This module examines the relationship between street trees, urban avifauna, and socioeconomic gradients in the highly urbanized county of Los Angeles, California. Using edited data from a published study, students will learn how to run and interpret a generalized linear model with negative binomial distribution in RStudio.

Backyard Beetles + Pollinators is a project to observe and evaluate plant-pollinator networks. This adaptation modifies the (adapted) modules for a non-lab course on conservation, conducted during a mix of in-person and remote students.

A common polymorphism in the alpha-actinin-3 (ACTN3) gene results in the lack of ACTN3 protein expression in fast twitch muscle fibers in ~16% of the human population (1). This genetic change has been linked with muscle performance in humans (2) but does not cause any known muscle disease (1). We have developed a series of laboratory modules that provide an authentic classroom research experience and which address the connection between science and society by examining the implications of ACTN3 genetic testing to improve sports training and performance. This article accompanies the lesson "The ACTN3 Polymorphism: Applications in Genetics and Physiology Teaching Laboratories," and summarizes background information that an instructor would need to implement the project in class.

This is a set of class notes rich in examples and ideas for modeling. There is some MatLab code in support of some of the activities.

A community of educators and scholars developing and using Molecular Case Studies (MCS), to explore the molecular basis of biological phenomena, understand real world problems, and their developing solutions at the interface of biology and chemistry.

This case study follows purveyors of peas, Joel E. and Jolene Greengiant, as they learn about the origin, biochemistry, genetics and eventual artificial selection of sweet (wrinkled) peas, all in the context of evolutionary biology.

BioMolViz is a community dedicated to advancing biomolecular visualization education. We provide training, teaching tools and validated visual literacy assessments. The BioMolViz Library—our online repository—delivers assessments to instructors worldwide.

This animation shows how mutations in an ion channel protein lead to the genetic disease cystic fibrosis. The animation also discusses how research on this protein has been used to develop treatments for the disease.

Biomolecular structure and function is emphasized as a core concept in a variety of community determined educational standards for biology and chemistry. Most curricula introduce students to the building blocks and principles of biomolecular structures, in introductory chapters of biology, biochemistry, cell biology, and chemistry courses, but very few engage students in actively visualizing and exploring biomolecular structures throughout the course. Conversations with faculty teaching introductory courses, and/or developing and piloting molecular case studies, helped uncover the need for new resources, and professional development to support introduction of biomolecular exploration. To address this need, a group of faculty participating in a Faculty Mentoring Network in Spring 2022, gathered together resources and lessons that they had independently developed and collaboratively developed additional ones. An overview of the lessons will be presented here. Interested users are invited to pilot the lessons in Fall 2022.

Collection of resources that help teach biochemistry.

Enzyme lesson

Evolution of caffeine pathway

Lab or class activities

Hardy Weinberg lab

Teaching evolution remains a challenging task in biology education. Students enter the classroom with stubborn misconceptions and many traditional examples of the process of evolution may not resonate with students. This short role play activity is designed to easily integrate into any class session on evolution and provide students with a concrete, tangible example of natural selection. In addition, it specifically addresses several misconceptions about evolution. In this activity, students become a fictional population that is under a selection pressure. As students take on the role of a population, they are reminded of the requirements for natural selection, fall victim to a selection pressure, and observe the change in allele frequencies over time. In the context of a class session that focuses on the mechanisms of evolution, students are able to immediately visualize the process of natural selection. This role play only takes 10-15 minutes, requiring minimal class and preparation time. It has been successfully used in both introductory and non-majors' biology classrooms. Though simplified and fictional, this role play provides a concrete example as a foundation for students' growing understanding of evolution.

Primary image: Depicts visual representation of populations evolving.

Teaching evolution remains a challenging task in biology education. Students enter the classroom with stubborn misconceptions and many traditional examples of the process of evolution may not resonate with students. This short role play activity is designed to easily integrate into any class session on evolution and provide students with a concrete, tangible example of natural selection. In addition, it specifically addresses several misconceptions about evolution. In this activity, students become a fictional population that is under a selection pressure. As students take on the role of a population, they are reminded of the requirements for natural selection, fall victim to a selection pressure, and observe the change in allele frequencies over time. In the context of a class session that focuses on the mechanisms of evolution, students are able to immediately visualize the process of natural selection. This role play only takes 10-15 minutes, requiring minimal class and preparation time. It has been successfully used in both introductory and non-majors' biology classrooms. Though simplified and fictional, this role play provides a concrete example as a foundation for students' growing understanding of evolution.

Primary image: Depicts visual representation of populations evolving.

Students often enter introductory biology courses with misconceptions about evolution. For example, many students believe that traits arise when a species needs them or that evolutionary processes are goal-oriented. To address these and other misconceptions, we have developed an activity called "Boost Your Evolution IQ." Student groups compete against one another in a fast-paced, challenging quiz that is presented using PowerPoint. Questions get harder from beginning to end, and the stakes get higher: Each correct answer earns double points in round 2 and then triple points in round 3. Student collaboration throughout the activity helps reinforce the concepts in advanced students and allows struggling students to hear evolution explained in various ways. Further, the same misconception is often tested multiple times, allowing students to learn from their mistakes. This activity is useful as a review before an evolution exam or as a pre- and post-test. It may also be adapted for large classes using clicker technology. We provide a detailed explanation of the approach in the attached video (Supporting File S1).

Undergraduates are often expected to read scientific papers for class and submit assignments based on their understanding of the contents of these papers. Most courses, in our experience as students and TAs, do not spend time teaching students how to approach highly technical scientific reading. We believe that reading scientific papers and interpreting figures is a skill that can and should be taught in a classroom setting. This workshop was designed for Stanford undergraduates in the bioBUDS program. The goal of this workshop is to provide students with some of the tools to start reading and interpreting scientific papers for class or undergraduate research.

There are few instructional tools about data acquisition and management available for undergraduate students. I created this lesson as a Fellow of the Ethics Network for Course-Based Opportunities in Undergraduate Research (ENCOUR) to fill this gap by providing a lesson that introduces lab notebooks and builds connections to responsible and ethical conduct of research (RECR). While originally developed for a course-based undergraduate research experience (CURE) in microbiology, there are few disciplinary or course specific details included, making this resource easy to adapt to a variety of contexts. The lesson begins with a pre-class assignment which introduces students to the basics of keeping a lab notebook. The in-class instruction provides opportunities for student reflection, short lecture segments, and group work to identify and discuss the connections between data collection practices and RECR. Students who completed the lesson displayed a broader and more complete conception of the connections to RECR topics as well as the utility of the lab notebook.

Primary Image: Lab Notebook image (from this website used under Creative Commons license)

Higher education in STEM undoubtedly integrates the use of technology as a primary mode for content delivery to undergraduate students. This became especially salient throughout the shift to online education during the COVID-19 pandemic. Despite Learning Management Systems (LMSs) being the primary platform for delivering online instruction and fostering peer interactions, technologies embedded in LMSs do not maximize engagement, and therefore, students may not be able to share LMS materials with peers outside of the classroom. On the other hand, podcasts, episodic audio files that present information in a spoken word format, are commonly used in engaging students beyond the classroom across a variety of social media platforms. In contrast to traditional pedagogies, podcasts allow students to reflect on content rather than recite newly acquired information. This article outlines the basics of using podcasting in the classroom including recommendations for selection of podcast topics, formation of student groups, and production of a podcast, and highlights the anticipated student benefits along with potential applications. Previous studies have correlated student podcast usage to positive affectual experiences and learning outcomes, which play a role in Science, Technology, Engineering and Mathematics retention. Furthermore, since podcasts use audio rather than visual recordings, podcasts can thus foster inclusion by helping to avoid barriers posed by video recordings such as students’ low confidence, various invisible barriers, or being overly conscious of their appearance. We recommend utilizing podcasts as a teaching tool to empower students to reflect and actively collaborate to synthesize course content related to classroom instruction and beyond.

Primary Image: User audio equipment. This image represents the versatility of using everyday technology for audio recording. The image is not copyrighted and was downloaded from a copyright free site.

Learning to write a scientific manuscript is one of the most important and rewarding scientific training experiences, yet most young scientists only embark on this experience relatively late in graduate school after gathering sufficient data in the lab. Familiarity with the process of writing a scientific manuscript and receiving peer reviews often leads to a more focused and driven experimental approach as well as a better understanding of the scientific literature. To jump-start this training, we developed a protocol for teaching manuscript writing and reviewing in a course, appropriate for new graduate or upper-level undergraduate students in biology. First, students are provided a cartoon data set. Students are instructed to use their creativity to convert evidence into argument and then to integrate their interpretations into a manuscript, including a mechanistic model figure. After student manuscripts are submitted, manuscripts are redacted and distributed to classmates for peer review. We present our cartoon data sets (based on animal development and interbacterial competition), homework instructions, and grading rubrics as a new resource for the scientific community. We also describe methods for developing new data sets so that instructors can adapt this activity to other disciplines. Our data-driven manuscript writing exercise as well as the formative and summative assessments resulting from the peer review process enable students to practice scientific skills and concepts. In addition, students practice scientific communication, arguing from evidence, developing and testing hypotheses, the unique conventions of scientific writing, and the joys of scientific story telling.

Primary Image: Manuscript 101 Workflow Schema. In this series of structured activities, students transform cartoon data sets into manuscripts that then undergo peer review.

With the publishing of the Vision and Change report, we know it is best practice to include authentic research experiences in our undergraduate science lab classes. One big challenge in teaching so-called "wet lab" classes is figuring out a way to make sure students come to lab prepared to successfully complete their experiments. Molecular biology protocols are particularly challenging as they are typically long, detailed, and have multiple steps to complete. The most successful teaching practice I have tried is having students prepare for lab by hand-drawing flowcharts of the lab protocols. Drawing is a proven way to increase scientific understanding and requires students to engage with the lab materials before class. These flowcharts are due when students walk in to lab and more importantly, students use their flowcharts during lab. This teaching tool is easy to teach to students, simple to assess, and does not rely on any pre-existing knowledge of molecular biology or artistic skill. I have had great success using flowcharts as a teaching tool in both upper division and lower division classes as well as with both life science major and non-major students. Flowcharts have many potential applications beyond undergraduate "wet lab" classes including discussion courses and graduate research projects.

Modern molecular biology is a data- and computationally-intensive field with few instructional resources for introducing undergraduate students to the requisite skills and techniques for analyzing large data sets. This Lesson helps students: (i) build an understanding of the role of signal transduction in the control of gene expression; (ii) improve written scientific communication skills through engagement in literature searches, data analysis, and writing reports; and (iii) develop an awareness of the procedures and protocols for analyzing and making inferences from high-content quantitative molecular biology data. The Lesson is most suited to upper level biology courses because it requires foundational knowledge on cellular organization, protein structure and function, and the tenets of information flow from DNA to proteins. The first step lays the foundation for understanding cell signaling, which can be accomplished through assigned readings and presentations. In subsequent active learning sessions, data analysis is integrated with exercises that provide insight into the structure of scientific papers. The Lesson emphasizes the role of quantitative methods in research and helps students gain experience with functional genomics databases and data analysis, which are important skills for molecular biologists. Assessment is conducted through mini-reports designed to gauge students' perceptions of the purpose of each step, their awareness of the possible limitations of the methods utilized, and the ability to identify opportunities for further investigation. Summative assessment is conducted through a final report. The modules are suitable for complementing wet-laboratory experiments and can be adapted for different courses that use molecular biology data.

Modules showing how the NCBI database classifies and organizes information on DNA sequences, evolutionary relationships, and scientific publications. And a module working to identify a nucleotide sequence from an insect endosymbiont by using BLAST

In this lesson, we describe an easily adaptable lab module that can be used in existing undergraduate molecular biology lab courses to conduct authentic scientific research, published in CourseSource