The mathematical modeling of populations utilizing field-collected demographic data is an important component of lab curricula in a variety of undergraduate biology lab courses. During the global pandemic brought about by the SARS-CoV-2 virus in 2020, we successfully converted an in-person lab on demographic population modeling to a lab that could be run remotely. We used a Google Earth Web Project to simulate a population study of the Northern Spotted Owl. In the simulation, students collected both demographic and mark-recapture data, based on surveying images of Northern Spotted Owls as they navigated four different wildlife transects. After conducting the survey, students used the data to determine population size using the mark-recapture method, derived a life table, calculated the net reproductive rate, and used the information to assess the current management plan for the population studied. Here we outline the lesson and provide materials required to duplicate the lab or to use Google Earth to create a similar simulation centered around a different species in any location around the globe.

Primary Image: Population Ecology with Google Earth. This population ecology lesson utilizes the Google Earth Project to provide students a simulated mark-recapture study. This lesson framework can be applied to any species or location; we chose to focus our lesson on the Northern Spotted Owl.

Evolutionary trees communicate both the diversity and unity of life, a central and important scientific concept, as highlighted by the Vision and Change undergraduate biology education movement. Evolutionary trees and cladograms are diagrams viewed by biologists as Rosetta Stone-like in how well they convey an enormous amount of information with clarity and precision. However, the majority of undergraduates in introductory biology courses find the non-linear diagram confusing and do not immediately understand the tree-thinking central to interpreting the evolutionary tree’s branching structure. Go Extinct! is an original board game featuring land vertebrates (i.e., amphibians, mammals, birds and reptiles) and it is designed to engage students in reading this evolutionary tree. Go Extinct! won the Society for the Study of Evolution’s Huxley Award for outstanding outreach achievements in recognition for how the gameplay itself incentivizes students to identify clades and common ancestors on a stylized tree. The game can be completed in about 30 minutes, which allows instructors time to give follow-up activity sheets that help students transfer their new ability to read a stylized tree into the ability to read more traditional-looking trees found in textbooks and the literature. Overall, teaching the game, playing the game, and completing the follow-up transfer activity can be completed in a 50-minute section. Each game can serve up to 6 students, which means 3 games can cover a section of 18 students. Go Extinct! provides a fun and effective learning experience that students will remember and may even request to play again.

Primary Image: Biologists play Go Extinct! Students who play Go Extinct! gain a mastery of reading an evolutionary tree or cladogram. The winning strategy depends on identifying common ancestors of animal cards in your hand. Photo taken by the author.

Role-playing activities in the classroom promote students’ critical thinking, research, and communication skills. We present an activity where students debate a current controversy in conservation. In our case study, students debate the topic of wolf reintroduction in California. Each student is assigned a stakeholder role (e.g., rancher, environmental scientist, hunter, or politician) and a position (either pro or con). First, the whole class participates in a vote on the debate topic so as to register pre-debate sentiment. Then, in the first part of the activity (75 minutes or as homework), students prepare arguments with others representing their stakeholder group by reading the primary and secondary literature and answering guided questions. In the second part of the activity (75 minutes), students participate in a live debate divided into three sections: introductory arguments, questions from the jury, and concluding arguments. The whole class then votes again to decide the winner of the debate, leading to a discussion about which factors do and do not lead to changes in understanding and opinion. The interdisciplinary nature of this activity reinforces student knowledge on ecological networks, keystone species, and natural history, as well as introduces the importance of non-scientific stakeholders in conservation. While this case study focuses on the reintroduction of wolves in California, the activity can be adapted to the reintroduction of controversial species in other regions, or used as a framework for any debatable topic in conservation biology.

Primary Image: The reintroduction of the gray wolf Canis lupus is a controversial topic in conservation biology and environmental policy.

The central dogma of biology is a foundational concept that provides a scaffold to understand how genetic information flows in biological systems. Despite its importance, undergraduate students often poorly understand central dogma processes (DNA replication, transcription, and translation), how information is encoded and used in each of these processes, and the relationships between them. To help students overcome these conceptual difficulties, we designed a clicker-based activity focused on two brothers who have multiple nucleotide differences in their dystrophin gene sequence, resulting in one who has Duchenne muscular dystrophy (DMD) and one who does not. This activity asks students to predict the effects of various types of mutations on DNA replication, transcription, and translation. To determine the effectiveness of this activity, we taught it in ten large-enrollment courses at five different institutions and assessed its effect by evaluating student responses to pre/post short answer questions, clicker questions, and multiple-choice exam questions. Students showed learning gains from the pre to the post on the short answer questions and performed highly on end-of-unit exam questions targeting similar concepts. This activity can be presented at various points during the semester (e.g., when discussing the central dogma, mutations, or disease) and has been used successfully in a variety of courses ranging from non-majors introductory biology to advanced upper level biology.

The central dogma of biology is a foundational concept that provides a scaffold to understand how genetic information flows in biological systems. Despite its importance, undergraduate students often poorly understand central dogma processes (DNA replication, transcription, and translation), how information is encoded and used in each of these processes, and the relationships between them. To help students overcome these conceptual difficulties, we designed a clicker-based activity focused on two brothers who have multiple nucleotide differences in their dystrophin gene sequence, resulting in one who has Duchenne muscular dystrophy (DMD) and one who does not. This activity asks students to predict the effects of various types of mutations on DNA replication, transcription, and translation. To determine the effectiveness of this activity, we taught it in ten large-enrollment courses at five different institutions and assessed its effect by evaluating student responses to pre/post short answer questions, clicker questions, and multiple-choice exam questions. Students showed learning gains from the pre to the post on the short answer questions and performed highly on end-of-unit exam questions targeting similar concepts. This activity can be presented at various points during the semester (e.g., when discussing the central dogma, mutations, or disease) and has been used successfully in a variety of courses ranging from non-majors introductory biology to advanced upper level biology.

The central dogma of biology is a foundational concept that provides a scaffold to understand how genetic information flows in biological systems. Despite its importance, undergraduate students often poorly understand central dogma processes (DNA replication, transcription, and translation), how information is encoded and used in each of these processes, and the relationships between them. To help students overcome these conceptual difficulties, we designed a clicker-based activity focused on two brothers who have multiple nucleotide differences in their dystrophin gene sequence, resulting in one who has Duchenne muscular dystrophy (DMD) and one who does not. This activity asks students to predict the effects of various types of mutations on DNA replication, transcription, and translation. To determine the effectiveness of this activity, we taught it in ten large-enrollment courses at five different institutions and assessed its effect by evaluating student responses to pre/post short answer questions, clicker questions, and multiple-choice exam questions. Students showed learning gains from the pre to the post on the short answer questions and performed highly on end-of-unit exam questions targeting similar concepts. This activity can be presented at various points during the semester (e.g., when discussing the central dogma, mutations, or disease) and has been used successfully in a variety of courses ranging from non-majors introductory biology to advanced upper level biology.

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.

Our understanding of microbiomes, or the collection of microorganisms and their genes in a given environment, has been revolutionized by technological and computational advances. However, many undergraduate students do not get hands-on experiences with processing, analyzing, or interpreting these types of datasets. Recent global events have increased the need for effective educational activities that can be performed virtually and remotely. Here, we present a module that introduces STEM undergraduates to the bioinformatic and statistical analyses of bacterial communities using a combination of free, web-based data processing software. These lessons allow students to engage with the studies of microbiomes; gain valuable experiences processing large, high-throughput datasets; and practice their science communication skills. The lessons presented here walk students through two web-based platforms. The first (DNA Subway) is an easy-to-use wrapper of the popular QIIME (pronounced “chime”) pipeline, which performs quality control analysis of the raw sequence data and outputs a community matrix file with assigned bacterial taxonomies. The second, ranacapa, is an R Shiny App that allows students to compare microbial communities, perform statistical analyses and visualize community data. Students may communicate their findings with a written final report or oral presentation. While the lessons presented here use a sample dataset based on the gut-microbiome of the bean beetle (Callosobruchus maculatus), the materials are easily modified to use original next-generation amplicon sequence data from any host or environment. Additionally, options for alternative datasets are also provided facilitating flexibility within the curriculum.

Primary Image: Insects are an excellent example of a tractable biological system to study the relationship between an organism and its microbiome. Little is currently known about the gut-microbiome of many insects, such as the bean beetle (Callosobruchus maculatus).

Creating a hands-on lab that conveys important information while simultaneously allowing for student autonomy can be difficult. This is particularly true for the field of microbiology, in which labs often rely on “recipe-style” instructions and materials that can be difficult to scale up for larger class sizes. For these reasons, microbiology concepts are often left out of introductory biology labs, the ramifications of which have been made apparent during the recent COVID-19 virus pandemic. Fundamental microbiology concepts, e.g., the prevention of communicable diseases, are important to teach in introductory biology classrooms – often a student's only exposure to biology in their academic careers – in order to create a healthier community as a whole. Therefore, this general biology lab introduces an active-learning microbiology lab that teaches students about the microbial world. Students are first introduced to the three major types of symbioses and apply these concepts to microbial organisms on a symbiotic continuum. Next, the students are given examples of mutualistic bacteria, i.e., the human microbiome, through a mini lecture prepared by the instructor. The students are then introduced to examples of parasitic/pathogenic microbes that can interfere with human health and cause relatable diseases (e.g., diarrhea, STDs, and athlete’s foot). Students then apply this information through a short matching game before learning common practices used to prevent the spread of these pathogens, including an active learning exercise and video on how to wash their hands like healthcare professionals. Finally, students are asked to generate their own questions about microbes before working through a handout that guides the students through using the scientific method to address their questions. This exercise thus provides students with the autonomy to ask their own questions about microbes, design their own experiments, prepare growth media their own way, and present their findings in a way that is both scalable for large class sizes and reduces the burden of lab prep common for microbiology labs. 

Primary image: Microbes sampled from the iPhone of a curious individual. Fungal colonies can be seen as fuzzy, white or colorful mounds while bacteria appear as opaque, smooth streaks on the media.

In March 2020, institutions underwent a massive transition to distance learning as a result of the COVID-19 pandemic. With so little time to devise new materials to maximize learning in the new virtual environment, instructors devised a variety of innovative strategies for completing the Spring 2020 semester. While highly disruptive, the pandemic also brought mainstream attention to a wide array of scientific concepts and provided an opportunity to teach students about science in real-time. Teaching topics related to COVID-19 can be approached from many different disciplines such as virology, immunology, biochemistry, genetics, public health, pharmacology, systems biology, and synthetic biology. By bringing together lessons devised by each of the authors on their own, we offer a series of curriculum modules that can be used either collectively or in parts to provide students with a multidisciplinary look at the virus and to answer their own curiosity about the disease that will define their generation.

Primary image: 360-degree view of COVID-19. The primary image depicts a SARS-CoV-2 virion surrounded by the fields of study that are featured in our pedagogical activities.

Engaging and supporting introductory level students in authentic research experiences during required coursework is challenging. Plant bioactive compounds attract students' natural curiosity as they are found in many familiar items such as tea, coffee, spices, herbs, vegetables, essential oils, medicines, cleaning supplies, and pesticides. Over the course of one semester, students work in teams to design experiments in three experimental modules to test whether bioactive compounds have effects on Daphnia heart rate, antibacterial activity, or caterpillar behavior. In a fourth module, they research solutions to an environmental problem. Students are involved in multiple scientific practices as they make their own experimental decisions, analyze data including using statistics to carefully justify their preliminary conclusions, and have the opportunity to improve their experiment and repeat it. Iteration is also emphasized by the fact that students go through the whole process from design to presentation repeatedly for three experiments. In the process, students experience for themselves the real complexity of scientific investigations and what it takes to rigorously show cause-and-effect relationships. The pedagogical focus is on providing introductory students with a supportive structure in a way that empowers them to make informed experimental decisions and be successful. At the end of the semester, the majority of students displayed a strong sense of personal involvement and an appreciation of the difficulties of scientific experimentation in open-ended written reflections. Students reported that statistics was one of the most difficult yet valuable experiences in these labs and demonstrated significant gains on a statistical test.

Primary image: Summary of the Lesson showing that student decide on which bioactive compounds to test in three model organisms (image attributions listed in Acknowledgments).

Students are frequently overwhelmed by the complexity of metabolic pathways and they think they have "learned" the pathway when they have memorized the individual reactions.  This laboratory lesson helps students to understand the significance of individual reactions in the pathways leading to methionine synthesis in the budding yeast, Saccharomyces cerevisiae.  Students appreciate that methionine is one of only two sulfur-containing amino acids, and students do not find it difficult to follow the "yellow" sulfur atom in the pathway. In the lesson, students use three different yeast met strains, each of which lacks a single gene involved in methionine synthesis.  Working in groups of three, students identify the missing MET gene in each of the three deletion strains by analyzing the abilities of the deletion strains to grow on several defined media in which methionine has been replaced with alternative sulfur sources. Students also determine the position of mutant genes in the pathway relative to sulfite reductase, using indicator media that reacts with sulfide, the product of the reaction catalyzed by sulfite reductase. For the analysis, students prepare serial dilutions of yeast cultures and spot the dilution series on agar plates. This lesson is part of a semester-long research investigation into the evolutionary conservation of the genes involved in methionine synthesis. The lesson can also be used as a stand-alone exercise that teaches students about biochemical pathways, while reinforcing basic microbiological techniques.

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.

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.

Typical biochemistry labs exploring basic enzyme activity rely on costly, time-consuming protein purification and rarely explore enzyme function in situ. Further, complex purification procedures leave little room for novelty in experimental design. Here we present an inquiry-driven laboratory exercise for biochemistry undergraduates and adaptations for a general education science course. Each student designs a unique experiment to test their hypothesis regarding the nature of avocado browning in a three-hour span. In the presence of oxygen, polyphenol oxidases (PPO) catalyze oxidation of phenolic compounds into quinones, the polymerization of which creates the visible browning of many cut fruits. Avocado fruit, a source of both enzyme and substrate, is a safe, low-cost vehicle for semi-quantitative experimentation. During the incubation, biochemistry students use the Protein Data Bank and primary literature to understand the structure-function relationship of PPO and other molecular components of the avocado. Non-major students discuss how pH, temperature, and substrate availability affect PPO. Visible browning pigments appear on a controllable time scale. Students can photograph results to create a figure to accompany semi-quantitative analysis of experimental results in a single lab period. Since avocados are familiar foods and select test reagents are generally recognized as safe, the optimal protocol investigated in the lab can be further applied to best practices in the kitchen in everyday life, promoting the transfer of knowledge learned in the classroom to practical environments.

To vaccinate or not to vaccinate, that is the question. Much of the recent trend in society against vaccination is that the general population does not understand 1) how vaccines work and 2) how one's vaccination status can influence others. Further compounding this is rather low acceptance of the influenza vaccine, a vaccine which is sometimes not even effective against the strains predominantly in circulation. Through engaging in a conversation about the role of vaccines in immunity not only of oneself but also about surrounding persons, we can increase vaccine acceptance. Herein is a physical assay which illustrates the concept of herd immunity with differing levels of vaccinations within a population. Students will learn that low vaccination rates do little to nothing to stop disease spread and that a large portion of the population (80%) is necessary to achieve near-eradication. This lesson is able to be taught at multiple levels using supplies that can mostly be obtained at the grocery store. In addition to illustrating vaccination, this study approximates a direct enzyme-linked immunosorbent assay (ELISA), enabling students to better understand that technique and how it is used to diagnose disease as well as the interrelation between antigens and antibodies.

Participation in research provides personal and professional benefits for undergraduates. However, some students face institutional barriers that prevent their entry into research, particularly those from underrepresented groups who may stand to gain the most from research experiences. Course-based undergraduate research experiences (CUREs) effectively scale research availability, but many only last for a single semester, which is rarely enough time for a novice to develop proficiency. To address these challenges, we present the Pipeline CURE, a framework that integrates a single research question throughout a biology curriculum. Students are introduced to the research system - in this implementation, C. elegans epigenetics research - with their first course in the major. After revisiting the research system in several subsequent courses, students can choose to participate in an upper-level research experience. In the Pipeline, students build resilience via repeated exposure to the same research system. Its iterative, curriculum-embedded approach is flexible enough to be implemented at a range of institutions using a variety of research questions. By uniting evidence-based teaching methods with ongoing scientific research, the Pipeline CURE provides a new model for overcoming barriers to participation in undergraduate research.