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Investigating Evidence for Climate Change (Project EDDIE) with CO2 and 13CO2 data: adapted for R

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.

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Emily Rude onto climate change

Calling Bull Case Study — 99.9% Caffeine-free with R

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.

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Emily Rude onto Stats

My Twin Sister Case Study

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

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Emily Rude onto Genetics

Population Genetics: Limits to Adaptation

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.

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Emily Rude onto Evolution - gene flow

Investigating human impacts on stream ecology: locally and nationally

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?

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Final Project for Calling Bull

misinformation

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Redlining and Climate Change

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.

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Global Temperature Change in the 21st Century: An Introduction to Global Climate Models and Graphing in Excel (Adapted for Non-Majors)

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.

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Too much of a good thing? Exploring nutrient pollution in streams using bioindicators

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.

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Fourteen Recommendations to Create a More Inclusive Environment for LGBTQ+ Individuals in Academic Biology

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Using Zebrafish in a Developmental Biology Lab Course to Explore Interactions Between Development and the Environment

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.

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Differential Gene Expression during Xenopus laevis Development

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.

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Emily Rude onto Genetics

A Rapid Genetic Screen Using Wisconsin Fast Plants<sup>®</sup>: A Hands-On Approach to Inheritance of <i>de novo</i> Mutations

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.

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A Rapid Genetic Screen Using Wisconsin Fast Plants<sup>®</sup>: A Hands-On Approach to Inheritance of <i>de novo</i> Mutations

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.

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A Structured Inquiry Approach to Cotyledon Phenotyping

In this lab, students will work with messy data to try to answer the question “How do plants inherit cotyledon color?”

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Dynamic Daphnia: An inquiry-based research experience in ecology that teaches the scientific process to first-year biologists

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.

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Using Student Perceptions and Cooperative Learning to Unpack Primary Literature on Global Change

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.

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Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes

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.

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Emily Rude onto Genetics

Investigating Gene Expression and Cell Specialization in Axolotl Embryos

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.

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Designing an Asynchronous, Self-Led Aquatic Ecology Field Trip

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).

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Moths and Frogs and <em>E. coli</em>, Oh My!: Agent-based Modeling of Evolutionary Systems

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.

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Mapping a Mutation to its Gene: The "Fly Lab" as a Modern Research Experience

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.

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Sex and gender: What does it mean to be female or male?

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.

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A Muscular Dystrophy Case Study Illustrating the Phenotypic Effects of Mutation

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.

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Honoring the Complexity of Genetics: Exploring the Role of Genes and the Environment Using Real World Examples

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).

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