As biology becomes more data driven, teaching students data literacy skills has become central to biology curriculum. Despite a wealth of online resources that teach researchers how to use R, there are few that offer practical laboratory-based exercises, with teaching resources such as keys, learning objectives, and assessment materials. Here, we present a modular set of lessons and lab activities to help teach R through the platform of RStudio. Both software applications are free and open source making this curriculum highly accessible across various institutions. This curriculum was developed over several years of teaching a graduate level computational biology course. In response to the pandemic, the class was shifted to be completely online. These resources were then migrated to GitHub to make them broadly accessible to anyone wanting to learn R for the analysis of biological datasets. In the following year, these resources were used to teach the course in a flipped format, which is the lesson plan presented here. In general, students responded well to the flipped format, which used class time to conduct live coding demos and work through challenges with the instructor and teaching assistant. Overall, students were able to use these skills to practice analyzing and interpreting data, as well as producing publication quality graphics. While the modules presented range from very basic, doing simple summary statistics and plotting, to quite advanced, where R is integrated onto the command line, teachers should feel free to pick and choose which elements to incorporate into their own curriculum.

Primary Image: R‐Mini‐Course: An Introduction to R. The primary image was generated with BioRender to be a small representation of the applicability of R that we cover in our course.

Scientists have the tools and knowledge to develop safe, effective vaccines, from trials to vials. This resource addresses the process by which vaccines are designed, tested and regulated. Key concepts include 1. Mechanisms of immune recognition for SARS CoV 2 2. Vaccines vs therapeutics 3. Vaccine types and sources - nucleic acid, viral vector and attenuated/inactive vaccines 4. Vaccine development pipeline 5. Exploratory research and vaccine design for SARS-CoV-2 - spike protein target 6. Vaccine production 7. Testing and clinical trials 8. Challenge trials 9. Regulatory review and approval

In this lesson, students interpret a map of species occurrences. Then, students view and reflect on an interview with biologist Dr. Jennifer Dean, whose research includes the map that they interpreted.

An introduction to the Scientific Method for Introductory Biology students using plant and animal richness and environmental data from ephemeral ponds and permanent wetlands.

PhyloCards are educational trading cards that teach people about biodiversity, conservation, and ecosystem relationships. We used this educational tool to explore the Wissahickon Valley's biodiversity in Philadelphia, PA, and to engage our college students in learning more about our local species and environmental issues. This activity aims to teach about native and non-native species, food chains, and the human impact on the local ecosystem. The game integrates core ecological concepts like biodiversity and species interactions while touching on human-environment interactions.

This activity picks up from Module 1 where students chose the plant they wanted to represent their botanical history. In that module, they each identified their plant’s family and were given its scientific name. Module 2 provides students with an overview of the four major groups of land plants (bryophytes, ferns and allies, gymnosperms, and angiosperms), as well as familiarizing students with organisms that are often mistaken for plants (e.g., fungi, lichens, algae). Students will also be introduced to the Linnaean hierarchy as applied to major plant groups. Once students become familiar with plant characteristics and distinguishing features for major groups, they will be able to identify the group their own plant belongs to.

In order to introduce students to the concept of molecular diversity, we developed a short, engaging online lesson using basic bioinformatics techniques. Students were introduced to basic bioinformatics while learning about local on-campus species diversity by 1) identifying species based on a given sequence (performing Basic Local Alignment Search Tool [BLAST] analysis) and 2) researching and documenting the natural history of each species identified in a concise write-up. To assess the student’s perception of this lesson, we surveyed students using a Likert scale and asking them to elaborate in written reflection on this activity. When combined, student responses indicated that 94% of students agreed this lesson helped them understand DNA barcoding and how it is used to identify species. The majority of students, 89.5%, reported they enjoyed the lesson and mainly provided positive feedback, including “It really opened my eyes to different species on campus by looking at DNA sequences”, “I loved searching information and discovering all this new information from a DNA sequence”, and finally, “the database was fun to navigate and identifying species felt like a cool puzzle.” Our results indicate this lesson both engaged and informed students on the use of DNA barcoding as a tool to identify local species biodiversity.

Primary Image: DNA Barcoded Specimens. Crane fly, dragonfly, ant, and spider identified using DNA barcoding.

Speciation provides a framework for classifying biodiversity on Earth and is a central concept in evolutionary biology. To help undergraduate students learn about speciation, we designed a student-centered lesson that uses active-learning techniques (e.g., clicker questions, small group work, and whole class discussion) and compares multiple species concepts (morphological, biological, and phylogenetic) using giraffes as an example. Giraffes were chosen as the focus of this lesson because they are familiar and have broad appeal to students; are in danger of becoming extinct; and have ecological, economic, and cultural importance. Students also learn about contemporary giraffe conservation issues and the current debate in the literature regarding the total number of giraffe species. Students then apply their knowledge by working in small groups on speciation scenarios that highlight organisms across the tree of life. Student understanding is assessed using multiple-choice pre/post-test questions, in-class clicker questions with peer discussion, and exam questions. Here we provide details about the lesson and report that student learning is improved.

Prokaryote gene regulation: Lac

Hemocytometer

HeLa Cells

The goal of this article is to describe an active learning exercise that can be used in a variety of advanced microbiology courses, including bacterial physiology, ecology, or systems biology. The gut microbiome is a multi-species bacterial community that is impacted by outside factors, such as the food we consume or treatments with antibiotics, and impacts our health. In this active learning experience; students start with a simple 'pasta' simulation of a gut microbiome, adapted from a previously published lesson, where different types of pasta in a plastic bag simulate different bacteria in the gut and the composition of the pasta types is representative of diet related differences in the microbiome. Students will then mimic an antibiotic treatment by removing certain pasta/bacteria and replacing them with beans/different bacteria. Next, students will analyze the gut microbiome at the level of phylum, genus, or species. With the help of assigned scientific literature, students will learn how the composition of the gut microbiome responds to diet, a process that is accompanied by the synthesis of bacterial fermentation and other bacterial metabolic products that elicit a molecular response in the host intestinal cells. Students will gain an initial understanding of how these changes impact human health. Through this experience, students will increase their knowledge of bacterial metabolic pathways and products, improve their understanding of the complex community that constitutes the microbiome, analyze the microbiome at multiple systematic levels, and apply their knowledge in a context that is relevant to human health.

Contagious diseases are unavoidable realities of life. Thus, understanding pathogens and their respective diseases is important in many biological subfields including evolution, ecology, health sciences, microbiology, and others. While all college students will have encountered pathogenic diseases at some point in their lives, many will not have studied them in a classroom setting. As a result, students may not be able to accurately formulate a comprehensive definition of pathogenic disease on their own. Here, I provide an engaging activity where students construct a definition of pathogenic disease based on their lived experiences using the think-pair-share technique. Students are asked to define pathogenic disease individually, then in small groups, and finally as an entire class. At the end of this activity, the class will have agreed upon one definition for pathogenic disease. Following this, the students are asked to put their new definition into practice by completing a categorization activity where they must sort different diseases into the following categories: genetic, environmental, or pathogenic. This immediate application of new knowledge helps foster long-term learning. Students were highly engaged with the material, and this lesson also fostered a sense of classroom community as it encouraged students to share their knowledge while completing the categorization assignment. An end-of-term review activity showcased that the students were able to recall the information learned during this lesson at the end of the course. This lesson is easy to implement and can help students understand pathogenic disease in both introductory and advanced courses.

Primary Image: Think Pair Share! How to define pathogenic disease. Several desks are arranged in a circle. The question “How do you define pathogenic disease?” is written along the bottom. In the middle of the circle of desks there is a thought bubble with a symbol of people talking within it.

Lecture-based introductory biology courses are typically content-heavy as instructors strive to provide students with foundational knowledge in a broad range of topics.  One topic traditionally covered is cellular respiration, the series of enzymatic reactions that results in the formation of ATP, the energy currency in cells, from carbohydrates.  Cellular respiration is often difficult for students in these classes because the topic is both complex and ‘invisible’ – the students can’t observe the process.  In an attempt to overcome these difficulties and enhance student learning, we describe how the board game Mousetrap™ (Hasbro, Milton Bradley) can be adapted to model cellular respiration.  Mousetrap™ is ideal for this adaptation due to its 3-dimensionality, the necessary assembly of its 3D components and the interdependence of its 3D components. In the classroom, the pieces of the game are re-assigned into the three stages of cellular respiration (glycolysis, Krebs Cycle, electron transport chain); after each stage is discussed in lecture, students assemble that part of the board game.  By the end of class, the game is completely assembled, providing students with a workable model of the entire cellular respiration pathway.  Students then trigger the mousetrap to visualize the complete, dynamic process and ‘make ATP’ (i.e., catch the mouse).  Mousetrap™ serves as a dynamic, interactive, active learning tool that helps students build a basic, but accurate model for cellular respiration that can be used as a scaffold for subsequent upper-level courses or for more complex discussions related to fermentation, toxicology, and/or enzymatic regulation. 

Helping students understand where they should provide citations in research manuscripts is an essential aspect of training them in the responsible and ethical conduct of research. This Lesson comprises about 35 minutes of in-class work to help students learn how to avoid plagiarism. The Lesson is ideally integrated into a course in which a research report will be written. It introduces students to professional norms and explores the ethical “gray areas” surrounding the topic of citation. First, small student groups discuss case studies to reach a consensus on the question, “Is this plagiarism?” After a report-out to identify emergent themes, students then evaluate a paragraph from a published primary research manuscript and discuss why some sentences have citations and others do not. The choice of manuscript excerpt is flexible, based on teacher preferences and course subject area. This Lesson integrates critical instruction in research ethics that is applied to the science skill of communicating results. Student progress can be monitored using a summative homework-style assessment, in which students are tasked to determine which sentences in a paragraph should have citations and then to rank those sentences in order of how confident the group is that a citation is required. By the end of the Lesson, students have explored the definition of plagiarism and the ethical norms and processes for identifying when a citation is necessary.

Primary image: Text Duplication. Copying the work of others is plagiarism unless a proper citation is provided (copyright Joseph Ross).

Immunology is relevant to our everyday lives, driving a need for more engaging and inclusive undergraduate immunology education. One way to engage a diverse group of learners is by teaching them how to read and interpret the scientific literature. This introduction can be challenging for immunology research, which often includes jargon and significant background information. The lesson described here meets this challenge by first teaching students the basics of reading a journal article. Students then read a seminal research article in the field and discuss the data and conclusions via think-pair-share in the classroom. This lesson teaches students the overall structure of a journal article, how to read a journal article, and the ability to read and interpret a research article’s findings. Additionally, students learn specifically about the organization and expression of the genes encoding B-cell receptors.

Primary Image: Image portrays the computer a student will use to read the literature while thinking about the B-cell receptor (shown here in secreted form as antibodies). Image was created using BioRender.

This module contains exercises designed to help students understand how solute concentrations affect the direction and rate of osmosis. Students are given different scenarios to predict the direction of water movement, calculate the rate of change in mass and create graphs to determine the isotonic concentration.

The multistep nature of tumorigenesis is a foundational concept in the context of Cancer Biology. Many students do not appreciate the complex nature of cancer development nor do they understand how scientists are able to unravel the molecular pathways that lead to tumorigenesis. In this small group activity, students are presented with background information about the multistep nature of tumorigenesis and complete a priming activity that allows them to brainstorm and discuss experimental design. Students are then presented with data from the landmark manuscript, published in 1998 by Vogelstein et al., describing the first pathway of genetic alterations associated with colorectal tumor development. Using selected pieces of the manuscript, students answer discussion questions and analyze the data presented in the paper. Using their analysis, students are able to create a scientifically valid molecular model of colorectal development that matches the model presented in the literature. The group activity can be followed by a whole class discussion about current knowledge about colorectal tumor development.

Flow Cytometry

In this activity, students will explore the concept of binary fission, generation time, and bacterial growth curves, with an emphasis on the log phase. Students will use semi-log graphs and linear graphs to plot bacterial cell growth.

New stop-motion ‘candymation’ videos of mitosis and meiosis, plus Instructor Guides and problem sets.

Many undergraduate students receive little guidance on how to critically read, interpret data within, or present information from the primary scientific literature before they begin senior independent research experiences or enter professional or graduate school. To provide guidance on reading and formally presenting scientific information, I incorporated a two-part Journal Club Project into my 400-level developmental neurobiology class. In this project, students worked in teams throughout the semester to present primary scientific literature to the rest of the class and incorporate peer and instructor feedback into their work. Student work was facilitated by different grading rubrics for the two parts of the Journal Club Project. Each of these grading rubrics contained elements to guide the process of delivering and the presentation of scientific content within student talks. Here, I will provide a detailed description of and share my instructions and grading rubrics for the Journal Club Project.

Primary Image: Students delivering a journal club presentation. Two students incorporating peer evaluation feedback from a past talk into their final Journal Club Project presentation.

Visualizing kinetic processes can be an impediment to student mastery of basic science coursework. To remedy this obstacle, I created an educational program called Biology from Molecules to Embryos^© (BioME), which provides 28 animated lessons for genetics and embryology. To provide access to the international educational community, BioME has been posted as an interactive, open access website. Empirical data demonstrates that BioME is an efficacious educational resource, which elicits positive student perception of its utility. The animated lessons are useful for student self-study. For instructors who choose to display BioME lessons as visual aids for their presentations, explanatory text can be hidden so that it does not compete with the instructors’ verbal explanations. For instructors who would not choose to use premade lessons, downloadable excerpts are provided. These excerpts are short presentations of specific topics that can be incorporated at any point of a lesson according to the instructor’s preference and student needs. To provide opportunities for self-quizzing and to summarize key points, multiple PopUp files are provided for most lessons. To allow students to actively access their mastery of the material and to take advantage of the testing effect, multiple-choice practice questions are also provided with each lesson. The level of these questions ranges from first-order recall to third-order application. The higher order questions promote deep processing by requiring students to deduce answers by actively integrating material within and across lessons. Thus, BioME can help to advance the understanding of biological sciences and promote the usage of animations to present dynamic processes.

Primary Image: BioME Animations. Sequential images of ovulation represent the dynamic progressions of BioME animations.

This module introduces activities that allow students to walk through the cell cycle and mitotic cell division processes. As part of the activities, students learn about and apply knowledge of chromosomal behavior to identify different stages of mitotic cell division in plant and animal cells. They also calculate and compare mitotic indices for normally dividing and cancerous cells. Students apply quantitative and statistical concepts such as sample size, mean, standard deviation, and standard error of the mean to discuss the impact of sample sizes on interpretation of biological data (i.e., normally dividing and tumor cells, in this case).