type and mutant proteins. These computer-generated models can be 3-D printed allowing students to better visualize the protein structure. The overall goal is to use student-centered laboratory activities to demonstrate the relationship between DNA sequence, protein structure/function, and phenotype.

The process of cell specialization is critical to the formation and function of tissues in animals and plants. Although gene expression, including the regulation of transcription, is taught in most introductory cell biology courses, the relationship between differential gene expression and the formation of specialized cell types is challenging to understand for even upper-level life science students. In order to decrease this learning gap, I have developed a suite of in-class problem-solving activities and a lab experiment on Axolotl embryos that support student learning and integration of content related to differential gene expression and cell specialization. Although axolotls are best known as a model system for tissue regeneration, recent advances in genomic and molecular tools has increased their application as a model for studying gene expression during embryonic development as well. I tested the activities in an upper-level undergraduate course and found an increase in student understanding of the importance of differential gene expression during cell specialization processes, and the techniques used to study these processes, particularly Real Time quantitative PCR (RTqPCR). Teachers can examine student understanding of techniques and concepts using in-class assignments, exam questions, homework assignments and laboratory notebook assignments. Importantly, by analyzing a specific gene associated with a specialized cell type during different axolotl embryonic stages, students connect and integrate molecular, cellular and organismal level concepts of differential gene expression and cell specialization. This engagement deepens their understanding of the gene expression processes involved in cell specialization and of the role of model systems in biological research.

Due to the COVID-19 pandemic and increasing need to teach students online, aquatic scientists are looking for ways to give students field experiences virtually. Asynchronous, self-led field trips are emerging as a solution. However, due to the varying circumstances surrounding students and the dangers of exploring near water alone, asynchronous field trips need to be designed with equity, inclusivity, and safety in mind. Here, I provide a guide to creating inclusive field trips meant to introduce students to making qualitative scientific observations about aquatic ecosystems. This guide for designing an asynchronous, self-led aquatic ecology field trip explains how to: i) gauge whether this type of activity is suitable for your students, ii) promote safety and equity in choosing field trip sites, iii) build a community of learners while in a virtual setting, iv) prepare students for their individual trips, v) create a step-by-step worksheet to lead students through the activity, and vi) improve the experience for future classes.

Primary image: Backyard River: Standing on a bridge looking over the Rillito River flowing through urban Tucson (photo taken by the author).

In evolution classrooms, introducing and reinforcing the idea of genetic drift and random selection can be challenging, as can be reinforcing appropriate mental models of evolution. Agent-based models offer students the opportunity to conduct a model-based inquiry into the impacts of different features on the outcomes in evolutionary systems, helping to build, test, and expand their mental models of evolution. In this lesson—through independent investigation, model-based inquiry, and discussions with peers—students are introduced to the ways that agent-based models can be used to make predictions and test hypotheses about evolutionary systems. This lesson uses the NetLogo modeling environment, which comes preloaded with several useful teaching models and can be manipulated in an easy-to-use graphical interface. We use three models: a model of peppered moths focused on environmental pressures and natural selection, a red queen model focused on the competitive coevolution of snakes and frogs, and a genetic drift model of E. coli. Together, these models help reinforce evolutionary concepts in a hands-on, student-driven environment while improving their understanding of the utility of computing in evolution research. This lesson can be modified to suit courses of varying student levels and has been successfully adapted to online or lecture-based learning environments.

Although genetics is an invaluable part of the undergraduate biology curriculum, it can be intimidating to students as well as instructors: Students must reduce their reliance on memorization and dive deep into quantitative analysis, and instructors must make a long, rich history of genetics experiments clear, coherent, and relevant for students. Our Lesson addresses these challenges by having students map an unknown mutation to its gene using a modern suite of genetic tools. Students receive a Drosophila melanogaster strain with a mutation that causes the normally flat wing to bend at distinct sites along its length. Although we recently mapped this mutation to its gene, here we have renamed it "crumpled wing" (cw), an example of a pseudonym that you could use in the classroom. Like many standard "fly labs" that are taught at undergraduate institutions, this Lesson reinforces classic genetics concepts: students selectively mate fly strains to determine mode of inheritance, test Mendel's Laws, and three-point map an unknown mutation relative to known markers. But here, we expand on this tradition to simulate a more modern primary research experience: we greatly increase mapping resolution with molecularly-defined transgene insertions, deletions, and duplications; then cross-examine our data with key bioinformatic resources to identify a short-list of candidate cw genes. After extensive data interpretation and integration, students have been able to map cw to a single gene. This Lesson has a flexible design to accommodate a wide range of course structures, staffing, budgets, facilities, and student experience levels.

This lesson provides three activities to engage non-science major students in a discussion about sex, gender, gender identity, and sex determination. Students prepare for the lesson by reading a short article titled Sex and gender: What is the difference? and responding with research topics that would be most appropriate for one term over the other (sex vs. gender). This forms the basis of the first activity in which students brainstorm what it means to be female or male, and then identify whether each idea is related to a sex or gender characteristic, followed by a whole class discussion. The second activity is a clicker question with four published journal article titles, and students identify which is the least appropriate use of the term gender. The final activity involves a case study of María José Martínez-Patiño who failed a sex test in 1985 and was denied the right to compete as a female in the World University Games. In the case study, students grapple with the physiology of androgen insensitivity and what ultimately determines a persons' sex and gender identity. Non-science major students find these activities accessible and engaging, and each activity serves as a formative assessment for both the teacher and student. Summative assessments evaluate the students' level of confidence related to each of the three learning outcomes, and their understanding of terminology, context, and examples of sex and gender.

Mutations in genes can lead to a variety of phenotypes, including various human diseases. Students often understand that a particular mutation in a single gene causes a disease phenotype, but it is more challenging to illustrate complex genetic concepts such as that similar mutations in the same gene cause very different phenotypes or that mutations in different genes cause similar phenotypes. We originally designed this lesson to build off of the CourseSource lesson “A clicker-based case study that untangles student thinking about the processes in the central dogma,” but it can also stand alone. In our lesson, students read or listen to a real-life case study featuring a patient who doggedly pursues the underlying genetic cause of her own disease—muscular dystrophy—and stumbles upon a similar mutation in the same gene that gives an athlete the seemingly opposite phenotype: pronounced muscles. The lesson also leads the students to overlay their understanding of the central dogma and mutation on protein function and disease, compares muscular dystrophy to the disease progeria, and concludes with an ethical challenge. We tested the lesson as both an independent homework assignment, as well as a small group in-class worksheet and both formats were successful.

Primary Image: Line drawing of a space filling diagram of the LMNA protein illustrating mutations that lead to progeria.

Historically, undergraduate genetics courses have disproportionately focused on the impact of genes on phenotypes, rather than multifactorial concepts which consider how a combination of genes, the environment, and gene-by-environment interactions impacts traits. Updating the curriculum to include multifactorial concepts is important to align course materials to current understanding of genetics, and potentially reduce deterministic thinking, which is the belief that traits are solely controlled by genes. Currently there are few resources to help undergraduate biology instructors incorporate multifactorial concepts into their genetics courses, so we designed this lesson that centers on familiar, real-world examples. During this lesson, students learn how to distinguish between genetic and environmental sources of variation, and examine and interpret examples of how phenotypic variation can result from a combination of gene and environmental variation and interactions. This lesson, which is designed for both in-person and online classrooms, engages students in small group and large group discussion, figure interpretation, and provides questions that can be used for both formative and summative assessments. Results from assessment questions suggest that students found working through models depicting the interactions between genotypes and environments beneficial for their understanding of these complex topics.

Primary Image: Mendel’s laws of alternative inheritance of peas. A photo taken by W.F.R. Weldon of variation in color and texture of peas. Reprinted with permission from Biometrika (Weldon WFR. 1902. Mendel’s laws of alternative inheritance in peas).

Constructing a robust understanding of homologous chromosomes, sex chromosomes, and the particulate nature of genes is a notoriously difficult task for undergraduate biology students. In this lesson, students expand their knowledge of human chromosome pairs by closely examining autosomes, sex chromosomes, and the non-homologous elements of the human X and Y sex chromosomes. In this four- part guided activity, students will learn about the structure and function of human autosomal and sex chromosomes, view and interpret gene maps, and gain familiarity with basic bioinformatics resources and data through use of the National Center for Biotechnology Information (NCBI) website. (Student access to computers with Internet connectivity is required for the completion of all Investigations within this lesson.) By viewing chromosomes and gene maps, students will be able to contrast expectations for homologous autosomal chromosome pairs and sex chromosome pairs, as well as gain a deeper understanding of the genetic basis for human chromosomal sex determination. In the last part of this lesson, students can also begin to understand how genetic mutations can lead to sex-reversal. The lesson, as presented, is intended for an introductory biology course for majors, but could be modified for other audiences. In addition, each exercise (“Investigation”) within the lesson can be used independently of the others if an instructor wishes to focus on only a subset of the learning objectives and provide the necessary context.  Options to extend the lesson related to interpreting phylogenies, and contrasting definitions of sex and gender are also provided.

The biology classroom is not separate from the greater context of society; social issues can and should be presented in connection with the content. Here we present an example of antiracist teaching using the molecular/cellular biology of cancer in an introductory biology course as a topic through which to address historic racial disparities. Through this lesson, students analyzed biological science through the lens of social justice, specifically looking at disparities of cancer incidence with ties to health outcomes and environmental racism. The synchronous activity begins with personal tie-ins to the broader subject of cancer and then dives into the molecular regulation involved in creating cancerous phenotypes. Cancer biology is explored using an active-learning style based in process-oriented guided inquiry learning (POGIL) tactics. Multiple levels of assessments pushed students to grapple with data about racial health disparities and make explicit connections between these data and molecular mechanisms of cancer formation. This paper provides activity worksheets, an activity timeline, an example of assessment items, and teacher preparation for other instructors who want to emulate this lesson either directly or as an example of adjusting other science topics towards this lens. For those teaching in different topics, we offer advice and examples to help instructors to include social justice lenses into their science teaching.

Primary image: Malignant History. Artwork by Heidi-Marie Wiggins and Jeannette Takashima.

A strong understanding of distinct gene components and the ability to retrieve relevant information from gene databases are necessary to answer a diverse set of biological questions. However, often there is a considerable gap between students’ theoretical understanding of gene structure and applying that knowledge to design laboratory experiments. In order to bridge that gap, our lesson focuses on how to take advantage of readily available gene databases, after providing students with a strong foundation in the central dogma and gene structure. Our instructor-led group activity aids students in navigating the gene databases on their own, which enables them to design experiments and predict their outcomes. While our class focuses on cardiomyocyte differentiation, classes with a different focus can easily adapt our lesson, which can be conducted within a single class period. Our lesson elicits high engagement and learning outcomes from students, who gain a deeper understanding of the central dogma and apply that knowledge to studying gene functions.

Primary Image: Gene structure at various levels of expression and retrieval of corresponding biological information from gene databases. This image contains a screenshot from the NCBI Database, which is an open source: National Center for Biotechnology Information. 2021. SOX2 SRY-box transcription factor 2.

Undergraduate education and long-term science literacy are enhanced by integrating data projects with public datasets and creating analysis summaries. Underutilized public datasets are often generated by community-based or citizen science projects to address conservation issues supported by local residents. The objectives of this course activity are for students to contribute to a community science project, observe local species diversity, develop biodiversity questions, and apply data science techniques. Engaging students in these local projects enhances their understanding of the scientific process and its broader impacts on their community. The City Nature Challenge (CNC) is an annual global community science event where students participate by documenting species observations with the iNaturalist application, similar to localized BioBlitz events. Students are guided through using the iNaturalist database to practice biodiversity calculations then data is collected through participation in CNC (or a BioBlitz event an instructor arranges for their class). Spreadsheet software is used by students to organize, analyze, and summarize their relevant data to their peers. Students join the iNaturalist community of observers, which includes professional and non-professional naturalists. Therefore, students can see the themselves as scientists by contributing locally relevant data to a global and digital community of scientists. Experience working with large datasets such as the CNC iNaturalist dataset is essential for STEM careers and building data literacy. Implementing these experiences in classrooms will provide students unique opportunities to learn more about local biodiversity, develop interdisciplinary skills and positively influence a global network of scientists.

Primary image: Students recording biodiversity observations in an open field. At the annual Macaulay Honors College BioBlitz, students are divided into teams to explore a specific NYC park and record the animal and plant life they observed, which they later used to generate biodiversity reports including the species richness and abundances for the park.

To facilitate understanding of the fundamental genetic concept of the genotype-phenotype relationship in our introductory biology students, we designed an engaging multi-week series of related lessons about canine genetics in which students explore and answer the question, "How does the information encoded in DNA lead to physical traits in an organism?" Dogs are an excellent model organism for students since the genetic basis for complex morphological traits of various breeds is an active area of scientific research and dog DNA is easily accessible. Additionally, examination of students' pets offers a relatable, real-world, connection for students. Of the more than 19,000 genes that control canine genetics, simple genetic mutations in three genes are largely responsible for the coat variations of dogs –specifically, the genes that control hair length, curl, and the presence/absence of furnishings. In our lessons, students collect DNA samples from dogs, isolate and amplify targeted sections of DNA through polymerase chain reactions (PCR), and then sequence and analyze DNA for insertions and single nucleotide polymorphism (SNP) mutations. Utilizing gel electrophoresis and bioinformatics tools, students connect how the physical manifestation of traits is rooted in genetic sequences. Students also participate in discussions of scientific literature, group collaboration to construct a final poster, and presentation of their findings during a mock scientific poster conference. Through this module students engage in progressive exploration of genetic and molecular techniques that reveal how simple variations in a few DNA sequences in combination lead to a broad diversity of coat quality in domestic dog breeds.

Primary image. Genetic Analysis of Canine Coat Morphologies. Three dogs with differing coat morphologies analyzed by students (A, B, C), an agarose gel post-electrophoresis (D), and a chromatogram of a DNA sequence highlighting a relevant mutation (E). This collage contains original images taken by authors and course participants.

Growing calls in science education reform have emphasized wide-scale engagement of first-year undergraduate students in authentic research experiences; however, large course enrollments, inadequate student experience, limited resources and departmental inertia often create obstacles to reaching this goal. To help overcome these obstacles, the Department of Biology at James Madison University (JMU) has developed a cost-effective, scalable, and transferable semester-long (14-week) course-based undergraduate research experience (CURE) designed for large enrollment introductory biology labs. In this series of labs, first-year students use DNA barcoding to engage in authentic research practices drawn from the fields of ecology, molecular biology, and bioinformatics. These labs enable students to identify local species of plants, fungi, and invertebrates using student-generated DNA barcode sequences, which are then shared through a public database. Since their implementation at JMU in 2016, students in these labs have created and shared over 1,500 unique DNA barcode sequences and documented over 300 local species of plants, fungi, and invertebrates. These data are being used in an ongoing project comparing the biodiversity of forest edge versus forest interior habitats, but the labs are adaptable to almost any habitat or taxonomic group. In this article, we provide detailed descriptions of the content, logistics, and implementation of this 14-week series of labs. To our knowledge, this is among the largest-enrollment CUREs being offered to first-year undergraduates in the United States, and we hope that it can be useful to other institutions interested in documenting biodiversity and engaging introductory biology students in authentic research.

Biostatistics Using R: A Laboratory Manual was created with the goals of providing biological content to lab sessions by using authentic research data and introducing R programming language to biology majors.

Modern molecular biology is a data- and computationally-intensive field with few instructional resources for introducing undergraduate students to the requisite skills and techniques for analyzing large data sets. This Lesson helps students: (i) build an understanding of the role of signal transduction in the control of gene expression; (ii) improve written scientific communication skills through engagement in literature searches, data analysis, and writing reports; and (iii) develop an awareness of the procedures and protocols for analyzing and making inferences from high-content quantitative molecular biology data. The Lesson is most suited to upper level biology courses because it requires foundational knowledge on cellular organization, protein structure and function, and the tenets of information flow from DNA to proteins. The first step lays the foundation for understanding cell signaling, which can be accomplished through assigned readings and presentations. In subsequent active learning sessions, data analysis is integrated with exercises that provide insight into the structure of scientific papers. The Lesson emphasizes the role of quantitative methods in research and helps students gain experience with functional genomics databases and data analysis, which are important skills for molecular biologists. Assessment is conducted through mini-reports designed to gauge students' perceptions of the purpose of each step, their awareness of the possible limitations of the methods utilized, and the ability to identify opportunities for further investigation. Summative assessment is conducted through a final report. The modules are suitable for complementing wet-laboratory experiments and can be adapted for different courses that use molecular biology data.

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