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.

Students build on fundamental concepts of ecosystem production and carbon cycling, combining this knowledge with open long-term data from ecological and meteorological networks to uncover the environmental drivers of carbon fluxes.

Using a case study approach, this lesson examines colonialism as an ongoing force affecting nature, culture, and society by focusing on decades of tribally led efforts resulting in recent federal approval of four Klamath River dams. Chinook Salmon are not only endangered keystone species among the Pacific Northwest, but they also play invaluable roles to the communities that rely on them. Using the Four-Dimensional Ecology Education Framework (4DEE) combined with aspects of environmental sociology, this module encourages students to critically examine the causes and consequences of salmon population decline. Further, students will evaluate the decision-making involved in the largest dam removal by critiquing different stakeholder perspectives through a role-playing activity. With the conclusion of this module, students will recognize the opportunity imposed by climate change as a vehicle for social action and the integration of various forms of knowledge as a driver in making more equitable ecological decisions for our futures.

This module contains a sequence of activities designed for an undergraduate ecology lesson on stage-structured population models or life tables that use published data. Two versions are provided: Version A emphasizes stage-structured population models and asks students to construct matrix models using data from a common garden experiment with two locally-adapted subspecies the a biennial plant, Gilia capitata. Version B focuses on life tables and survivorship curves by comparing the Gilia capitata data with data on Bighorn sheep and Monk seals. Both versions contain an initial introductory activity and an optional follow-up activity in which students conduct a sensitivity analysis to determine effects of climate change (version A) or conservation scenarios (version B).

Use Part 1 for Discussion 4 in BIOL240 F2024

Students follow the steps of a tiny data science project from start to finish. They are given a research question "Are the number of cases of yellow fever associated with global average precipitation?" The students locate the data from the World Health Organization and Environmental Protection Agency, download it, and use the merged and cleaned data to see whether the evidence supports the hypothesis that yellow fever cases are higher in wetter than drier years. The activity is intended to be used early in a course to prepare introductory students to eventually explore their own questions.

Creating your own database is an excellent way for students to learn the trials and tribulations of data collection and management. Construction of three simple databases using a spreadsheet is described here and basic summary statistics are provided.

Social Justice Dialogues in STEM 2 is a resource to help facilitate conversations around various social contexts within STEM classroom.

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.

The goal of this article is to describe a variation of an active learning exercise that was previously published by the same author under a similar title. The variation describes modifications instructors can use to make the exercise suitable for online course delivery. The exercise is split into several parts. Part I is taught asynchronously via three consecutive videos. Part II is taught synchronously via Blackboard Collaborate Ultra (or similar). There is a follow up assignment that students do in groups as part III. The active learning exercise is a 'pasta' simulation of the gut microbiome. In the asynchronous part I of this exercise, students are virtually given a plastic bag/gut with different types of pasta/gut bacteria. Six different bags resemble the gut microbiome under six different diets. The instructor mimics an antibiotic treatment by removing two types of pasta/gut bacteria and replacing them with beans/environmental bacteria from a second plastic bag. In the synchronous part II of the exercise, students read multiple review articles and assign bacterial names to the pasta types under the respective diet. They then use the same articles to identify metabolic byproducts that these bacteria produce. In a follow up assignment that constitutes part III, students investigate signal transduction pathways in the human host cells and the potential diseases that can result from a high fat diet.

Original lesson: The Impact of Diet and Antibiotics on the Gut Microbiome

Human Ecology resources

We all know that understanding family history is important to understanding our place in the world. To help students learn to appreciate plants, this activity will connect family memories to specific plants that were important to them or to their ancestors. This is referred to as “botanical history.” Students will interview family members to identify a specific plant they will use for the remaining nine modules. The plant the students choose is ideally one that holds historical significance to their family (e.g., an apple tree that has provided fruits for many generations, or a houseplant that has been divided or shared on special occasions). The students will then share their stories with the class and compare the plants they have chosen with their classmates.

A thorough understanding of glycolysis forms a foundation for students to analyze subsequent topics in metabolism, a core competency recognized by multiple national societies for biology and biochemistry. However, when confronted with the names of over ten chemicals and enzymes, along with various energy inputs and outputs, students can regard glycolysis as a daunting memorization task. Here we describe a card sorting activity in which small groups of students work out the steps of the glycolysis pathway before any lectures on the topic. They examine the chemical structures of glycolytic intermediates and deduce their logical order. Subsequent analysis of the reactions and the role of cofactors and substrates is reinforced with a POGIL worksheet. In the process, the students engage in productive discussions of topics often introduced didactically in lecture. The activity was implemented at six different institutions in small (~12 students) and large classrooms (100+ students), and can be adapted to hybrid/online formats. This highly engaging exercise has been well-received by students and instructors in various undergraduate course contexts.

Primary Image: Rediscovering glycolysis. Students working on the card sorting activity in small groups. Photo taken by Dr. Lauren Genova.

A thorough understanding of glycolysis forms a foundation for students to analyze subsequent topics in metabolism, a core competency recognized by multiple national societies for biology and biochemistry. However, when confronted with the names of over ten chemicals and enzymes, along with various energy inputs and outputs, students can regard glycolysis as a daunting memorization task. Here we describe a card sorting activity in which small groups of students work out the steps of the glycolysis pathway before any lectures on the topic. They examine the chemical structures of glycolytic intermediates and deduce their logical order. Subsequent analysis of the reactions and the role of cofactors and substrates is reinforced with a POGIL worksheet. In the process, the students engage in productive discussions of topics often introduced didactically in lecture. The activity was implemented at six different institutions in small (~12 students) and large classrooms (100+ students), and can be adapted to hybrid/online formats. This highly engaging exercise has been well-received by students and instructors in various undergraduate course contexts.

Primary Image: Rediscovering glycolysis. Students working on the card sorting activity in small groups. Photo taken by Dr. Lauren Genova.

Rapid advances in genomics and bioinformatics, the vast amount of data generated by next-generation sequencing, and the penetration of the ‘-omics’ into many areas of biology have created a need for students with hands-on experience with computational and ‘big data’ methods. Additionally, laboratory experience in the isolation, identification, and characterization of unknown bacteria is a vital part of a microbiology student’s training. This lesson is a course-based undergraduate research experience (CURE) focusing on Salmonella enterica, a common and relatively low-virulence foodborne pathogen. In Module 1, students isolate and identify S. enterica strains from stream sediment, poultry litter, or other sources. They conduct phenotypic evaluation of antimicrobial resistance (AMR) and can search for plasmids. Isolates’ whole genomes may be sequenced by the United States FDA or public health laboratories, typically at no charge. In Module 2, students learn basic methods of genome assembly, analysis, annotation, and comparative genomics. They use easily accessible, primarily web-based tools to assemble their genomes and investigate areas of interest including serotype, AMR genes, and in silico evidence of mobile genetic elements. Either module can be used as a standalone learning experience. After course completion, students will be able to isolate and identify Salmonella from natural sources, and use computational analysis of microbial genomic data, particularly of the Enterobacteriaceae. This lesson offers undergraduate microbiologists a genuine research experience and a real-world microbiology application in genomic epidemiology, as well as a valuable mix of field, laboratory, and computational skills and experiences.

Activities related to teaching tree-thinking skills in evolutionary biology

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.

One key to student success in introductory and cell biology courses is a foundational knowledge of cellular respiration. This is a content area in which students often harbor misconceptions that make cellular respiration particularly challenging to teach. Conventional approaches presenting cellular respiration as a complex series of isolated steps creates a situation where students tend to memorize the steps but fail to appreciate the bigger picture of how cells transform and utilize energy. Instructors frequently struggle to find ways to motivate students and encourage deeper learning. The learning goals of this cellular respiration lesson are to understand energy transfer in a biological system, develop data analysis skills, practice hypothesis generation, and appreciate the importance of cellular respiration in everyday life. These goals are achieved by using a case study as the focal point. The case-based lesson is supported with student-centered instructional strategies, such as individual and group activity sheets, in-class group discussions and debate, and in-class clicker questions. This lesson has been implemented at two institutions in large enrollment introductory biology courses and in a smaller upper-division biochemistry course.

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.

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.