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).

Cell division is a key concept in cell biology. While there are many popular activities to teach students the stages of mitosis, most make use of simple schematics, cartoons, or textbook diagrams. Others engage students in acting out the stages, or modeling them with physical objects (i.e. noodles, pipe cleaners). These approaches are useful for developing student knowledge and comprehension of the stages of cell division, but do not readily convey the real-life processes of mitosis. Moreover, they do not teach students how cell biologists study these processes, nor the difficulties with imaging real cells. Here, we provide an activity to reinforce student knowledge of mitosis, demonstrate how data on mitosis and other dynamic cellular processes can be collected, and introduce methods of data analysis for real cellular images using research-quality digital images from a free public database. This activity guides students through a virtual experiment that can be easily scaled for large introductory classes or low-resource settings. The activity focuses on experimentally determining the timing of the stages of cell division, directing the attention of students to the tasks that are completed at each stage and promoting understanding of the underlying mechanisms. Before the experiment, the students generate testable predictions for the relative amount of time each step of mitosis takes, provide a mechanistic reason for their prediction, and explain how they will test their predictions using imaging data. Students then identify the stages of cell division in a curated set of digital images and determine how to convert their data into relative amount of time for each phase of mitosis. Finally, students are asked to relate their findings to their original predictions, reinforcing their increasing understanding of the cell cycle. Students praised the practical application of their knowledge and development of image interpretation skills that would be used in a cell biology research setting.

This module introduces the exponential growth of cells in the context of understanding cell division. It is intended for an introductory biology audience.

Authentic research experiences are effective in fostering self-efficacy and increasing retention in STEM, particularly among minoritized student populations. Many instructors have sought to bring these to a wide range of students in the form of course-based undergraduate research experiences (CUREs). However, implementing CUREs can be challenging, especially at under-resourced institutions. To introduce an authentic inquiry-based experience without increasing the monetary, time, or teaching resources needed, we converted an existing traditional laboratory exercise into an inquiry-based lab at California State University Dominguez Hills (CSUDH), a Hispanic- and minority-serving comprehensive university. This inquiry-based module allows students to use the scientific process while focusing on investigating factors influencing diffusion through a dialysis membrane. Students engaged in activities such as gathering preliminary data, formulating hypotheses, designing experiments, and analyzing results, which helped students to increase their self-efficacy. Although many inquiry-based labs have been adapted from “cookbook” type lab activities, this example uniquely discusses making these changes in an under-resourced, majority-minority university. Similarly designed modules that utilize existing resources and require minimal instructor expertise may be more accessible to a wider range of institutions, including those more similar to CSUDH, than traditional CUREs. We used a pre- and post-survey to demonstrate the efficacy of this approach in enhancing student understanding of scientific processes as well as increasing belonging among students from historically-minoritized groups. Here we provide insights and practical guidelines for incorporating inquiry-based labs in undergraduate biology education, particularly in under-resourced institutions serving diverse student populations.

Primary Image: Students were asked to plan an experiment to test a hypothesis based on diffusion through a dialysis tubing membrane. This group of students hypothesized that if they hydrolyzed starch using heat first, it would be able to move through the membrane. Although their hypothesis was not supported, they were able to complete a report including generating a figure. Student Figure Legend: FIG 1 Room Temperature Starch beaker contents & Heated Starch beaker contents. The Iodine Test shows a negative result/no reaction.

Lecture-Free Classroom

Traditionally-trained undergraduate students often lack an understanding of science as an active process that yields the information presented in their textbooks. One result has been a call for more research experiences built into traditional introductory undergraduate courses, now commonly referred to as course-based undergraduate research experiences (CUREs). The laboratory module presented in this paper used an established four-step pedagogical framework to simplify and streamline the development and implementation process of a CURE in an introductory biology laboratory setting. A unique six-week CURE was designed for undergraduates enrolled in a cell biology lab that employs Saccharomyces cerevisiae as a eukaryotic model organism. Students address a research problem that is of interest to the scientific community: Do select chemicals in the environment have adverse effects on the mitotic cell division? Students are first introduced to S. cerevisiae, its life cycle, morphology, growth curve generation and analysis, and the laboratory techniques required to cultivate this organism. Working in groups, students then act as scientists to research primary literature, ask an original question, develop a testable hypothesis, collaborate with peers, design and conduct an experiment, analyze and interpret data, and present their work to their peers. In addition, students are involved in multiple levels of iterative work, including addressing problems or inconsistencies, ruling out alternative explanations, and/or gathering additional data to support assertions.

Cell Project

Photosynthesis is a process by which plants synthesize glucose and oxygen in presence of sunlight through light dependent reactions by utilization of sunlight, water to synthesize oxygen, ATP and NADPH and light-independent reactions to synthesize carbon dioxide and carbohydrates. Cellular respiration is a metabolic pathway that breaks down glucose through glycolysis, pyruvate oxidation, citric acid / Krebs cycle and oxidative phosphorylation. Primary producers produce energy and consumers derive energy from primary producers. Primary productivity is the accumulation of energy in form of biomass. Integrating biological science and mathematics helps to understand how differential regulation of factors impacting metabolic pathways and processes impact primary productivity.

Osmosis is a process by which by which solvent move from a region of lower solute concentration to region of higher solute concentration through a semi-permeable membrane. Cells utilize the process osmosis and osmotic pressure to transport substance in and out of the cell cytoplasm. Solution is made up of solute and solvent - concentration of a solution is the measure of the amount of solute that has been dissolved in a given quantity of solvent or solution. Spectrophotometer can be used to measure the optical density of the solution which relates to the change in concentration of the solution. As the concentration in any biological system will change the cells shape, size and number will change in that micro-environment.

Genetic Code

This Excel module explores how drugs are processed and absorbed in the human body.

CIVID-19 Model

SIR Modelling