This QUBES module is focused towards AP Environmental studies courses. It includes hypothesis testing, transect sampling, Shannon Diversity Index, and scatter plot and bar graph creation in excel.

Introduction to Primate Data Exploration and Linear Modeling with R was created with the goal of providing training to undergraduate biology research students on data management and statistical analysis using authentic data of Cayo Santiago rhesus macaques.

Instructional Videos

Lab Math Resources

This resource promotes inclusive learning by using all free platforms to extend the central dogma to an applied experience. Genomics is focused on with literature reviews that are performed to identify genes implicated in a clinical condition. Transcriptomics with data mining of RNAseq acquisition is followed by protein sequence acquisition and modeling. Teaching and learning of communication in the process of science is the final focus.

Resources for the Advanced Molecular Biology course (Applied Biosciences Itinerary)

The exploitation of African elephants in the form of ivory poaching is exacerbated by warfare. The affects of this anthropogenic evolutionary force on the African savanna elephant (Loxodonta africana) in the Gorongoas National Park in Mozambique was investigated (Campbell-Staton, et. al. 2021) after the Mozambican civil war (1997-1992).  This multipart lesson is based on this research.  Here, we explore allele frequencies, phenotypic data, and the use of a chi-squared test to determine if the population is in Hardy-Weinberg Equilibrium.  Because one gene influencing tusklessness is X-linked, we also explore inheritance of the trait, using hemophilia as an example.  The data used in this part of the lesson are simulated data based on reports from Zambia.

In this activity students explore and analyze real, authentic research data paired with HHMI’s “Selection for Tuskless Elephants” video in a hands-on investigation of human impacts on elephant evolution.

In this activity students explore and analyze real, authentic research data paired with HHMI’s “Selection for Tuskless Elephants” video in a hands-on investigation of human impacts on elephant evolution using the R-Shiny App, Serenity.

This educational game allows teams of students to try to control a simulated epidemic in United States snake populations using their epidemiological and ecological knowledge. It combines a "choose your own adventure", scenario-based website with an agent based model (run in the free NetLogo program).

A compelling reason to learn something can make all the difference in students’ motivation to learn it.  Motivation, in turn, is one of the key attitudes that drives learning.  This story presents students with a compelling puzzle of a fatherless snake.  The puzzle motivates students to learn about meiosis and mitosis, since the only way to explain the origin of the fatherless baby is by mastering details of meiosis.  During the process, students work through the major steps in meiosis, compare and contrast mitosis and meiosis, and apply their understanding to predict how meiosis “went wrong” to produce an unusual offspring that did not originate through union of an egg and a sperm.  This story can be adapted for introductory or advanced students and can be scaled from a brief introduction in a single lecture to a series of active learning exercises that could take two or more lecture periods.

This is an FMN participant supplement for the TIEE module "Global Temperature Change in the 21st Century," authored by Daniel R. Taub and Gillian S. Graham in 2011.

This module examines the complicated co-evolution of Lice, Humans, and Great Apes

Introductory genetics laboratory published as GSA Learning Resource

This is an adaptation to work in R of Investigating Evidence for Climate Change (Project) by Hage, M. 2020. Students will investigate geologic and modern evidence for global temperature and atmospheric CO2 change using ice-core data and Mauna Loa records.

This is an adaptation of Calling Bull's Case Study on how caffeine free is hot chocolate versus coffee in order to make it into a student project that uses R.

A young boy wonders why his twin sister can roll his tongue, but he cannot. Case centers on meiosis.

This module introduces gene flow in the context of understanding the persistence of maladaptive traits in some populations. It is intended for an introductory biology audience.

This is a modification of an original TIEE Module, investigating these questions: How does nutrient pollution impact stream ecosystems locally and nationally? How does land cover change impact nutrient pollution?

misinformation

Redlining was a racist, legal practice and its impacts are measurable in terms of environmental variables in US cities today. This resource examines redlining, urban environments, and climate change.

Students link human behavior in various climate change scenarios to predicted temperature outcomes at both local (their assigned Latitude) and global (Latitudinal trends) scales. This adaptation is intended to be more accessible to non-majors.

Students use data on nitrogen and phosphorus levels in streams and macrobenthic insect biodiversity to consider issues of nutrient pollution and stream health while learning to filter, summarize, and plot data.

Important learning outcomes for biology students include the ability to develop experiments as well as pull together concepts across their coursework. The field of developmental biology, especially environmental influences on development (eco-devo), provides a framework for connecting concepts including tissue dynamics, cell signaling, and physiology. An eco-devo framework also provides opportunities for experiments that are relevant to student interests and/or experiences by encompassing topics such as the impact of environmental contamination or maternal health on development. Here we present a guided course-based undergraduate research experience (CURE) for students to work with zebrafish embryos as a foundation for the design and execution of their own novel research project. The guided experiment that is performed first in this lesson explores how the weed killer atrazine might affect development of zebrafish, even though atrazine would not be expected to impact animals. The student-developed independent experiment is planned during the guided experiment and then performed in subsequent weeks by students in the second part of this lesson. The independent experiment allows students to investigate a research question related to their own interests. These experiments can be modified for a variety of courses depending on the instructor's curriculum, time constraints, and goals for the experiment. Students are particularly engaged in the lesson because it enables them to investigate their ideas and interests.

In Developmental Biology classes, students are challenged with understanding how differential gene expression guides embryonic development. It can be difficult for students to realize that genes need to be turned on or off at the right time and place in order for development to proceed normally. In this lab, students working in groups perform experiments with live embryos and visualize differential gene expression allowing them to become invested in their experiment and curious about the results. This lab also addresses the benefits of Xenopus laevis as a model organism and allows students to observe the changes Xenopus embryos undergo during early embryonic stages. After the students have chosen and fixed two stages of Xenopus embryos, they perform an in situ hybridization on the embryos to visualize gene expression at two different developmental stages. They then compare their results with those from other lab groups who analyzed their embryos for different genes. The students self-reported that they better understood the concept of differential gene expression during vertebrate development and enjoyed doing this series of lab experiments working with live materials.

Some concepts in genetics, such as genetic screens, are complex for students to visualize in a classroom and can be cumbersome to undertake in the laboratory. Typically, very large populations are needed, which can be addressed by using micro-organisms. However, students can struggle with phenotyping microbes. For macroscopic organisms, the number of offspring produced, and the generation time can be challenging. I developed this lesson as a small-scale genetic screen of Fast Plants^®. These plants are amenable to teaching labs as they have simple growth requirements, a short generation time, and produce numerous seeds that can be stored for years. Seeds used for this screen are purchased pre-treated with a DNA damaging agent, removing the need for in-house use of mutagens. Also, students can screen the phenotypes without specialized equipment. The initial lesson begins with an examination of the first generation of plants. Later their offspring are screened for altered phenotypes. Students responded well to having full-grown plants available on the first day of the lab project. This lesson fostered student collaboration, as they worked with class datasets. Differences in growth due to mutagenesis treatment in the first generation were clear to students who had not worked with plants before. Identifying plants with altered phenotypes in the next generation was more of a challenge. This lesson incorporates key concepts such as somatic and germline mutations, the impact of such mutations on phenotype, and the inheritance of mutation alleles, and provides a hands-on way to illustrate these concepts.

Primary Image: Fast Plant^® phenotype differences observed in the M2 generation. This pot contains three full-sibling M2 seedlings from a single M1 parent plant. The seed of their parent plant received 50 Krads of radiation. Plants 1 and 2 are of standard height, while plant 3 is greatly elongated. Image by AL Klocko.

Some concepts in genetics, such as genetic screens, are complex for students to visualize in a classroom and can be cumbersome to undertake in the laboratory. Typically, very large populations are needed, which can be addressed by using micro-organisms. However, students can struggle with phenotyping microbes. For macroscopic organisms, the number of offspring produced, and the generation time can be challenging. I developed this lesson as a small-scale genetic screen of Fast Plants^®. These plants are amenable to teaching labs as they have simple growth requirements, a short generation time, and produce numerous seeds that can be stored for years. Seeds used for this screen are purchased pre-treated with a DNA damaging agent, removing the need for in-house use of mutagens. Also, students can screen the phenotypes without specialized equipment. The initial lesson begins with an examination of the first generation of plants. Later their offspring are screened for altered phenotypes. Students responded well to having full-grown plants available on the first day of the lab project. This lesson fostered student collaboration, as they worked with class datasets. Differences in growth due to mutagenesis treatment in the first generation were clear to students who had not worked with plants before. Identifying plants with altered phenotypes in the next generation was more of a challenge. This lesson incorporates key concepts such as somatic and germline mutations, the impact of such mutations on phenotype, and the inheritance of mutation alleles, and provides a hands-on way to illustrate these concepts.

Primary Image: Fast Plant^® phenotype differences observed in the M2 generation. This pot contains three full-sibling M2 seedlings from a single M1 parent plant. The seed of their parent plant received 50 Krads of radiation. Plants 1 and 2 are of standard height, while plant 3 is greatly elongated. Image by AL Klocko.

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.

E-book in .pdf format and customizable .iba format

Scientists have discovered that microplastic pollution is ubiquitous in the environment, but the small size of these microscopic pollutants prohibits most people from recognizing their prevalence. This river-based field lesson will introduce environmental science students to this emerging environmental concern, and encourages them to explore microplastics in their local waterways with sample collection, density separation and field-based microscopy. Students will appreciate the opportunity to connect to this topic from anywhere in the world, allowing them to see microplastics with their own eyes and without the use of sophisticated equipment. In addition, this lesson helps students recognize their own personal impact on microplastic pollution and identify ways to reduce their creation of microplastics.

The five Phanerozoic mass extinctions were central in shaping biodiversity on Earth today. Due to increasing biodiversity losses, there is debate about whether we are currently undergoing a sixth mass extinction. To help students better understand these issues and explore the ongoing debate, we developed a lesson that uses active learning approaches including small-group work, poll questions, and whole-class discussion. This lesson provides an overview of major events in Earth’s history, an introduction to extinction and mass extinction, and past and present conservation efforts. Students were assessed using two short take-home assignments, in-class poll questions, and quiz questions. Here we provide detail about the lesson and summarize student performance on the assessments.

Primary image: This image was adapted from work shared under a Creative Commons License (https://commons.wikimedia.org/wiki/File:Nature_timespiral_vertical_layout.png)

In this module, students will be investigating a louse gene with an unknown function to determine if it might be important in the evolution of the louse ecomorphs.

Growth Mindset presentation

In this Lunch with a Scientist episode, we discuss Genome Sequencing and Bioinformatics with National Institute of Standards and Technology (NIST) biologist Nate Olson, Ph.D.

Genetics is a fascinating topic of biology. Establishing relevance is a key component of student learning. To increase learning, this resource includes summaries and teaching guides for integrating four different podcasts into a genetics course. Lecturing through podcasts has been shown to be received well by students and improve their understanding of concepts. Using podcasts to provide context and significance to a course would further enhance their learning and interest in the course.

Biomolecular structure and function is emphasized as a core concept in a variety of community determined educational standards for biology and chemistry. Most curricula introduce students to the building blocks and principles of biomolecular structures, in introductory chapters of biology, biochemistry, cell biology, and chemistry courses, but very few engage students in actively visualizing and exploring biomolecular structures throughout the course. Conversations with faculty teaching introductory courses, and/or developing and piloting molecular case studies, helped uncover the need for new resources, and professional development to support introduction of biomolecular exploration. To address this need, a group of faculty participating in a Faculty Mentoring Network in Spring 2022, gathered together resources and lessons that they had independently developed and collaboratively developed additional ones. An overview of the lessons will be presented here. Interested users are invited to pilot the lessons in Fall 2022.

This resource pairs DNA barcoding databases with Biodiversity databases. Students collect their insect specimens in the field and use BLAST and BOLD to identify their species. They then use biodiversity databases to obtain information on the species' distribution, recently submitted observations, and life history stage.

The exploitation of African elephants in the form of ivory poaching is exacerbated by warfare. The affects of this anthropogenic evolutionary force on the African savanna elephant (Loxodonta africana) in the Gorongoas National Park in Mozambique was investigated (Campbell-Staton, et. al. 2021) after the Mozambican civil war (1997-1992).  This multipart lesson is based on this research.  Here, we explore allele frequencies, phenotypic data, and the use of a chi-squared test to determine if the population is in Hardy-Weinberg Equilibrium.  Because one gene influencing tusklessness is X-linked, we also explore inheritance of the trait, using hemophilia as an example.  The data used in this part of the lesson are simulated data based on reports from Zambia.

Teach a Course-based Undergraduate Research Experience (CURE) using digitized natural history collections data to test hypotheses on sexually dimorphic wing melanization patterns of Pieris rapae butterflies. This inclusive CURE can be implemented in in-person, online, and hybrid formats, synchronously or asynchronously, and requires only student access to a computer and the internet.

For the Fall 2022 BIOME Working Group, we have developed a plug-and-play CURE model that will allow educators to pick and choose CURE resources, centered on microbial diversity and ecology, to allow students to learn the process of science, specific methods, and science communication. Students will be able to publish original data to the OneHealth Initiative and other databases. The resources will be further developed in a Spring 2023 FMN, to expand the model of a plug-and-play CURE.

This interdisciplinary pedagogical case study focuses on differences between rural and urban coyotes at the levels of organismal and community ecology, including how their gut microbiomes could affect their behaviour. The health and fitness of rural and urban coyote populations vary dramatically with the latter being poor as a result of their consumption of carbohydrate-rich anthropogenic food, compared to a more natural protein-rich diet. This difference is associated with altered gut microbiome composition. The case explores how altered microbiomes can influence behavior changes through the gut-brain axis. Cross talk between the brain and gut microbiome involves multiple physiological systems including the immune, endocrine, and nervous systems. This case showcases the interdisciplinary nature of science by having students explore the connection between these macro and micro-level systems. It is based on a manuscript by Sugden et al. (2020) supporting the existence of distinct gut microbiomes in rural and urban coyotes. Interdisciplinary connection - Immunology+Microbiology+Ecology+Animal Behavior

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.

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.

Hands-on research experiences are important opportunities for students to learn about the nature of inquiry and gain confidence in solving problems. Here, we present an inquiry-based lesson plan that investigates the foraging behavior of sciurid rodents (squirrels) in local habitats. Squirrels are an ideal study system for student research projects because many species are diurnal, easy to watch, and inhabit a range of habitats including college campuses. In this activity, instructors identify appropriate field sites and focal species, while students generate questions and brainstorm predictions in small groups regarding factors that might influence behavioral trade-offs in sciurids. Students conduct observational surveys of local squirrels in pairs using a standardized protocol and upload their data to a national database as part of the multi-institutional Squirrel-Net (http://squirrel-net.org). Instructors access the nationwide dataset through the Squirrel-Net website and provide students with data for independent analysis. Students across the country observe and record a range of squirrel species, including behaviors and habitat characteristics. The national dataset can be used to answer student questions about why squirrels behave in the way they do and for students to learn about authentic analyses regarding behavior trade-offs. Additionally, the lesson is designed to be modified across a range of inquiry levels, from a single two-hour laboratory activity to a unit- or semester-long student-driven course-based research experience. Our activity highlights the value of using observational data to conduct research, makes use of the Squirrel-Net infrastructure for collaboration, and provides students equitable access to field-based projects with small mammals.

Primary image: Students observe squirrel behaviors on the campus of Colorado Mesa University.

Additional Squirrel-Net Articles:

• An Introduction to the Squirrel-Net Teaching Modules
• ​Sorry to Eat and Run: A Lesson Plan for Testing Trade-off in Squirrel Behavior Using Giving Up Densities (GUDs) 
• How Many Squirrels Are in the Shrubs? A Lesson Plan for Comparing Methods for Population Estimation
• Squirrels in Space: Using Radio Telemetry to Explore the Space Use and Movement of Sciurid Rodents
• Squirreling from Afar: Adapting Squirrel-Net Modules for Remote Teaching and Learning
   

With the publishing of the Vision and Change report, we know it is best practice to include authentic research experiences in our undergraduate science lab classes. One big challenge in teaching so-called "wet lab" classes is figuring out a way to make sure students come to lab prepared to successfully complete their experiments. Molecular biology protocols are particularly challenging as they are typically long, detailed, and have multiple steps to complete. The most successful teaching practice I have tried is having students prepare for lab by hand-drawing flowcharts of the lab protocols. Drawing is a proven way to increase scientific understanding and requires students to engage with the lab materials before class. These flowcharts are due when students walk in to lab and more importantly, students use their flowcharts during lab. This teaching tool is easy to teach to students, simple to assess, and does not rely on any pre-existing knowledge of molecular biology or artistic skill. I have had great success using flowcharts as a teaching tool in both upper division and lower division classes as well as with both life science major and non-major students. Flowcharts have many potential applications beyond undergraduate "wet lab" classes including discussion courses and graduate research projects.

The Inside and Outside the Body activity helps students develop a conceptual understanding of anatomical barriers such as skin and mucus membranes that separate internal cells and fluids from the external environment. This short exercise prepares students for lessons in both anatomy and physiology and reflects recommendations from policy documents that suggest teaching core concepts. Understanding processes such as absorption, gradients and flow, and body defenses relies on the core concept of anatomical barriers. Instructors can use the concepts taught in this activity in subsequent discussions of topics such as immune tolerance of the fetus, the devastating impact of burns, and the sites of gas exchange.

With the publishing of the Vision and Change report, we know it is best practice to include authentic research experiences in our undergraduate science lab classes. One big challenge in teaching so-called "wet lab" classes is figuring out a way to make sure students come to lab prepared to successfully complete their experiments. Molecular biology protocols are particularly challenging as they are typically long, detailed, and have multiple steps to complete. The most successful teaching practice I have tried is having students prepare for lab by hand-drawing flowcharts of the lab protocols. Drawing is a proven way to increase scientific understanding and requires students to engage with the lab materials before class. These flowcharts are due when students walk in to lab and more importantly, students use their flowcharts during lab. This teaching tool is easy to teach to students, simple to assess, and does not rely on any pre-existing knowledge of molecular biology or artistic skill. I have had great success using flowcharts as a teaching tool in both upper division and lower division classes as well as with both life science major and non-major students. Flowcharts have many potential applications beyond undergraduate "wet lab" classes including discussion courses and graduate research projects.

This is a presentation highlighting some issues at the intersection of STEM, Open, and Social Justice. The audience is STEM education professionals and professional developers. The presentation was originally given at SERC in February 2023.

Survey findings for the learning community (LC), Social Justice Dialogues in STEM Ed, facilitated by Drs. Bryan Dewsbury (Florida Institute of Technology) and Desiree Forsythe (Rochester Institute of Technology) – with support from Dr. Kaitlin Bonner (St. John Fisher College). The LC included five synchronous sessions from April 6th through May 31st, aimed to explore difficult dialogues of social inequities in STEM classrooms using short readings, discussions, and mini-workshops.

Hands-on research experiences are important opportunities for students to learn about the nature of inquiry and gain confidence in solving problems. Here, we present an inquiry-based lesson plan that investigates the foraging behavior of sciurid rodents (squirrels) in local habitats. Squirrels are an ideal study system for student research projects because many species are diurnal, easy to watch, and inhabit a range of habitats including college campuses. In this activity, instructors identify appropriate field sites and focal species, while students generate questions and brainstorm predictions in small groups regarding factors that might influence behavioral trade-offs in sciurids. Students conduct observational surveys of local squirrels in pairs using a standardized protocol and upload their data to a national database as part of the multi-institutional Squirrel-Net (http://squirrel-net.org). Instructors access the nationwide dataset through the Squirrel-Net website and provide students with data for independent analysis. Students across the country observe and record a range of squirrel species, including behaviors and habitat characteristics. The national dataset can be used to answer student questions about why squirrels behave in the way they do and for students to learn about authentic analyses regarding behavior trade-offs. Additionally, the lesson is designed to be modified across a range of inquiry levels, from a single two-hour laboratory activity to a unit- or semester-long student-driven course-based research experience. Our activity highlights the value of using observational data to conduct research, makes use of the Squirrel-Net infrastructure for collaboration, and provides students equitable access to field-based projects with small mammals.

Primary image: Students observe squirrel behaviors on the campus of Colorado Mesa University.

Additional Squirrel-Net Articles:

• An Introduction to the Squirrel-Net Teaching Modules
• ​Sorry to Eat and Run: A Lesson Plan for Testing Trade-off in Squirrel Behavior Using Giving Up Densities (GUDs) 
• How Many Squirrels Are in the Shrubs? A Lesson Plan for Comparing Methods for Population Estimation
• Squirrels in Space: Using Radio Telemetry to Explore the Space Use and Movement of Sciurid Rodents
• Squirreling from Afar: Adapting Squirrel-Net Modules for Remote Teaching and Learning
   

using NEON data with R

Ibuprofen

In this activity, students are introduced to phylogenetic trees and networks as tools for analyzing evolutionary relationships.

Educational games are one active and effective way of engaging students with material while also providing additional motivation to tackle challenging concepts. A particularly popular game concept is the escape room, where students need to work in groups to solve a series of puzzles to prevent disaster from occurring in an imaginary universe, all within a specified amount of time. This paper presents a general guide to constructing an escape room for undergraduate classrooms. Unlike many recently published educational escape rooms, this template does not use any laboratory-based components, making it widely applicable to any class and any level, although it will be most easily adapted to classes that do include analytical components. The puzzles in the game escalate from remembering and understanding concepts to applying and evaluating techniques and data. Unlike many other games and puzzles, an escape room does not reveal the final answers until the allocated time is up, which forces students to work through challenging questions and find solutions within their group to advance in the game. The game provides students many instances for formative assessment and encourages helpful discussions surrounding misconceptions and core course content while they escalate through the challenges.

Estimating the population sizes of animals is a key skill for any student interested in ecology, conservation, or management. However, counting animals in natural habitats is difficult, and the many techniques that exist each rely on assumptions that can bias results. Most wildlife courses teach one or two of these methods, but rarely are students given an opportunity to compare approaches and explore how underlying assumptions affect the accuracy of estimates. Here, we describe a hands-on activity in which students estimate the size of a single population of animals using multiple methods: strip censuses, scat counts, and camera traps. They then compare the estimates and evaluate how the assumptions of each model (e.g., random use of habitats and animal behavior) bias the results. Finally, students submit their data to a national database that aggregates observations across multiple institutions as part of Squirrel-Net (http://squirrel-net.org). They can then analyze the national dataset, permitting exploration of these questions across a broader variety of habitats and species than would be possible at any single institution. Extensions of this activity guide students to enumerate the advantages and disadvantages of each method in different contexts and to select the most appropriate method for a given scenario. This activity and the database focus on estimating population sizes of squirrels, which are diurnal, charismatic, easily identified, and present in a wide range of habitats (including many campuses), but the same methods could be broadly used for other terrestrial species, including birds, amphibians, reptiles, or invertebrates.

Primary image: Students estimate the population density of small mammals in a natural area near Grand Junction, CO.

Additional Squirrel-Net Articles:

• An Introduction to the Squirrel-Net Teaching Modules
• Squirreling Around for Science: Observing Sciurid Rodents to Investigate Animal Behavior
• Sorry to Eat and Run: A Lesson Plan for Testing Trade-off in Squirrel Behavior Using Giving Up Densities (GUDs)
• Squirrels in Space: Using Radio Telemetry to Explore the Space Use and Movement of Sciurid Rodents
• Squirreling from Afar: Adapting Squirrel-Net Modules for Remote Teaching and Learning

Despite increased awareness of the lack of equity and inclusion in the STEMM classroom, lessons on DEI topics are treated as separate to the scientific curriculum being taught. Rarely are intentional reflections and conversations on the lack of representation integrated into the lessons themselves. This lesson, titled “Discovery and Invention”, was developed to guide students through an exploration of the history of a topic—in this case, fermentation—followed by reflections and discussion on the culture of science and how it highlights certain individuals over others. Reflections allow students to explore and discuss their own scientific self-identity and sense of belonging in science. This fermentation lesson was designed to be integrated into a unit introducing students to microbial ecosystems, but it can be adapted for other topics as well, to suit the instructor’s needs.

Primary Image: Rosalind Franklin with microscope in 1955. MRC Laboratory of Molecular Biology. Creative Commons Attribution-Share Alike 4.0 Downloaded from commons.wikimedia.org on November 1, 2021 by authors.

This could be used in conjunction with nature serve tool?

First publication to mark launching of BRISCLab. The outcomes from the catalyst project will be shared first.

Teach a Course-based Undergraduate Research Experience (CURE) using digitized natural history collections data to test hypotheses on sexually dimorphic wing melanization patterns of Pieris rapae butterflies. This inclusive CURE can be implemented in in-person, online, and hybrid formats, synchronously or asynchronously, and requires only student access to a computer and the internet.

Use ImageJ to analyze morphological characters in digital images of natural history specimens. Skills are transferable to many organisms and other morphological measurements.

Students in non-majors’ biology courses may not choose careers that require biology content knowledge; however, all will encounter science in their lives. We redesigned a non-majors introductory biology course to support students in considering the importance of biology in their own lives. Our intent was to provide students with skills to engage in scientific reasoning, apply biological concepts, and increase their interest in the subject. One of the components we created to achieve these goals was a series of three Real World Scenarios (RWS). These RWSs consisted of existing case studies to which we added structured group discussion and individual reflection papers. These elements allowed students to grapple with a complex topic with peers, be exposed to viewpoints different from their own, and then have time to reflect and consider their own thoughts before they made an individual decision. We implemented these RWSs in both the face-to-face (F2F) and online sections. Students in both sections reported finding the assignments useful to help them connect the science to their own lives and appreciated the opportunity to interact with their peers and be exposed to differing viewpoints. We provide information on how we set up the assignment and provide suggestions for additional improvements.

Primary Image: The image depicts students engaged in a classroom discussion (obtained through Microsoft Word Stock Images).

Cellular respiration is a daunting topic for many students in introductory biology courses. Students are challenged at conceptual and factual levels, since instruction covers multiple metabolic pathways occurring across different cellular compartments, involving abstract energy and electron transfers through diverse chemical reactions. Lecture-based instruction may clearly convey details of cellular respiration to students, but the complexity of this topic suggests alternative, active learning strategies may improve student comprehension and retention. I designed an original board game as a teaching tool for cellular respiration, targeted at improving learning outcomes for advanced high school, introductory undergraduate, and upper-level undergraduate biology students. “Aerobic Respiration: The Board Game” applies multiple learning strategies (quiz questions, student-completed study table, visual, tactile and quantitative learning, and game-play) with the goal that students are simultaneously entertained and invested in understanding this complex topic. Initial application in a small undergraduate introductory biology section (ca. 25–30 students) suggested improved student understanding of some aspects of cellular respiration. Use in a longer class or lab period and simplification of game board design and instructions should improve effectiveness of the game. Students had significantly favorable perceptions of the game as a learning tool. Included game board and game cards are provided to reflect multiple student academic levels, and are fully editable. Ordering information for materials and game pieces is also included.

Primary Image: Example setup for Aerobic Respiration: The Board Game.

There are few feasible models for marine-focused inquiry laboratory activities, a notable shortcoming for instructors seeking to engage their students in meaningful, course-based research experiences (CUREs). We describe a multi-week CURE that investigates the symbiosis between hermit crabs and the hydrozoan Hydractinia spp. Although much is known about hermit crab biology, ecology, and behavior, little is known about Hydractinia, and less is known about the relationship between the two symbionts. Given their small size, low cost, and relative ease of maintenance, colonized hermit crabs may be useful subjects for student-driven research projects. We discuss our experiences with this system and offer adopters a suite of resources for in-lab implementation.

Organismal life cycles are often presented as a set of facts to memorize in undergraduate biology courses. This approach is cognitively demanding for students and fails to convey how central life cycle diversity is in shaping ecological and evolutionary processes. Understanding the causes and consequences of life cycles is especially important when studying parasites with multiple life cycle stages for passing through diverse hosts. We designed a two-part lab activity to help our students gain a better understanding of the ecological interactions driven by parasite life cycles. Part I is a structured guide to reading a peer-reviewed journal article. Part II is a guided exercise in summarizing and interpreting mock experimental data involving a trematode parasite life cycle. These assignments helped students (1) understand how parasite life cycles shape ecological interactions with their hosts, (2) practice making predictions about species interactions using core ecological principles, and (3) practice quantitative reasoning and graph literacy skills by visualizing and interpreting data. We first used this activity as a self-guided lab exercise for an upper-division undergraduate parasitology class that switched from in-person to asynchronous-remote mid-semester. The stepwise structure of the activity allowed us to pinpoint the links in the chain of biological reasoning where students struggled most to guide target topic reviews in subsequent lectures. Here, we provide a summary of the activity, our experience with the activity, and suggestions for adapting the activity for a synchronous-remote or in-person class.

Seafood Choices

Cellular respiration game

Genome search

The relationship between protein structure and function is a foundational concept in undergraduate biochemistry. We find this theme is best presented with assignments that encourage exploration and analysis. Here, we share a series of four assignments that use open-source, online molecular visualization and bioinformatics tools to examine the interaction between the SARS-CoV-2 spike protein and the ACE2 receptor. The interaction between these two proteins initiates SARS-CoV-2 infection of human host cells and is the cause of COVID-19. In assignment I, students identify sequences with homology to the SARS-CoV-2 spike protein and use them to build a primary sequence alignment. Students make connections to a linked primary research article as an example of how scientists use molecular and phylogenetic analysis to explore the origins of a novel virus. Assignments II through IV teach students to use an online molecular visualization tool for analysis of secondary, tertiary, and quaternary structure. Emphasis is placed on identification of noncovalent interactions that stabilize the SARS-CoV-2 spike protein and mediate its interaction with ACE2. We assigned this project to upper-level undergraduate biochemistry students at a public university and liberal arts college. Students in our courses completed the project as individual homework assignments. However, we can easily envision implementation of this project during multiple in-class sessions or in a biochemistry laboratory using in-person or remote learning. We share this project as a resource for instructors who aim to teach protein structure and function using inquiry-based molecular visualization activities.

Primary image: Exploration of SARS-CoV-2 spike protein: student generated data from assignments I - IV. Includes examples of figures submitted by students, including a sequence alignment and representations of 3D protein structure generated using UCSF Chimera. The primary image includes student generated data and a cartoon from Pixabay, an online repository of copyright free art. 

Students will learn about infectious disease and the immune response to infection by investigating different types of tests (PCR, antigen, and antibody tests) to detect the SARS-CoV-2 viral genetic material, antigens, or anti-SARS-CoV-2 antibodies. In the activity, students will apply core concepts and competencies from Vision & Change (https://visionandchange.org/). The activity uses a jigsaw format, with students choosing one of three specialities (epidemiologist, infectious disease doctor, or immunologist) and completing an assignment, either in-class or as homework, based on their speciality. In groups, students first hold a conference by speciality, then teams with representatives from each speciality discuss possible conclusions using results from the three different tests for a hypothetical patient.

To complement AbleWeb BRCA1 activity

Most molecular biology and biological sciences students understand that the polymerase chain reaction (PCR) is used to amplify DNA. However, we have found that some students experience conceptual misunderstandings, a lack of detailed comprehension of the PCR process, or difficulties with troubleshooting and predicting the effects of alterations to the standard PCR process. We hypothesized that a problem-based learning approach that incorporates a kinesthetic modeling of the PCR process could address these problems. During this hands-on learning activity, students “amplified” a specific region of template DNA through three cycles of PCR using a “toolkit” composed of a) intertwined, supercoiled, and double-stranded yarn representing template DNA, b) short wax sticks representing primers, and c) long wax sticks representing the PCR products. Instructors can introduce a variety of assessments, including real-time image capture of the models, pre- and post-activity assessment quizzes, and homework assignment to gauge student learning. We administered identical four-question quizzes worth 12 points to 28 undergraduate students before and after the activity. The mean score on the post-quiz was three points higher than the pre-quiz score, demonstrating a 75% increase in score. Moreover, we found that students who began the activity with lower levels of understanding experienced the most significant learning gains. This hands-on, student-centered, kinesthetic activity allowed students to (i) visualize PCR processes, (ii) construct a model of the PCR process, (iii) correct common misconceptions and sources of confusion, and (iv) actively engage in the learning process.

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.

Some concepts in genetics, such as genetic screens, are complex for students to visualize in a classroom and can be cumbersome to undertake in the laboratory. Typically, very large populations are needed, which can be addressed by using micro-organisms. However, students can struggle with phenotyping microbes. For macroscopic organisms, the number of offspring produced, and the generation time can be challenging. I developed this lesson as a small-scale genetic screen of Fast Plants^®. These plants are amenable to teaching labs as they have simple growth requirements, a short generation time, and produce numerous seeds that can be stored for years. Seeds used for this screen are purchased pre-treated with a DNA damaging agent, removing the need for in-house use of mutagens. Also, students can screen the phenotypes without specialized equipment. The initial lesson begins with an examination of the first generation of plants. Later their offspring are screened for altered phenotypes. Students responded well to having full-grown plants available on the first day of the lab project. This lesson fostered student collaboration, as they worked with class datasets. Differences in growth due to mutagenesis treatment in the first generation were clear to students who had not worked with plants before. Identifying plants with altered phenotypes in the next generation was more of a challenge. This lesson incorporates key concepts such as somatic and germline mutations, the impact of such mutations on phenotype, and the inheritance of mutation alleles, and provides a hands-on way to illustrate these concepts.

Primary Image: Fast Plant^® phenotype differences observed in the M2 generation. This pot contains three full-sibling M2 seedlings from a single M1 parent plant. The seed of their parent plant received 50 Krads of radiation. Plants 1 and 2 are of standard height, while plant 3 is greatly elongated. Image by AL Klocko.