Cellular respiration, a common topic among introductory and cellular biology curricula, is a complex biological process that exemplifies core biological concepts, including systems, pathways and transformation of energy, and structure and function relationships. Unfortunately, many students struggle to understand cellular respiration and its associated concepts. To help students with their understanding of cellular respiration, we developed a lesson that uses computational modeling and simulations through an on-line modeling platform, Cell Collective (learn.cellcollective.org). Computational models and simulations allow students to observe and influence the dynamics of complex biological systems not observable in static diagrams from textbooks. In our lesson, students explore different aspects of cellular respiration by making changes to the system. For each perturbation, students investigate the underlying mechanistic causes by iteratively predicting the mechanism, testing their prediction with simulations, interpreting and reporting on their findings, and reflecting upon their prediction until they can accurately describe the underlying mechanism. Because the lesson is self-contained and requires little guidance from the teacher, the lesson can be implemented in a wide-variety of settings without the need for many changes to existing curricula.

While there are several available lessons for teaching introductory biology students about diffusion, facilitated diffusion, and active transport, fewer materials exist to support upper-division students' understanding of the proteins that mediate these forms of transport. In the 1970s, mitochondrial pyruvate carrier (MPC) proteins were predicted to import pyruvate from the cytoplasm into mitochondria for cellular respiration. Yet it was not until 2012 that the identity of the proteins responsible for this transport was confirmed in two seminal publications. In this Lesson, students will use their background knowledge of transport mechanisms to analyze data from those papers to determine which of the predicted MPC proteins are actually part of the mitochondrial pyruvate transporter. Student will also learn how scientists test whether a protein is necessary and sufficient. The Lesson is written in the style of process-oriented guided inquiry learning (POGIL). POGIL is a teaching approach that requires students to work collaboratively in small groups to answer a set of questions based on scientific data. Questions in the POGIL activity, called the problem set, are structured so that each question leads to the next, helping to guide students to a deeper understanding of the content. During this Lesson, the instructor acts as a facilitator to guide student learning. Several forms of assessment are included within the Lesson, allowing instructors to assess learning gains. This Lesson has been used multiple times by over 10 faculty in an upper-division Cell Biology course and can also be used in other upper-division biology courses.

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. 

Photosynthesis is a conceptually challenging topic. The small scale at which photosynthesis takes place makes it difficult for students to visualize what is occurring, and students are often overwhelmed by all of the details of the process. This activity uses a freely-available comic to make learning photosynthesis more approachable and to help students identify their own misconceptions and questions about the process. This activity is appropriate for any college-level introductory biology course and although it was designed for an online class, it could be adapted for in-person learning. In this activity, students work through a four-part online module. Each part consists of readings and videos containing background information on the steps of photosynthesis followed by the corresponding portion of a comic on photosynthesis. Students then use the background information in the module and the comic to identify their own misconceptions and questions and post these in an online discussion forum. The online module is followed by a live session in which the instructor uses the student discussion posts to clarify any remaining questions. Learning about photosynthesis in the unique visual format of a comic allows students to more easily visualize a process that they cannot see with their own eyes. Students enjoyed this activity because it makes learning photosynthesis fun and less intimidating. This lesson is powerful because it allows the instructor to hear from all students in the course via the discussion forum and then tailor the live discussion session to cover student identified problem topics.

Primary Image: Overview of photosynthesis comic. This image comes from Jay Hosler’s comic Photosynthesis or “gimme some sugar” (© 2020 Jay Hosler, used with permission from the author).

Materials created for an upper level ABM course. Prerequisite: Students have taken either (a) another modeling course, or (b) the introductory computer science sequence.

Students access NOAA data to conduct an analysis to look at differences between locations in heat stress and ultimately the amount of coral bleaching in 2005

This module assesses the role of wildfire in the eastern US and its impact on bird communities using NEON bird survey data from pre- and post- a major wildfire in the Great Smoky Mountains National Park (GRSM) in November 2016.

A participatory live-coding lesson on working with NEON phenology data and fitting a sine-wave model to determine when different species get and lose their leaves.

These are the materials for Math 214 offered at Rhodes College.

Students evaluate long term (100+ years) trends in temperature and precipitation, and then isolate a shorter time span (20 years) in which to evaluate the correlation between spring temps and the earliest reported calling dates for MN frogs and toads

Use the calling bull course to introduce students to data, ethics, visualization, and R.

We describe Presentation Enhanced Learning (PEL), a flexible, lecture-free, field-tested teaching format to promote problem-based, active learning in upper-division or graduate biological sciences courses.  PEL may be implemented as a single, capstone event or as the organizing principle for an entire course.  In a PEL module, the lectures are replaced by student-led presentations created by their own backward design process and mapped to Bloom’s taxonomy.  Each presentation includes explicit assessment activities aligned with student learning outcomes (SLOs).  The instructor acts as a facilitator and guide inside and outside of class. Feedback concerning accuracy and the level of content coverage for each subject is provided by instructor via small groups meetings (before and after students deliver their in-class presentations).  This interactive time replaces instructor time devoted to traditional lecture preparation.  In our experience, these meetings initially last approximately three hours per week for courses that contain up to six groups of two to five students, with one group presenting per week.  The length of the meetings drops by approximately half, and the quality of the discussions and feedback improves, once students become familiar with the presentations style.  Assessment of student learning outcomes occurs through take-home exams, in-class assignments and assessment activities, individual and group presentation scores, and peer evaluation.  Specific grading rubrics, available to students in advance, guide all assessment scoring.  We have converted two entire lecture courses to a PEL format, resulting in increased critical thinking skills as determined by student answers to exam questions mapped to Bloom’s taxonomy.

This data module examines the relationship between mosquito vector ecology and climate across the east coast of the United States. The module is designed to merge core concepts in ecology with budding interests of the largely pre-heath student body.

Students will use data published by the World Health Organization to model the 2014 outbreak of the Ebola virus in West Africa. We begin with a simple exponential growth model and move through the modeling process to the logistic growth model.

Students will learn how to set up a population matrix model in R and use it for demographic analysis of a population, including projecting population growth, determining lambda and the stable age distribution, and conducting an elasticity analysis.

Students use small mammal data from the National Ecological Observatory Network to understand necessary steps of data management from data collection to data analysis by estimating small mammal population sizes using the Lincoln-Peterson model.

This 50 minute lecture on long-read sequencing technology covers the following items: 1) Review of RNA-Seq Short-read Sequencing, 2) Overview and benefits of Long-read Sequencing, 3) Oxford Nanopore Sequencing, and 4) Pacific Biosciences Sequencing.

The purpose of this semester-long Lesson is to give students an authentic, course-based undergraduate research experience during which they learn basic and advanced microbiological and molecular biology techniques. This project begins with the isolation of a suspected Streptomyces bacterium from a soil sample and concludes with its identification. Students collect data, regarding colony and cell morphology, biochemical characteristics, the production of secondary metabolites, and employs the PCR using custom-designed primers to the Streptomyces 16s rRNA gene. The project culminates with the identification of their soil isolate using the National Center for Biotechnology Information (NCBI) web site to perform nucleotide blasts. The blastn program provides the final piece of evidence used to confirm, or not, the identification of their isolate as a Streptomyces from 16s rRNA gene sequence data, hence the title “From Dirt to Streptomyces DNA. In addition, the Lesson focuses on the Streptomyces bacteria to address several ASM aligned goals and objectives. These include prokaryotic growth phases and ways in which interactions of microorganisms among themselves and with their environment is determined by their metabolic abilities.  In addition, this Lesson illustrates how microbial metabolism is important to a relevant societal issue, the need for new antibiotic discovery particularly given the rise of antibiotic resistance strains of clinically relevant bacteria. It also illustrates the microbial diversity of soil and the developmental/physiological strategies employed in such a competitive environment. This Lesson hopes to impart both the thrill and challenges associated with scientific discovery.

Primary image: Photomicrograph of Streptomyces colonies growing on ISP 2 agar. The Streptomyces are student isolates showing stages of morphological development. Photomicrograph by Marc A. Brodkin.

The students will analyze the human gut and vaginal microbiomes in healthy and diseased states using diversity of bacteria as determined by 16SrRNA sequence.

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

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

This interactive assignment engages students in a hands-on exploration of microbial diversity and the importance of microbes in ecosystems. Designed for General Biology II and Introduction to Microbiology courses, the activity accommodates class sizes of 10-30 students. Within a 55-minute class period, students work in groups to research, analyze, and present various microorganisms. This guide includes detailed steps for instructors, a student worksheet, a PowerPoint presentation with microbial images, and quizzes to assess student learning.

Students develop scatter plots of growth rings by tree diameters and determine the equation of their best fit line.

Students use published scientific data to determine which types of nanoparticles would be best to use to deliver cytotoxic drugs directly to cancer cells. Then they learn about the scientist who generated the data.

This classroom modeling project applies mathematical techniques to solve a problem related to drug dosage patterns. Suitable for high school or undergraduate students. Prerequisite: Calculus I.