Signaling and gene expression are fundamental to cell biology and developmental biology. Although these topics are highly interrelated, they typically appear in separate units in a course. We use a series of short problem-based learning exercises for two complementary purposes: 1) to promote a better understanding of the mechanisms of signal transduction; and 2) to reinforce students' understanding of cell- and tissue-specific gene expression. Moreover, the exercises promote synthesis of these two topics in the context of real biological problems. The first small-group exercise that we present poses questions about the implications of cell- or tissue-specific expression of signaling molecules, encouraging students to synthesize information when thinking about biological systems. The second exercise asks students to apply the principles of signal transduction to interpret data presented in a case study based on mutations in a MAP kinase pathway that cause Noonan syndrome. Both in-class exercises present opportunities for the students and the instructor to assess the students' understanding of signaling mechanisms. Finally, we include a set of guiding questions on the Wnt signaling pathway as an out-of-class assignment, to be followed by a quiz on Wnt signaling as a summative assessment.

I implemented Unit 5 of the "Climate of Change" module into two weeks of my nonmajors Environmental Science course to cover the concepts of atmospheric science, climate change, and data evaluation.

The BioSkills Guide comprises program- and course-level learning outcomes for the Vision and Change core competencies that elaborate what general biology majors should be able to do by the time they graduate.

Students typically find linear regression analysis of data sets in a biology classroom challenging. These activities could be used in a Biology, Chemistry, Mathematics, or Statistics course. The collection provides student activity files with Excel instructions and Instructor Activity files with Excel instructions and solutions to problems. Students will be able to perform linear regression analysis, find correlation coefficient, create a scatter plot and find the r-square using MS Excel 365. Students will be able to interpret data sets, describe the relationship between biological variables, and predict the value of an output variable based on the input of an predictor variable.

Using oVERT project models students examine examples of extant traditional lizards, snakes and limbless lizards and create phylogenies based on trait and genetic data.

place based cure

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces the idea of computers as tools to help understand aspects of biology.

This Practical Guide in the Bringing Bioinformatics into the Classroom series introduces the idea of computers as tools to help understand aspects of biology.

This module discusses mental and physical aspects of field safety. The module contains resources for supporting students and technicians in the field and guides supervisors as they write their own Right to Know document.

Genome Solver began as a way to teach undergraduate faculty some basic skills in bioinformatics; no coding or scripting is required. This pre-lesson introduces the BLAST tool.

In this lesson, learners will hear about research that focuses on bacterial antibiotic resistance and biofilm production. Students will see how antibiotic resistance is measured and interpret a graph measuring biofilm production of these bacterial soil isolates. Then, learners view and reflect on an interview with microbiology researcher Dr. Danielle Graham, who collected the data that they interpreted.

Decades of evidence support the premise that undergraduate research experiences are valuable endeavors for science students; however, a lack of knowledge about research and how to get involved can preclude equitable participation. We developed two in-class workshops to teach introductory biology students about undergraduate research experiences. In the first workshop, students are introduced to various types of undergraduate research, including faculty-mentored research, Course Based Undergraduate Research Experiences (CUREs), summer research experiences and research-related jobs and internships. Students hear first-hand accounts about research from undergraduates actively performing research and learn about the benefits and challenges associated with participating. In the second workshop, students learn how to effectively identify and secure research opportunities and engage in an exercise that teaches them how to write a professional email to potential research advisors. Students also work together to develop strategies for building resilience if faced with rejection from a faculty member or internship/job opportunity. The workshops utilize student speakers, think-pair-share activities, and class discussions to engage and inform students. By the end of the workshops, all students are familiar with undergraduate research and have the knowledge and skills needed to identify and secure a research opportunity. The workshops were designed for introductory biology students but can be adapted for students in related majors or at different stages of the academic journey.

Primary Image: Undergraduate research poster session at Sacramento State. Students present the discoveries they made through their course-based research experiences. Photograph was taken in-house. 

Bioassessment is an evaluation of the biological condition of a waterbody using biological surveys and other direct measurements of resident living organisms. Aquatic macroinvertebrates are important indicators of stream health: they are relatively long-lived, differentially sensitive to environmental stressors, and relatively easy to sample. This lesson is a hands-on introduction to the use of stream macroinvertebrates in assessing a stream’s biological condition. Students will learn how to (1) sample and identify stream macroinvertebrates and (2) conduct a rapid bioassessment to quantify ecosystem integrity based on the macroinvertebrate taxa that they collect. The lesson can be conducted with any number of students (although a second instructor would likely be needed for class sizes >20) and is appropriate for undergraduates of all levels.

Ideas for revamping my physiology lab

In this module, students use data from natural history collections to look at range shifts related to climate variables over different time periods.

Data driven curriculum module from Dryad Digital Repository

Use digitized natural history collection occurrence data from the Global Biodiversity Information Facility (GBIF) to map the distribution of the beaver in the state of Oregon from 1800-2020 using QGIS

In this lesson students will learn about the impacts of urbanization, and the conservation challenges it poses to wildlife, in particular avifauna. Introductory ecology topics such as the theory of island biogeography and habitat fragmentation will be discussed, and the student will learn about the beneficial role of native plants in urban residential landscaping. A focal paper will be used to better explore these topics, and data from this observational study will be utilized to introduce generalized linear models in the R programming environment. The student should have some prior basic knowledge of introductory ecology concepts, introductory statistics and have R studio installed on their computer with a basic understanding of this programming language. Upon completion of this lesson, students will learn how urban residential yards contribute to the overall green space in urbanized areas and be used as a conservation strategy to mitigate habitat loss. In R, the student will learn how to conduct statistical analyses and determine if the species area relationship and distance effects of the theory of island biogeography predict bird richness in this study system.

The video and exercise provides insight into how researchers are using digital data resources to investigate biodiversity in prairie fen wetlands.

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

This Practical Guide outlines a number of basic bioinformatics approaches that can be used to understand the molecular basis of genetic diseases.

A long-standing tradition uses strings of poppit beads of different colors to model meiosis, especially to show how segments of paired homologous chromosomes are recombined. Our use of orthodontic latex bands to model cohesion of sister chromatids, and plastic coffee stirrers as microtubules, extends what can normally be achieved with ‘standard’ commercial kits of beads, so emphasizing the importance of four key elements of meiosis: (a) the role of chromosome replication before meiosis itself begins; (b) pairing and exchange (chiasma formation) of homologous chromosomes during meiosis I; (c) centromere (kinetochore) attachment and orientation within/on the spindle during meiosis I and meiosis II; and (d) the differential loss of arm and centromere cohesion at onset of anaphase I and anaphase II. These are essential elements of meiosis that students best need to visualize, not just read and think about. Bead modeling leads them in that direction, as our gallery of figures and accompanying text show.

Primary image: Unassembled components of ‘PoppitMeiosis’ – a poppit bead exercise aimed at student learning of meiosis. Beads are snapped together to model bivalent chromosomes (on the right side), with double-stick tape (top) representing the synaptonemal complex, orthodontic latex bands representing cohesion rings, and coffee stirrers representing microtubule bundles that connect centromeres to the spindle poles.

Radical innovations in DNA sequencing technology over the past decade have created an increased need for computational bioinformatics analyses in the 21^st century STEM workforce. Recent evidence however demonstrates that there are significant barriers to teaching these skills at the undergraduate level including lack of faculty training, lack of student interest in bioinformatics, lack of vetted teaching materials, and overly full curricula. To this end, the James Madison University, Center for Genome & Metagenome Studies (JMU CGEMS) and other PUI collaborators are devoted to developing and disseminating engaging bioinformatics teaching materials specifically designed for streamlined integration into general undergraduate biology curriculum. Here, we have developed and integrated a fun introductory level lesson to command line next generation sequencing (NGS) analysis into a large enrollment core biology course. This one-off activity takes a crucial but mundane aspect of NGS quality control (QC) analysis and incorporates the use of Emoji data outputs using the software FASTQE to pique student interest. This amusing command line analysis is subsequently paired with a more rigorous research-grade software package called FASTP in which students complete sequence QC and filtering using a few simple commands. Collectively, this short lesson provides novice-level faculty and students an engaging entry point to learning basic genomics command line programming skills as a gateway to more complex and elaborated applications of computational bioinformatics analyses.

Primary image: Undergraduate students learn the basics of command line NGS quality analysis using the FASTQE and FASTP programs.

In this adaptation, students learn how CRISPR/Cas9 is used in bacterial immunity and gene editing. Students create both a gRNA target and a donor template to edit a gene. Mutations can be from the case study, Piwi Matter, or designed by the instructor.

Meiosis is well known for being a sticky topic that appears repeatedly in biology curricula. We observe that a typical undergraduate biology major cannot correctly identify haploid and diploid cells or explain how and why chromosomes pair before segregation. We published an interactive modeling lesson with socks to represent chromosomes and demonstrated that it could improve student understanding of ploidy (1). Here we present an improvement on that lesson, using DNA paper strips in place of socks to better demonstrate how and why crossing over facilitates proper segregation. During the lesson, student volunteers act out the roles of chromosomes while the whole class discusses key aspects of the steps. Strips of paper with DNA sequences are used to demonstrate the degrees of similarity between sister chromatids and homologous chromosomes and to prompt students to realize how and why homologous pairing must occur before cell division. We include an activity on Holliday Junctions that can be used during the main lesson, skipped, or taught as a stand-alone lesson.

Before undergraduate students take a genetics course they generally know cancer has a genetic basis and involves the proliferation of cells; however, many are uncertain about why only a subset of people have a predisposition to cancer and how that predisposition is inherited from one generation to the next.  To help students learn about these concepts, we designed a teaching unit that centers on a small-group, in-class activity.  During this activity students learn how to:

1. determine inheritance patterns for different types of cancer,
2. explain why a person with or without cancer can pass on a genetic predisposition to cancer, and
3. distinguish between proto-oncogenes and tumor suppressor genes. 

In addition to participating in the small-group activity, students watch short video clips from a documentary about breast cancer, answer clicker questions, and engage in a whole-class discussion.  A combination of pre/posttest results, clicker question answers, and performance on subsequent exam questions suggests that this unit helps students learn about the hereditary basis of cancer.

This module teaches about the three key steps that are involved in converting the pre-mRNA into a mature mRNA: 1) The addition of a 5’ cap, 2) The addition of a 3’ poly(A) tail, 3) The removal of introns through splicing.

In this module, students will learn to identify splice donor and acceptor sites that are best supported by RNA-Seq data, and use the canonical splice donor and splice acceptor sequences to identify intron-exon boundaries.

In this module, students will learn to identify the open reading frames for a given gene, and define the phases of the splice donor and acceptor sites.

This case study focuses on a specific enzyme Lactate Dehydrogenase (LDH) in the malarial parasite as a target for treating malaria.

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.

This lesson introduces the University of California Santa Cruz genome browser to students, walking them through some of the key features so that it can be used for analysis of gene structure.

This module explores how multiple different mRNAs and polypeptides can be encoded by the same gene. After completing this module students will be able to explain how alternative splicing of a gene can lead to different mRNAs.

A compelling reason to learn something can make all the difference in students’ motivation to learn it.  Motivation, in turn, is one of the key attitudes that drives learning.  This story presents students with a compelling puzzle of a fatherless snake.  The puzzle motivates students to learn about meiosis and mitosis, since the only way to explain the origin of the fatherless baby is by mastering details of meiosis.  During the process, students work through the major steps in meiosis, compare and contrast mitosis and meiosis, and apply their understanding to predict how meiosis “went wrong” to produce an unusual offspring that did not originate through union of an egg and a sperm.  This story can be adapted for introductory or advanced students and can be scaled from a brief introduction in a single lecture to a series of active learning exercises that could take two or more lecture periods.

There is an abundance (currently over 10¹⁶ DNA bases) of publicly available genetic sequence data and a dearth of trained genomicists to process and interpret it, necessitating more trained bioinformaticians with biological expertise. For example, thousands of data sets are deposited on NCBI's Sequence Read Archive with plans to use only part of the data generated, though much of this data could be used to address other important biological questions. Course-Based Undergraduate Research Experiences (CUREs) are growing in popularity as a way to engage undergraduates in a project-based learning experience to analyze data that could not otherwise be processed. Through CUREs, students can receive training in the most relevant and up-to-date skill sets used within the field. We present a lesson plan for a CURE centered around teaching genome annotation. This project is suitable as a four week module in an undergraduate/graduate cross-listed course and focuses on annotating streamlined organellar genomes. This module is similar to other programs, such as the Genomics Education Partnership. However, students are additionally provided with the opportunity to publish their annotated genomes to NCBI's GenBank. In addition, many students who have taken this course have gone on to pursue internships and careers using the bioinformatics skills gained.

s assistant professor in the department of medicine at Rutgers Robert Wood Johnson Medical School, Manisha Bajpai, PhD., led the Gastroenterology division’s clinical and translational research efforts funded by the NIH/NIDDK and grants from industry foundations. Her research initiative focused on early-stage biomarker discovery in Barrett’s esophagus and Inflammatory Bowel Diseases using various contemporary molecular biology, cell biology as well as Omics methods. In this lecture we will develop a basic understanding of the methods of the various ‘omics” approaches and discuss their potential in improving human health.

Two articles introducing the Human Genome Project-Write and asking questions about the ethics of the project.

A video that highlights the unspoken assumptions that we use in pedigree analysis.

Gene structure, transcription, translation, and alternative splicing are challenging concepts for many undergraduates studying biology. These topics are typically covered in a traditional lecture environment, but students often fail to master and retain these concepts. To address this problem we have designed a series of six Modules that employ an active learning approach using a bioinformatics tool, the genome browser, to help students understand eukaryotic gene structure and functionality. Students learn how to use a mirror site of the UCSC Genome Browser created by the Genomics Education Partnership while completing the Modules, which focus on gene structure, transcription, splicing, translation, and alternative splicing. The Modules are supplemented with short videos that illustrate key functionalities of the genome browser and fundamental concepts in processing transcripts. These materials have been used successfully to teach gene structure in many different settings, from community colleges to 4-year colleges and universities, encompassing advanced high school students to college seniors. Instructors can easily customize the Modules and/or select a subset for their curriculum. The Modules have helped our students learn about eukaryotic gene structure and expression, simultaneously acquiring skills in the use of a genome browser, and have prepared them to pursue genome annotation projects as independent research.

At the heart of scientific ways of knowing is the systematic collection and analysis of data, which is then used to propose an explanation of how the world works. In this two-day module, students in a large-lecture course are immersed in a biological problem related to the Central Dogma and gene expression. Specifically, students interpret experimental data in small groups, and then use those data to craft a scientific argument to explain how alternative splicing of a transcription factor gene may contribute to human cancer. Prior to the module, students are assigned a reading and provided PowerPoint slides outlining the basics of alternative splicing and refreshing their understanding of gene regulation. Students complete a pre-class assignment designed to reinforce basic terminology and prepare them for interpreting scientific models. Each day of the module, students are presented experimental data or biological models which they interpret in small groups, use to vote for viable hypotheses using clickers, and ultimately leverage in a culminating summary writing task requiring them to craft a data-driven answer to the biological problem. Despite the novelty of the argumentation module, students engage in all aspects (inside and outside of the classroom) of the activity and are connected across data, hypotheses, and course concepts to explain the role of alternative splicing in gene expression and cancer.

Primary image: Splicing it together. Students work together, interpreting primary data and models to investigate the effects alternative splicing may have on gene regulation and cancer.

At the heart of scientific ways of knowing is the systematic collection and analysis of data, which is then used to propose an explanation of how the world works. In this two-day module, students in a large-lecture course are immersed in a biological problem related to the Central Dogma and gene expression. Specifically, students interpret experimental data in small groups, and then use those data to craft a scientific argument to explain how alternative splicing of a transcription factor gene may contribute to human cancer. Prior to the module, students are assigned a reading and provided PowerPoint slides outlining the basics of alternative splicing and refreshing their understanding of gene regulation. Students complete a pre-class assignment designed to reinforce basic terminology and prepare them for interpreting scientific models. Each day of the module, students are presented experimental data or biological models which they interpret in small groups, use to vote for viable hypotheses using clickers, and ultimately leverage in a culminating summary writing task requiring them to craft a data-driven answer to the biological problem. Despite the novelty of the argumentation module, students engage in all aspects (inside and outside of the classroom) of the activity and are connected across data, hypotheses, and course concepts to explain the role of alternative splicing in gene expression and cancer.

Primary image: Splicing it together. Students work together, interpreting primary data and models to investigate the effects alternative splicing may have on gene regulation and cancer.

Understanding the central dogma and how changes in gene expression can impact cell function requires integration of several topics in molecular biology. Students often do not make the necessary connections between DNA structure, transcription, translation and how these processes work together to impact cell function. This lesson seeks to tie together these concepts through the use of data from primary literature, in the context of viral infection. This lesson asks students to think like scientists as they design experiments, make predictions and interpret and evaluate data from primary literature on how changes in the expression of a glucose transporter gene can alter the function of a cell through changes to glucose uptake and metabolism. This lesson incorporates the Vision and Change core concept of information flow and the core competency of quantitative reasoning. It also addresses The Genetics Society of America learning framework goal of Gene Expression and Regulation (How can gene activity be altered in the absence of DNA changes?). This lesson was taught in three sections of a small-enrollment undergraduate class and assessed summatively using a pre/post test and formatively using in class via personal response systems. This lesson describes the design, implementation and results of student assessment, and offers suggestions on how to adapt the materials to a variety of contexts including different class sizes, different units of introductory biology, and upper-level classes.

An online module utilizing probability and Punnett squares to introduce students to more complex genetic problems. The module emphasizes students' use of probability to solve the problems.

A strong understanding of distinct gene components and the ability to retrieve relevant information from gene databases are necessary to answer a diverse set of biological questions. However, often there is a considerable gap between students’ theoretical understanding of gene structure and applying that knowledge to design laboratory experiments. In order to bridge that gap, our lesson focuses on how to take advantage of readily available gene databases, after providing students with a strong foundation in the central dogma and gene structure. Our instructor-led group activity aids students in navigating the gene databases on their own, which enables them to design experiments and predict their outcomes. While our class focuses on cardiomyocyte differentiation, classes with a different focus can easily adapt our lesson, which can be conducted within a single class period. Our lesson elicits high engagement and learning outcomes from students, who gain a deeper understanding of the central dogma and apply that knowledge to studying gene functions.

Primary Image: Gene structure at various levels of expression and retrieval of corresponding biological information from gene databases. This image contains a screenshot from the NCBI Database, which is an open source: National Center for Biotechnology Information. 2021. SOX2 SRY-box transcription factor 2.

Mutations in genes can affect the encoded proteins in multiple ways, and some of these effects are counterintuitive. As for any other knowledge, students must create their own deep understanding of the Central Dogma. Students may not develop this understanding because they have limited opportunity to practice manipulating DNA sequences and classifying their effects. Such practice can improve student appreciation for the myriad possible effects of DNA change (mutation) on amino acid sequence. In this Lesson, a series of scaffolded exercises provides this opportunity. Students first identify gene sequences from an online database, create their own insertion/deletion mutations, and predict the effects. Students then use a web-based tool to translate and observe the effect of the mutation on protein sequence. Subsequent comparison of predicted and observed effects employs the chi-square test. Discussion of results with peers involves categorizing the types of possible effects. The lesson concludes with an exercise asking students to create a mutation with an intended effect on the protein. Together, the exercises integrate quantitative reasoning and statistical analysis, information literacy, and multiple Bloom's learning levels. Student progress is monitored using three formative and three summative assessments.

This is an online activity that provides an introduction to Punnett squares as a tool for visualizing genetic inheritance. The ratios of possible genotypes and phenotypes in offspring are considered. Both monohybrid and dihybrid crosses are examined.

This glossary defines the key terms that are used in the Understanding Eukaryotic Genes modules.

This is an introductory bioinformatics exercise intended for use in a genetics course.

Constructing a robust understanding of homologous chromosomes, sex chromosomes, and the particulate nature of genes is a notoriously difficult task for undergraduate biology students. In this lesson, students expand their knowledge of human chromosome pairs by closely examining autosomes, sex chromosomes, and the non-homologous elements of the human X and Y sex chromosomes. In this four- part guided activity, students will learn about the structure and function of human autosomal and sex chromosomes, view and interpret gene maps, and gain familiarity with basic bioinformatics resources and data through use of the National Center for Biotechnology Information (NCBI) website. (Student access to computers with Internet connectivity is required for the completion of all Investigations within this lesson.) By viewing chromosomes and gene maps, students will be able to contrast expectations for homologous autosomal chromosome pairs and sex chromosome pairs, as well as gain a deeper understanding of the genetic basis for human chromosomal sex determination. In the last part of this lesson, students can also begin to understand how genetic mutations can lead to sex-reversal. The lesson, as presented, is intended for an introductory biology course for majors, but could be modified for other audiences. In addition, each exercise (“Investigation”) within the lesson can be used independently of the others if an instructor wishes to focus on only a subset of the learning objectives and provide the necessary context.  Options to extend the lesson related to interpreting phylogenies, and contrasting definitions of sex and gender are also provided.

A lesson that requires students to work through a series of questions pertaining to the genetics of sickle cell disease and its relationship to malaria.

Genetics is a fascinating topic of biology. Establishing relevance is a key component of student learning. To increase learning, this resource includes summaries and teaching guides for integrating four different podcasts into a genetics course. Lecturing through podcasts has been shown to be received well by students and improve their understanding of concepts. Using podcasts to provide context and significance to a course would further enhance their learning and interest in the course.

This case aims to strengthen students’ understanding of molecular biology concepts through study of Fragile X Syndrome (FXS). Students begin by learning the cause and phenotypes of FXS and related conditions. Students then apply genetics knowledge to describe the inheritance of FXS. Knowledge of the central dogma of molecular biology helps students understand the impact of genetic and epigenetic changes on expression of the Fragile X mental retardation gene 1 and the impacts of the loss of the Fragile X Mental Retardation Protein on other protein production. As one example of the latter, students look at alterations in metabolic enzymes and consider ways to mitigate the phenotype, proposing treatments for FXS. Throughout the case, students are pointed to a clinical website and scientific literature to build their understanding. This case study also engages students in consideration of diversity and inclusion in conveying, interpreting, and acting on scientific information. Overall, this case can help students connect biological concepts to a real-world application while developing their abilities to think critically and comprehend scientific information.

Primary Image: “Fragile X metaphase spread,” showing human chromosomes with the Fragile X site highlighted with an arrow. This image was accessed via Creative Commons and available under license CC BY 4.0 (provider Europeana, source Wellcome Collection).

Students often shy away from tedious bioinformatics approaches to exploring their genomes. However, in our expanding digital world these skills are some of the most relevant and valuable. To increase students' interest in their own genomes, I have designed a computer-based laboratory lesson that was coupled with opportunity for the students to be genotyped by the consumer sequencing company, 23andMe. This lesson employs multiple open-access websites through which students explore a health-related single nucleotide polymorphism (SNP) in which they are most interested. Through a series of guided activities, students investigate the genomic region in which their SNP lies, investigate if there are any genome-wide association studies about this SNP, and then determine what model organism would be the best to use if they were to conduct future research about the gene in which the SNP lies. This module could be adapted as a supplement for a variety of Biology lecture or laboratory courses including but not limited to genetics and molecular biology.

In this essay, we present our strategy for implementing active learning strategies into an upper division course on Human Genetics. Our principal goal was to shift from a traditional didactic course design, to one that more clearly placed the responsibility for learning on to the course participants. A key part of our objective, was to incorporate active learning approaches that more saliently lend themselves to student contemplation of material. We pursued the goal of incorporating active learning in a variety of ways, including the use of personal response clicker questions, partner discussions, small group discussions, class-wide presentation of topical questions, and a final comprehensive individual presentation. The approaches we describe were effective and favorably received, as reflected in positive post-course reviews from student participants. The tools and techniques we integrated in our course design are flexible, and are widely applicable to other subjects and disciplines. Our hope is that these approaches may be flexibly adapted for a variety of different courses to improve course experiences for students and instructors alike.

It has been shown that active learning strategies used in the classroom can increase student learning and retention of information. We generated an active learning exercise that can be used in the classroom to explore the relationship between genes, mutations, cancer, and cancer therapeutics. The learning objectives for this exercise include defining and understanding the functional relationships between genes that regulate cell division, major types of mutations, and the onset of cancer. The active learning exercise begins with a take home quiz to define terms related to the information covered during the lecture portion of the class. Students are then divided into groups to generate a concept map that displays the interrelationships between these terms. Each group is then instructed to exchange their concept maps with another group, evaluate the map for accuracy, and identify targets for inhibiting or activating drug therapies. The lesson plan was implemented in undergraduate biology courses at two public universities. Survey data indicate that students perceived the activity helped increase their knowledge and understanding of the learning objectives.

Biodiversity is decreasing rapidly each year and agriculture is a large contributor. In order to minimize biodiversity loss, we must study how local and landscape management in agriculture impact different species in different ways. With this knowledge, policy makers and planners can create strategies to protect biodiversity in the most effective ways as possible.

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

Biology students require broad preparation for diverse careers including agriculture, natural resource management, and laboratory research. Concurrent with this need, employers are seeking applicants who have the scientific skills that allow them to solve problems related to locally relevant economic systems and develop ways to foster economic growth. To support these efforts, biology faculty from six different campuses in the University of Maine System collaborated to develop an economically relevant activity where students differentiate the roles light energy, carbon dioxide, and nutrients have in photosynthetic organisms. In addition, the activity addresses the relationship between photosynthesis and global carbon dioxide cycles, as well as the potential impacts of rising global atmospheric carbon dioxide on economic industries that rely on these processes. The activity was taught in 11 classrooms throughout the University of Maine System, and student performance was assessed using a multiple-choice pre/post-test, pre/post constructed response questions, in-class clicker questions with peer discussion, and exam questions. Here we report that the activity improved student learning and that combining the expertise of University of Maine System faculty and the Hurricane Island Center for Science and Leadership provided the opportunity to integrate biological concepts with economic development. Although the examples in this lesson have economic relevance in the state of Maine, the examples can be modified to align with other regional economic systems.

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 students who are already familiar with GIS to doing comparative analyses with large-scale community science (often called citizen science) data sets. Students will explore how we can use community science data to examine the spread and distribution of invasive species in different geographic locations. In the final step, students will identify different invasive species and determine if community science data accurately maps the threat these species pose.

Students learn about the importance of good data management and begin to explore QGIS and RStudio for spatial analysis purposes. Students will explore National Land Cover Database raster data and made-up vector point data on both platforms.

This exercise explores circumstances of urban heat islands in the United States using spatial data, including an exploration of heat island solutions.

This module is made up of four concepts. The goal of the first concept is to elicit an understanding of primate relatedness, phylogeny, and how specific characteristics are beneficial for life in an arboreal environment. The next concept explains the overarching trends in hominin evolution and the selective pressures that encouraged their development. Concept three examines specific fossils and the characteristics that are associated with them. This concept serves to provide a timeline of hominin evolution. The final concept encourages students to understand characteristics in the hominin lineage and how they relate to social behaviors. This concept ends by driving home the point that evolution is a dynamic and continual process.

This module examines the complicated co-evolution of Lice, Humans, and Great Apes

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.

Research experiences provide a valuable view into the world of science and a great way to explore new fields and careers while developing critical thinking skills. The development and maintenance of databases have allowed researchers to accelerate research in many fields, and understanding how to use them opens doors to actual data for scientific purposes. This resource will give students the opportunity to use research tools with published data to answer questions about immunological topics. The activities in this lesson can be used in Biology, Biotechnology, Microbiology, Bioinformatics, and Introductory Immunology courses. In addition, this activity includes a Student Activity and Instructor Notes with solutions and extra guidance for educators.

Teaching resources, especially active learning pedagogy, are scarce for toxicology compared to what is available for other disciplines. Ecological and human health risk assessment are important aspects of toxicology and are routinely used by government agencies to regulate the registration and usage of many chemicals. Most traditional toxicology classes do not cover how such risk assessments are carried out in real-world scenarios. We developed this case study to introduce concepts and processes of ecological and human health risk assessment in pesticide registration by the U.S. EPA. In Part 1, dialogues among three college friends introduce organic food, pesticides, and the concept of risk. Part 2 and Part 3 build on Part 1 and focus on ecological risk assessment and human health risk assessment, respectively. At the end of each section, students select appropriate exposure and toxicity endpoints to perform a mini-risk assessment and draw conclusions regarding risk. In Part 4, students examine real pesticide monitoring data in various foods and perform basic data organization and analysis. This case is appropriate for upper-level college students taking toxicology or other environmental science related courses. With modifications, the case study may also be suitable for introductory level environmental and biological science students.

Primary image: Assortment of fruit. This image shows some common fruit and fruit drinks.

Teaching resources, especially active learning pedagogy, are scarce for toxicology compared to what is available for other disciplines. Ecological and human health risk assessment are important aspects of toxicology and are routinely used by government agencies to regulate the registration and usage of many chemicals. Most traditional toxicology classes do not cover how such risk assessments are carried out in real-world scenarios. We developed this case study to introduce concepts and processes of ecological and human health risk assessment in pesticide registration by the U.S. EPA. In Part 1, dialogues among three college friends introduce organic food, pesticides, and the concept of risk. Part 2 and Part 3 build on Part 1 and focus on ecological risk assessment and human health risk assessment, respectively. At the end of each section, students select appropriate exposure and toxicity endpoints to perform a mini-risk assessment and draw conclusions regarding risk. In Part 4, students examine real pesticide monitoring data in various foods and perform basic data organization and analysis. This case is appropriate for upper-level college students taking toxicology or other environmental science related courses. With modifications, the case study may also be suitable for introductory level environmental and biological science students.

Primary image: Assortment of fruit. This image shows some common fruit and fruit drinks.

The ability to collate information from diverse scientific resources and effectively employ scientific writing is an essential skill for scientists. This lesson describes a semester-long project entitled “Pick Your Poison,” which is designed for use in a one-semester Toxicology course. Students are each assigned to or choose their own individual toxicant as a case study from a pre-selected list of toxicants (poisons) that align with the theme of the course. As content is covered in the course, students complete ten scaffolded, low-stakes writing modules that are shared with groupmates of 4–5 students. Each module covers a major feature of the toxicant, such as chemical features, characteristics of absorption, distribution, metabolism, and elimination (ADME), and organ-specific toxicities. Students share their work with their group mates and the instructor, peer review one another’s work, and then edit their original post as appropriate to produce a concise, 3–4 paragraph product. At the end of the course, students compile their writing modules into an article in the format of the Encyclopedia of Toxicology. This project can be adapted to any toxicology course through alteration of the content and number of modules and/or the type of final deliverable. Several evidence-based and inclusive teaching practices are included, such as writing-to-learn, peer review, and low-stakes assessments.

Primary Image: A picture of the online discussions for two of the ten modules.

Could use for visit to k-12

Multicellular biofilms constructed by microbes are key aspects of microbiology with significant implications in various fields, including medicine, environmental science, and biotechnology. While bacteria spend nearly all their lives in biofilms, many students do not study them in detail in a course setting. Consequentially, students have misperceptions that microbes exist as free-living single-cell organisms and cannot understand the biofilm lifestyle accurately. Here, I present a comprehensive and engaging lab lesson plan designed for students to explore the concepts of biofilm lifestyle and compare biofilms to cities using a think-group-share strategy. Students are asked to individually define biofilms and relate them to living in a city, followed by forming small groups, and then discussing them as an entire class. The class will understand the different aspects of biofilms in each step of the life cycle from colonization to dispersal. Subsequently, the students will put their knowledge into practice by completing an activity where they must sort different functional activities into the following steps in the biofilm life cycle: colonization, formation, maturation, and dispersal. This analogy-based activity encourages comparative analysis and fosters long-term learning. I observed that students actively participated in the learning activity, which also cultivated a sense of class community during the sharing session. An end-of-module review activity six weeks later showed that the students could still recall the knowledge learned during the lesson. This lesson activity has several advantages: it is easy for the teacher to implement within 20–30 minutes and convenient for the students to engage with biofilm biology.

Primary Image: Comparison of a biofilm to a city. The biofilm has similar analogies to a city. 

Students evaluate evidence for evolution of Darwin's finches using authentic research data sets collected by Peter and Rosemary Grant.

Case Study for Genetics or Molec Lab

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.

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.

Developing student creativity and ability to develop a testable hypothesis represents a significant challenge in most laboratory courses. This lesson demonstrates how students use facets of molecular evolution and bioinformatics approaches involving protein sequence alignments (Clustal Omega, Uniprot) and 3D structure visualization (Pymol, JMol, Chimera), along with an analysis of pertinent background literature, to construct a novel hypothesis and develop a research proposal to explore their hypothesis. We have used this approach in a variety of institutional contexts (community college, research intensive university and primarily undergraduate institutions, PUIs ) as the first component in a protein-centric course-embedded undergraduate research experience (CURE) sequence. Built around the enzyme malate dehydrogenase, the sequence illustrates a variety of foundational concepts from the learning framework for Biochemistry and Molecular Biology. The lesson has three specific learning goals: i) find, use and present relevant primary literature, protein sequences, structures, and analyses resulting from the use of bioinformatics tools, ii) understand the various roles that non-covalent interactions may play in the structure and function of an enzyme. and iii) create/develop a testable and falsifiable hypothesis and propose appropriate experiments to interrogate the hypothesis. For each learning goal, we have developed specific assessment rubrics. Depending on the needs of the course, this approach builds to an in-class student presentation and/or a written research proposal. The module can be extended over several lecture and lab periods. Furthermore, the module lends itself to additional assessments including oral presentation, research proposal writing and the validated pre-post Experimental Design Ability Test (EDAT). Although presented in the context of course-based research on malate dehydrogenase, the approach and materials presented are readily adaptable to any protein of interest.

Primary image: Mind map of the hypothesis development.

Providing undergraduate life-science students with a course-based research experience that utilizes cutting-edge technology, is tractable for students, and is manageable as an instructor is a challenge. Here, I describe a multi-week lesson plan for a laboratory-based course with the goal of editing the genome of budding yeast, Saccharomyces cerevisiae. Students apply knowledge regarding advanced topics such as: CRISPR/Cas9 gene editing, DNA repair, genetics, and cloning. The lesson requires students to master skills such as bioinformatics analysis, restriction enzyme digestion, ligation, basic microbiology skills, polymerase chain reaction, and plasmid purification. Instructors are led through the technical aspects of the protocols, as well as the teaching philosophy involved throughout the laboratory experience. As it stands, the laboratory lesson is appropriate for 6-8 weeks of an upper-level undergraduate laboratory course, but may be adapted for shorter stints and students with less experience. Students complete the lesson with a more realistic idea of life science research and report significant learning gains. I anticipate this lesson to provide instructors and students in undergraduate programs with a hands-on, discovery-based learning experience that allows students to cultivate skills essential for success in the life sciences.

This interdisciplinary pedagogical case study focuses on differences between rural and urban coyotes at the levels of organismal and community ecology, including how their gut microbiomes could affect their behaviour. The health and fitness of rural and urban coyote populations vary dramatically with the latter being poor as a result of their consumption of carbohydrate-rich anthropogenic food, compared to a more natural protein-rich diet. This difference is associated with altered gut microbiome composition. The case explores how altered microbiomes can influence behavior changes through the gut-brain axis. Cross talk between the brain and gut microbiome involves multiple physiological systems including the immune, endocrine, and nervous systems. This case showcases the interdisciplinary nature of science by having students explore the connection between these macro and micro-level systems. It is based on a manuscript by Sugden et al. (2020) supporting the existence of distinct gut microbiomes in rural and urban coyotes. Interdisciplinary connection - Immunology+Microbiology+Ecology+Animal Behavior

Use GEOLocate to assign geographic coordinates to natural history collections specimens

Best practices for designing educational modules using biodiversity data

An appreciation of organismal diversity is a requirement for understanding evolution and ecology, and can serve as a source of amazement and wonder that inspires students to enjoy biology. However, biodiversity can be a challenging subject to teach: it often turns into a procession of facts to memorize and a disorienting list of Latin names. To help engage students in this topic, we developed an activity in which each student contributes to a class "biodiversity tour" of strange and intriguing species. Students in our large-enrollment introductory biology course use the Internet to find a species that interests them and that they think will interest their peers. They research their species and complete a worksheet to report their findings. Then they meet in discussion sections of ~32 students (in person or online) where each student gives a brief presentation about their species using a slide they have prepared, producing a lively, crowd-sourced, rapid-fire nature documentary. The performance for their peers motivates students to find the strangest species possible. Students overwhelmingly reported that this activity taught them something new about life on Earth and increased their interest in our planet's species. Many students also reported that this activity caused them to talk to someone about biology outside of the class and increased their personal connection to the natural world, suggesting that it helped them see the relevance of biology to their everyday lives. This simple activity can enrich an introductory biology course of almost any size.

Primary image: Photos of some of the species chosen by students in Fall 2019.

Students predict changes to tadpole morphology and coloration after considering characteristics of the predator species and the prey themselves then test their own hypotheses (typically with t-tests or ANOVA) by collecting novel data via image...

Role-playing activities in the classroom promote students’ critical thinking, research, and communication skills. We present an activity where students debate a current controversy in conservation. In our case study, students debate the topic of wolf reintroduction in California. Each student is assigned a stakeholder role (e.g., rancher, environmental scientist, hunter, or politician) and a position (either pro or con). First, the whole class participates in a vote on the debate topic so as to register pre-debate sentiment. Then, in the first part of the activity (75 minutes or as homework), students prepare arguments with others representing their stakeholder group by reading the primary and secondary literature and answering guided questions. In the second part of the activity (75 minutes), students participate in a live debate divided into three sections: introductory arguments, questions from the jury, and concluding arguments. The whole class then votes again to decide the winner of the debate, leading to a discussion about which factors do and do not lead to changes in understanding and opinion. The interdisciplinary nature of this activity reinforces student knowledge on ecological networks, keystone species, and natural history, as well as introduces the importance of non-scientific stakeholders in conservation. While this case study focuses on the reintroduction of wolves in California, the activity can be adapted to the reintroduction of controversial species in other regions, or used as a framework for any debatable topic in conservation biology.

Primary Image: The reintroduction of the gray wolf Canis lupus is a controversial topic in conservation biology and environmental policy.

Traditional Ecological Knowledge (TEK) is based on deep understanding of systems from observations made over hundreds to thousands of years. This resource connects TEK to modern conservation through media and primary literature interpretation.

Metacognitive approach to improving students ability to read complex science articles.

This project focuses on the use of data analysis problems to introduce students to specific topics in microbiology and to give them practice in the interpretation of figures and tables of data. Each problem is based on a single journal article and includes five to eight multiple-choice questions.

In this activity, students will analyze raw data obtained from an experiment that explores the effect of overexpressing the Ssk protein in order to strengthen the intestinal barrier and prevent bacteria from leaking out of the gut and into the hemolymph, which is the fruit fly equivalent to blood in the circulatory system. Using Excel, students will fit an exponential function to the few known data points and will then interpolate the missing data points and extrapolate a few future data points. They will also learn how they can fit a linear model by transforming the data (applying the logarithmic function) and use that model to estimate the missing data points. This activity involves both statistical analysis and mathematical modeling as well as displaying the usefulness of mathematical models for biological data analysis.

Students use their number sense to make observations and come up with reasonable guesses or explanations for the patterns shown. These are some specifically for microbiology.

A user guide and video instructions for GBIF

A module guiding students through the process of building a biodiversity dataset using field data and protocols derived for a study of the invasive aquatic plant species, European frog-bit (Hydrocharis morsus-ranae L.). 

A novel activity was designed to introduce students to the concepts of natural selection and life history using an active-learning, constructivist format. It consisted of two parts: 1) a brief introduction to the basic mechanism of natural selection, and 2) a game that introduces life-history strategies. The activity was designed for use in the college classroom. It was shown to be an effective means of fostering a deep and transferrable conceptual understanding of the principles of natural selection specifically through the lens of life-history strategies. The activity is available in the supporting materials. It takes approximately one 50-minute period to complete.

Primary Image: Student Performing Life History Activity, a picture of a student filling out the life history game component of this activity.

A novel activity was designed to introduce students to the concepts of natural selection and life history using an active-learning, constructivist format. It consisted of two parts: 1) a brief introduction to the basic mechanism of natural selection, and 2) a game that introduces life-history strategies. The activity was designed for use in the college classroom. It was shown to be an effective means of fostering a deep and transferrable conceptual understanding of the principles of natural selection specifically through the lens of life-history strategies. The activity is available in the supporting materials. It takes approximately one 50-minute period to complete.

Primary Image: Student Performing Life History Activity, a picture of a student filling out the life history game component of this activity.

Students generate predictions and test three hypotheses about how biodiversity is affected by urbanization over time using citizen science generated bird count data and land use data from 13 locations in Florida over a 10 year time span

Targeting undergraduate students in lower-division ecology courses, this module guides students through authentic research. The purpose of this project is to provide hands-on research experience to enhance students' skills and confidence in the field of ecology. Within the module, students conduct a research project that allows them to: (1) explore recent studies in urban ecology, introducing the ecological research tools of camera traps and citizen science; (2) gain experience as a citizen scientist, generating data for different projects in Zooniverse; (3) write a hypothesis based on two possible research questions; and (4) analyze and test their hypothesis. The two possible research questions are: How do species’ diel activity patterns differ between land cover types (e.g., forest vs. anthropogenic)? How do diel activity patterns differ between/among species? Data for analysis is obtained through Snapshot USA. Through the module, students obtain skills in constructively reading and evaluating research papers, constructing testable hypotheses and predictions, using Excel to calculate Chi-Square and P-Values, interpreting statistical evidence, and presenting research findings.

Students will navigate through different stations experiencing simulations of adaptations, manipulations of 3D examples, and making connections to the standards to formulate hypotheses about certain adaptations and how they manifest in the morphology.

In this lesson students 1) become familiar with various graphs that are used to study diversity patterns within and across sites, 2) learn about some of the questions that can be addressed by metabarcoding studies, and 3) reflect on an interview with evolutionary ecologist Maria Rebolleda Gomez, who collected the data used in the lesson.

Traditional Ecological Knowledge is based on deep understanding of systems from observations made over hundreds to thousands of years. This resource connects Traditional Ecological Knowledge to modern conservation through media and primary literature interpretation. The adaptation of this research aims to link the material to the ecological concept of the intermediate disturbance hypothesis and to highlight ecologists whose careers have focused on the concept.

Stream reach metabolism integrates organism respiration & production to provide a valuable ecosystem measure that varies as a function of biotic & abiotic factors. As a powerful indicator of whole system functioning, it is important students can estimate stream metabolism. This field lesson engages students in study of ecosystem metabolism through its components, production & respiration. Students connect to the reach through guided reflection, predict and explore dissolved oxygen, investigate metabolism drivers in a matching game of diel oxygen curves from streams around the world, and collect & analyze diel dissolved oxygen data. This is designed for mid to upper-level undergraduates to complete in one 2-hour field visit at a wadable reach of run habitat, and a 30-minute analysis session. This lesson complements lessons including hydrogeomorphology, field sketching, organismal studies, ecosystem energetics, mapping, any that provide an ecosystem or energetic framework (RCC, Fluvial Landscape Ecology) to student understanding of flowing waters. Additionally, it can be replicated in space and time to highlight the relative importance of the key drivers of ecosystem metabolism.

Scientists have discovered that microplastic pollution is ubiquitous in the environment, but the small size of these microscopic pollutants prohibits most people from recognizing their prevalence. This river-based field lesson will introduce environmental science students to this emerging environmental concern, and encourages them to explore microplastics in their local waterways with sample collection, density separation and field-based microscopy. Students will appreciate the opportunity to connect to this topic from anywhere in the world, allowing them to see microplastics with their own eyes and without the use of sophisticated equipment. In addition, this lesson helps students recognize their own personal impact on microplastic pollution and identify ways to reduce their creation of microplastics.

A lecture will be hosted by the educator. The first four sections cover factual information and in the activity students will draw conclusions about spore germination. The last section will highlight a scientist and current trends in mycology.

Environmental health is a field of study within public health that is concerned with human-environment interactions, and specifically, how the environment influences public well-being. In this module, students will explore how environmental pollution impacts public health through comparing cancer rates of areas with known environmental pollutants to the national average through a t-test. Students can further their knowledge by comparing the concentrations of atmospheric pollutants in areas with known sources to control sites without such sources. Project EDDIE modules are designed with an A-B-C structure to make them flexible and adaptable to a range of student levels and course structures.

A foundational knowledge of the relationship between structure and function is critical to understanding how enzymes work. The seemingly invisible nature of these molecular interactions makes it challenging for undergraduate students to conceptualize the dynamic changes that occur during a catalytic cycle. In this Lesson, we describe an interactive, collaborative modeling activity that we use in introductory biology courses to teach students how enzymes catalyze chemical reactions. First, the students imagine a fictitious enzyme and its associated reaction, and use modeling compound to demonstrate the progression of the reaction while focusing on the three-dimensional shape of active site and substrate in facilitating this catalysis. Second, they then select one of four types of enzymatic regulation (competitive inhibition, allosteric inhibition, allosteric activation, or feedback inhibitions) to incorporate into their model. They then demonstrate these reactions to groups of peers. This student-centered approach uses active learning and peer instruction to provide students with prompt feedback to strengthen their understanding of the inter-relatedness of structure and function. This modeling activity concludes with student reflection and discussion, and student learning is assessed with exam questions.

Teaching scientific literacy skills can help combat the propagation of misinformation online. This lesson is intended to give students practice identifying reliable scientific information on the Internet, in the context of vaccine safety. It was designed for a first-year seminar taught fully through remote instruction but can be adapted for any in-person or blended course. It can also be easily modified to use for other biologically-relevant topics and is especially well suited for controversial topics. This lesson consists of three activities. First, students review an article about identifying reliable Internet resources and search online for vaccine safety information. Then, students meet in small groups to review and rank the resources that each of them found from most to least reliable, referencing the criteria laid out by the CRAAP test (Currency, Relevance, Accuracy, Authority, Purpose). After ranking each resource, students reflect on how their thinking about online resources has changed during the activity and how they will evaluate scientific information online in the future. Finally, students use the reliable resources that they and their classmates compiled during the activity as references to write about how the biology of vaccines relates to the five Core Concepts. Following this lesson, 100% of student groups were able to correctly identify at least one reliable and unreliable online resource and 95% of groups were able to articulate particular qualities of resources that helped them establish their reliability. Further, 100% of groups could articulate how their thinking had changed throughout this activity.

Primary Image: A drawing of vaccines and a vial, used with permission from Pixabay. 

As the basic unit of life, cells are a foundational concept for all of biology. Before students can appreciate how eukaryotic cells function either in isolation or in higher order and multicellular organisms, they must first have a basic understanding of the organelles that make up these cells. The primary objective of this lesson is to provide a fun and engaging way for students to learn the function and arrangement of eukaryotic organelles. This lesson uses familiar and easy to learn games, such as Pictionary® and Bingo, to help students enrolled in introductory, non-majors biology courses better recognize cellular organelles and understand their functions.

cellular respiration and weight loss

Surface to area volume-detailed

surface area to volume ratio

University capstone projects can offer science students a rich research experience that illustrates the process of doing scientific research, and can also help students better choose future academic and career pathways. While capstone projects are an effective component of students' learning in the sciences, they are resource and labor intensive for supervising faculty and are not always logistically feasible in understaffed and/or under-resourced departments and colleges. A good compromise is to incorporate a significant research component into upper division classes. This article documents a project I have incorporated into a plant ecology course that I teach every spring. This project gives students a taste of what practicing ecologists do in their professional lives. Students learn how to survey vegetation and environmental factors in the field, apply several statistical analysis techniques, formulate testable hypotheses relevant to a local plant community, analyze a large shared data set, and communicate their findings both in writing and in a public presentation. Over the weeks required for this project, students learn that doing science is quite different from how they typically learn about science. Most say that, while this project is one of the hardest they have completed in their time in university, they appreciate being treated like a fellow scientist rather than as "just a student." Additionally, students' findings often reveal complex and subtle interactions in the plant community sampled, providing further insight to and examples of emergent properties of biological communities.

A successful scientist combines skill, creativity, and the art of persuasion to excel in his or her field of study. Critically important for the professional scientist is the ability to not only conduct research, but also to conceive a project and obtain funding to support research goals. As students grow in their scientific process skills over the course of their training, they are often surprised by the structures and processes used by professional scientists to procure funds for their work. We describe a semester-long experience in which students engage the process of science to design an innovative research plan on a topic that is relevant to the scientific community and society. Research teams seek funding to pursue a novel, high-impact research question, and submit proposals for peer review in a mock NSF-style study section. The module design uses a scaffolded series of writing and peer review activities, and culminates in a Pecha Kucha event in which students orally pitch and defend their proposal and vote for the best in session. The module may be scaled and adapted to suit a wide range of contexts where proposal writing and peer review is emphasized.

To prepare biology undergraduates to be able to read and evaluate the primary literature, it is beneficial to teach students how to write documents in the style of professional science style manuscripts. By breaking manuscripts into individual section assignments, we can distribute instruction across a four-year undergraduate curriculum to scaffold writing practice mastery. These skills are aided by peer review, writing tutor instruction, and assignment repetition. Students gain not only competency in writing about the discipline, but can better understand and critically evaluate the written work of others. The science writing and communication skills gathered over the course of this curricular framework provide all students with expertise in accessing science themselves and disseminating science to others.

Reading primary scientific literature enhances students’ understanding of material, increases their self-efficacy, and critical thinking skills. However, scientific articles often present multiple challenges to the students, the first among them is the unfamiliar nature of scientific texts: their high information density, formal language, and abundance of scientific jargon. In this lesson, students are taught the Talking to the Text method to metacognitively read scientific texts. The Talking to the Text method, which is part of the Reading Apprenticeship approach, enables students to have a metacognitive conversation with a scientific text, annotating it with their own questions, connections to previous knowledge, predictions, and drawings. The method is introduced through instructor’s modeling, individual practice, peer interactions, and class discussions. The collaborative approach of this lesson normalizes the struggles that students face when reading complex scientific texts. We have successfully used the Talking to the Text method in an introductory biology course with diverse students who often do not have experience in reading dense scientific texts. We find that this method promotes inclusion and holds students accountable to address what they do not understand in the text. In a survey, half of the students indicated that they were still using the method at the end of the semester. Students commented that the method improved their understanding of concepts, built their metacognitive skills, and helped them connect new information with what they already know. We believe that this method can be valuable for all students who are starting to read complex scientific texts.

Primary Image: Using Talking to the Text to metacognitively read scientific literature. A student reads a scientific text using the Talking to the Text method. The student engages in metacognitive conversation with the text by identifying the confusing parts of the text, making connections between new and existing knowledge, and drawing pictures of concepts or experiments.

A compilation of videos to support teaching the concepts and protocols for discovering and working with phage.

Week 1 Potential

Week 1 Potential

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.

This multi part case on hemoglobin structure as it relates to oxygen binding and sickle cell disease focuses on utilizing bioinformatics and molecular visualization tools to learn about the sickle cell disease, its cause, symptoms and possible cures.

This 3 part case on sickle cell disease focuses on visualizing and understanding the molecular basis of its cause, symptoms, complications, management, treatment, and possible cures.

The mathematical modeling of populations utilizing field-collected demographic data is an important component of lab curricula in a variety of undergraduate biology lab courses. During the global pandemic brought about by the SARS-CoV-2 virus in 2020, we successfully converted an in-person lab on demographic population modeling to a lab that could be run remotely. We used a Google Earth Web Project to simulate a population study of the Northern Spotted Owl. In the simulation, students collected both demographic and mark-recapture data, based on surveying images of Northern Spotted Owls as they navigated four different wildlife transects. After conducting the survey, students used the data to determine population size using the mark-recapture method, derived a life table, calculated the net reproductive rate, and used the information to assess the current management plan for the population studied. Here we outline the lesson and provide materials required to duplicate the lab or to use Google Earth to create a similar simulation centered around a different species in any location around the globe.

Primary Image: Population Ecology with Google Earth. This population ecology lesson utilizes the Google Earth Project to provide students a simulated mark-recapture study. This lesson framework can be applied to any species or location; we chose to focus our lesson on the Northern Spotted Owl.

Evolutionary trees communicate both the diversity and unity of life, a central and important scientific concept, as highlighted by the Vision and Change undergraduate biology education movement. Evolutionary trees and cladograms are diagrams viewed by biologists as Rosetta Stone-like in how well they convey an enormous amount of information with clarity and precision. However, the majority of undergraduates in introductory biology courses find the non-linear diagram confusing and do not immediately understand the tree-thinking central to interpreting the evolutionary tree’s branching structure. Go Extinct! is an original board game featuring land vertebrates (i.e., amphibians, mammals, birds and reptiles) and it is designed to engage students in reading this evolutionary tree. Go Extinct! won the Society for the Study of Evolution’s Huxley Award for outstanding outreach achievements in recognition for how the gameplay itself incentivizes students to identify clades and common ancestors on a stylized tree. The game can be completed in about 30 minutes, which allows instructors time to give follow-up activity sheets that help students transfer their new ability to read a stylized tree into the ability to read more traditional-looking trees found in textbooks and the literature. Overall, teaching the game, playing the game, and completing the follow-up transfer activity can be completed in a 50-minute section. Each game can serve up to 6 students, which means 3 games can cover a section of 18 students. Go Extinct! provides a fun and effective learning experience that students will remember and may even request to play again.

Primary Image: Biologists play Go Extinct! Students who play Go Extinct! gain a mastery of reading an evolutionary tree or cladogram. The winning strategy depends on identifying common ancestors of animal cards in your hand. Photo taken by the author.

Role-playing activities in the classroom promote students’ critical thinking, research, and communication skills. We present an activity where students debate a current controversy in conservation. In our case study, students debate the topic of wolf reintroduction in California. Each student is assigned a stakeholder role (e.g., rancher, environmental scientist, hunter, or politician) and a position (either pro or con). First, the whole class participates in a vote on the debate topic so as to register pre-debate sentiment. Then, in the first part of the activity (75 minutes or as homework), students prepare arguments with others representing their stakeholder group by reading the primary and secondary literature and answering guided questions. In the second part of the activity (75 minutes), students participate in a live debate divided into three sections: introductory arguments, questions from the jury, and concluding arguments. The whole class then votes again to decide the winner of the debate, leading to a discussion about which factors do and do not lead to changes in understanding and opinion. The interdisciplinary nature of this activity reinforces student knowledge on ecological networks, keystone species, and natural history, as well as introduces the importance of non-scientific stakeholders in conservation. While this case study focuses on the reintroduction of wolves in California, the activity can be adapted to the reintroduction of controversial species in other regions, or used as a framework for any debatable topic in conservation biology.

Primary Image: The reintroduction of the gray wolf Canis lupus is a controversial topic in conservation biology and environmental policy.

The central dogma of biology is a foundational concept that provides a scaffold to understand how genetic information flows in biological systems. Despite its importance, undergraduate students often poorly understand central dogma processes (DNA replication, transcription, and translation), how information is encoded and used in each of these processes, and the relationships between them. To help students overcome these conceptual difficulties, we designed a clicker-based activity focused on two brothers who have multiple nucleotide differences in their dystrophin gene sequence, resulting in one who has Duchenne muscular dystrophy (DMD) and one who does not. This activity asks students to predict the effects of various types of mutations on DNA replication, transcription, and translation. To determine the effectiveness of this activity, we taught it in ten large-enrollment courses at five different institutions and assessed its effect by evaluating student responses to pre/post short answer questions, clicker questions, and multiple-choice exam questions. Students showed learning gains from the pre to the post on the short answer questions and performed highly on end-of-unit exam questions targeting similar concepts. This activity can be presented at various points during the semester (e.g., when discussing the central dogma, mutations, or disease) and has been used successfully in a variety of courses ranging from non-majors introductory biology to advanced upper level biology.

The central dogma of biology is a foundational concept that provides a scaffold to understand how genetic information flows in biological systems. Despite its importance, undergraduate students often poorly understand central dogma processes (DNA replication, transcription, and translation), how information is encoded and used in each of these processes, and the relationships between them. To help students overcome these conceptual difficulties, we designed a clicker-based activity focused on two brothers who have multiple nucleotide differences in their dystrophin gene sequence, resulting in one who has Duchenne muscular dystrophy (DMD) and one who does not. This activity asks students to predict the effects of various types of mutations on DNA replication, transcription, and translation. To determine the effectiveness of this activity, we taught it in ten large-enrollment courses at five different institutions and assessed its effect by evaluating student responses to pre/post short answer questions, clicker questions, and multiple-choice exam questions. Students showed learning gains from the pre to the post on the short answer questions and performed highly on end-of-unit exam questions targeting similar concepts. This activity can be presented at various points during the semester (e.g., when discussing the central dogma, mutations, or disease) and has been used successfully in a variety of courses ranging from non-majors introductory biology to advanced upper level biology.

The central dogma of biology is a foundational concept that provides a scaffold to understand how genetic information flows in biological systems. Despite its importance, undergraduate students often poorly understand central dogma processes (DNA replication, transcription, and translation), how information is encoded and used in each of these processes, and the relationships between them. To help students overcome these conceptual difficulties, we designed a clicker-based activity focused on two brothers who have multiple nucleotide differences in their dystrophin gene sequence, resulting in one who has Duchenne muscular dystrophy (DMD) and one who does not. This activity asks students to predict the effects of various types of mutations on DNA replication, transcription, and translation. To determine the effectiveness of this activity, we taught it in ten large-enrollment courses at five different institutions and assessed its effect by evaluating student responses to pre/post short answer questions, clicker questions, and multiple-choice exam questions. Students showed learning gains from the pre to the post on the short answer questions and performed highly on end-of-unit exam questions targeting similar concepts. This activity can be presented at various points during the semester (e.g., when discussing the central dogma, mutations, or disease) and has been used successfully in a variety of courses ranging from non-majors introductory biology to advanced upper level biology.

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.

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)

Our understanding of microbiomes, or the collection of microorganisms and their genes in a given environment, has been revolutionized by technological and computational advances. However, many undergraduate students do not get hands-on experiences with processing, analyzing, or interpreting these types of datasets. Recent global events have increased the need for effective educational activities that can be performed virtually and remotely. Here, we present a module that introduces STEM undergraduates to the bioinformatic and statistical analyses of bacterial communities using a combination of free, web-based data processing software. These lessons allow students to engage with the studies of microbiomes; gain valuable experiences processing large, high-throughput datasets; and practice their science communication skills. The lessons presented here walk students through two web-based platforms. The first (DNA Subway) is an easy-to-use wrapper of the popular QIIME (pronounced “chime”) pipeline, which performs quality control analysis of the raw sequence data and outputs a community matrix file with assigned bacterial taxonomies. The second, ranacapa, is an R Shiny App that allows students to compare microbial communities, perform statistical analyses and visualize community data. Students may communicate their findings with a written final report or oral presentation. While the lessons presented here use a sample dataset based on the gut-microbiome of the bean beetle (Callosobruchus maculatus), the materials are easily modified to use original next-generation amplicon sequence data from any host or environment. Additionally, options for alternative datasets are also provided facilitating flexibility within the curriculum.

Primary Image: Insects are an excellent example of a tractable biological system to study the relationship between an organism and its microbiome. Little is currently known about the gut-microbiome of many insects, such as the bean beetle (Callosobruchus maculatus).

At the heart of scientific ways of knowing is the systematic collection and analysis of data, which is then used to propose an explanation of how the world works. In this two-day module, students in a large-lecture course are immersed in a biological problem related to the Central Dogma and gene expression. Specifically, students interpret experimental data in small groups, and then use those data to craft a scientific argument to explain how alternative splicing of a transcription factor gene may contribute to human cancer. Prior to the module, students are assigned a reading and provided PowerPoint slides outlining the basics of alternative splicing and refreshing their understanding of gene regulation. Students complete a pre-class assignment designed to reinforce basic terminology and prepare them for interpreting scientific models. Each day of the module, students are presented experimental data or biological models which they interpret in small groups, use to vote for viable hypotheses using clickers, and ultimately leverage in a culminating summary writing task requiring them to craft a data-driven answer to the biological problem. Despite the novelty of the argumentation module, students engage in all aspects (inside and outside of the classroom) of the activity and are connected across data, hypotheses, and course concepts to explain the role of alternative splicing in gene expression and cancer.

Primary image: Splicing it together. Students work together, interpreting primary data and models to investigate the effects alternative splicing may have on gene regulation and cancer.

At the heart of scientific ways of knowing is the systematic collection and analysis of data, which is then used to propose an explanation of how the world works. In this two-day module, students in a large-lecture course are immersed in a biological problem related to the Central Dogma and gene expression. Specifically, students interpret experimental data in small groups, and then use those data to craft a scientific argument to explain how alternative splicing of a transcription factor gene may contribute to human cancer. Prior to the module, students are assigned a reading and provided PowerPoint slides outlining the basics of alternative splicing and refreshing their understanding of gene regulation. Students complete a pre-class assignment designed to reinforce basic terminology and prepare them for interpreting scientific models. Each day of the module, students are presented experimental data or biological models which they interpret in small groups, use to vote for viable hypotheses using clickers, and ultimately leverage in a culminating summary writing task requiring them to craft a data-driven answer to the biological problem. Despite the novelty of the argumentation module, students engage in all aspects (inside and outside of the classroom) of the activity and are connected across data, hypotheses, and course concepts to explain the role of alternative splicing in gene expression and cancer.

Primary image: Splicing it together. Students work together, interpreting primary data and models to investigate the effects alternative splicing may have on gene regulation and cancer.

A compelling reason to learn something can make all the difference in students’ motivation to learn it.  Motivation, in turn, is one of the key attitudes that drives learning.  This story presents students with a compelling puzzle of a fatherless snake.  The puzzle motivates students to learn about meiosis and mitosis, since the only way to explain the origin of the fatherless baby is by mastering details of meiosis.  During the process, students work through the major steps in meiosis, compare and contrast mitosis and meiosis, and apply their understanding to predict how meiosis “went wrong” to produce an unusual offspring that did not originate through union of an egg and a sperm.  This story can be adapted for introductory or advanced students and can be scaled from a brief introduction in a single lecture to a series of active learning exercises that could take two or more lecture periods.

Parthenogenesis accompanying article

The mathematical modeling of populations utilizing field-collected demographic data is an important component of lab curricula in a variety of undergraduate biology lab courses. During the global pandemic brought about by the SARS-CoV-2 virus in 2020, we successfully converted an in-person lab on demographic population modeling to a lab that could be run remotely. We used a Google Earth Web Project to simulate a population study of the Northern Spotted Owl. In the simulation, students collected both demographic and mark-recapture data, based on surveying images of Northern Spotted Owls as they navigated four different wildlife transects. After conducting the survey, students used the data to determine population size using the mark-recapture method, derived a life table, calculated the net reproductive rate, and used the information to assess the current management plan for the population studied. Here we outline the lesson and provide materials required to duplicate the lab or to use Google Earth to create a similar simulation centered around a different species in any location around the globe.

Primary Image: Population Ecology with Google Earth. This population ecology lesson utilizes the Google Earth Project to provide students a simulated mark-recapture study. This lesson framework can be applied to any species or location; we chose to focus our lesson on the Northern Spotted Owl.

In this lesson, students discuss anti-predator defense mechanisms and the types of cues defenses provide to predators. Students then interpret graphs of behavior of arthropod predators when presented with different phenotypes of color polymorphic tortoise beetles. Finally, students view and reflect on an interview with Dr. Lynette Strickland, the biologist who collected the data that they interpreted.

DNA replication, mutation

Multiple Alleles

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.

In March 2020, institutions underwent a massive transition to distance learning as a result of the COVID-19 pandemic. With so little time to devise new materials to maximize learning in the new virtual environment, instructors devised a variety of innovative strategies for completing the Spring 2020 semester. While highly disruptive, the pandemic also brought mainstream attention to a wide array of scientific concepts and provided an opportunity to teach students about science in real-time. Teaching topics related to COVID-19 can be approached from many different disciplines such as virology, immunology, biochemistry, genetics, public health, pharmacology, systems biology, and synthetic biology. By bringing together lessons devised by each of the authors on their own, we offer a series of curriculum modules that can be used either collectively or in parts to provide students with a multidisciplinary look at the virus and to answer their own curiosity about the disease that will define their generation.

Primary image: 360-degree view of COVID-19. The primary image depicts a SARS-CoV-2 virion surrounded by the fields of study that are featured in our pedagogical activities.

Engaging and supporting introductory level students in authentic research experiences during required coursework is challenging. Plant bioactive compounds attract students' natural curiosity as they are found in many familiar items such as tea, coffee, spices, herbs, vegetables, essential oils, medicines, cleaning supplies, and pesticides. Over the course of one semester, students work in teams to design experiments in three experimental modules to test whether bioactive compounds have effects on Daphnia heart rate, antibacterial activity, or caterpillar behavior. In a fourth module, they research solutions to an environmental problem. Students are involved in multiple scientific practices as they make their own experimental decisions, analyze data including using statistics to carefully justify their preliminary conclusions, and have the opportunity to improve their experiment and repeat it. Iteration is also emphasized by the fact that students go through the whole process from design to presentation repeatedly for three experiments. In the process, students experience for themselves the real complexity of scientific investigations and what it takes to rigorously show cause-and-effect relationships. The pedagogical focus is on providing introductory students with a supportive structure in a way that empowers them to make informed experimental decisions and be successful. At the end of the semester, the majority of students displayed a strong sense of personal involvement and an appreciation of the difficulties of scientific experimentation in open-ended written reflections. Students reported that statistics was one of the most difficult yet valuable experiences in these labs and demonstrated significant gains on a statistical test.

Primary image: Summary of the Lesson showing that student decide on which bioactive compounds to test in three model organisms (image attributions listed in Acknowledgments).

Students are frequently overwhelmed by the complexity of metabolic pathways and they think they have "learned" the pathway when they have memorized the individual reactions.  This laboratory lesson helps students to understand the significance of individual reactions in the pathways leading to methionine synthesis in the budding yeast, Saccharomyces cerevisiae.  Students appreciate that methionine is one of only two sulfur-containing amino acids, and students do not find it difficult to follow the "yellow" sulfur atom in the pathway. In the lesson, students use three different yeast met strains, each of which lacks a single gene involved in methionine synthesis.  Working in groups of three, students identify the missing MET gene in each of the three deletion strains by analyzing the abilities of the deletion strains to grow on several defined media in which methionine has been replaced with alternative sulfur sources. Students also determine the position of mutant genes in the pathway relative to sulfite reductase, using indicator media that reacts with sulfide, the product of the reaction catalyzed by sulfite reductase. For the analysis, students prepare serial dilutions of yeast cultures and spot the dilution series on agar plates. This lesson is part of a semester-long research investigation into the evolutionary conservation of the genes involved in methionine synthesis. The lesson can also be used as a stand-alone exercise that teaches students about biochemical pathways, while reinforcing basic microbiological techniques.

To facilitate understanding of the fundamental genetic concept of the genotype-phenotype relationship in our introductory biology students, we designed an engaging multi-week series of related lessons about canine genetics in which students explore and answer the question, "How does the information encoded in DNA lead to physical traits in an organism?" Dogs are an excellent model organism for students since the genetic basis for complex morphological traits of various breeds is an active area of scientific research and dog DNA is easily accessible. Additionally, examination of students' pets offers a relatable, real-world, connection for students. Of the more than 19,000 genes that control canine genetics, simple genetic mutations in three genes are largely responsible for the coat variations of dogs –specifically, the genes that control hair length, curl, and the presence/absence of furnishings. In our lessons, students collect DNA samples from dogs, isolate and amplify targeted sections of DNA through polymerase chain reactions (PCR), and then sequence and analyze DNA for insertions and single nucleotide polymorphism (SNP) mutations. Utilizing gel electrophoresis and bioinformatics tools, students connect how the physical manifestation of traits is rooted in genetic sequences. Students also participate in discussions of scientific literature, group collaboration to construct a final poster, and presentation of their findings during a mock scientific poster conference. Through this module students engage in progressive exploration of genetic and molecular techniques that reveal how simple variations in a few DNA sequences in combination lead to a broad diversity of coat quality in domestic dog breeds.

Primary image. Genetic Analysis of Canine Coat Morphologies. Three dogs with differing coat morphologies analyzed by students (A, B, C), an agarose gel post-electrophoresis (D), and a chromatogram of a DNA sequence highlighting a relevant mutation (E). This collage contains original images taken by authors and course participants.

To facilitate understanding of the fundamental genetic concept of the genotype-phenotype relationship in our introductory biology students, we designed an engaging multi-week series of related lessons about canine genetics in which students explore and answer the question, "How does the information encoded in DNA lead to physical traits in an organism?" Dogs are an excellent model organism for students since the genetic basis for complex morphological traits of various breeds is an active area of scientific research and dog DNA is easily accessible. Additionally, examination of students' pets offers a relatable, real-world, connection for students. Of the more than 19,000 genes that control canine genetics, simple genetic mutations in three genes are largely responsible for the coat variations of dogs –specifically, the genes that control hair length, curl, and the presence/absence of furnishings. In our lessons, students collect DNA samples from dogs, isolate and amplify targeted sections of DNA through polymerase chain reactions (PCR), and then sequence and analyze DNA for insertions and single nucleotide polymorphism (SNP) mutations. Utilizing gel electrophoresis and bioinformatics tools, students connect how the physical manifestation of traits is rooted in genetic sequences. Students also participate in discussions of scientific literature, group collaboration to construct a final poster, and presentation of their findings during a mock scientific poster conference. Through this module students engage in progressive exploration of genetic and molecular techniques that reveal how simple variations in a few DNA sequences in combination lead to a broad diversity of coat quality in domestic dog breeds.

Primary image. Genetic Analysis of Canine Coat Morphologies. Three dogs with differing coat morphologies analyzed by students (A, B, C), an agarose gel post-electrophoresis (D), and a chromatogram of a DNA sequence highlighting a relevant mutation (E). This collage contains original images taken by authors and course participants.

Typical biochemistry labs exploring basic enzyme activity rely on costly, time-consuming protein purification and rarely explore enzyme function in situ. Further, complex purification procedures leave little room for novelty in experimental design. Here we present an inquiry-driven laboratory exercise for biochemistry undergraduates and adaptations for a general education science course. Each student designs a unique experiment to test their hypothesis regarding the nature of avocado browning in a three-hour span. In the presence of oxygen, polyphenol oxidases (PPO) catalyze oxidation of phenolic compounds into quinones, the polymerization of which creates the visible browning of many cut fruits. Avocado fruit, a source of both enzyme and substrate, is a safe, low-cost vehicle for semi-quantitative experimentation. During the incubation, biochemistry students use the Protein Data Bank and primary literature to understand the structure-function relationship of PPO and other molecular components of the avocado. Non-major students discuss how pH, temperature, and substrate availability affect PPO. Visible browning pigments appear on a controllable time scale. Students can photograph results to create a figure to accompany semi-quantitative analysis of experimental results in a single lab period. Since avocados are familiar foods and select test reagents are generally recognized as safe, the optimal protocol investigated in the lab can be further applied to best practices in the kitchen in everyday life, promoting the transfer of knowledge learned in the classroom to practical environments.

To vaccinate or not to vaccinate, that is the question. Much of the recent trend in society against vaccination is that the general population does not understand 1) how vaccines work and 2) how one's vaccination status can influence others. Further compounding this is rather low acceptance of the influenza vaccine, a vaccine which is sometimes not even effective against the strains predominantly in circulation. Through engaging in a conversation about the role of vaccines in immunity not only of oneself but also about surrounding persons, we can increase vaccine acceptance. Herein is a physical assay which illustrates the concept of herd immunity with differing levels of vaccinations within a population. Students will learn that low vaccination rates do little to nothing to stop disease spread and that a large portion of the population (80%) is necessary to achieve near-eradication. This lesson is able to be taught at multiple levels using supplies that can mostly be obtained at the grocery store. In addition to illustrating vaccination, this study approximates a direct enzyme-linked immunosorbent assay (ELISA), enabling students to better understand that technique and how it is used to diagnose disease as well as the interrelation between antigens and antibodies.

Participation in research provides personal and professional benefits for undergraduates. However, some students face institutional barriers that prevent their entry into research, particularly those from underrepresented groups who may stand to gain the most from research experiences. Course-based undergraduate research experiences (CUREs) effectively scale research availability, but many only last for a single semester, which is rarely enough time for a novice to develop proficiency. To address these challenges, we present the Pipeline CURE, a framework that integrates a single research question throughout a biology curriculum. Students are introduced to the research system - in this implementation, C. elegans epigenetics research - with their first course in the major. After revisiting the research system in several subsequent courses, students can choose to participate in an upper-level research experience. In the Pipeline, students build resilience via repeated exposure to the same research system. Its iterative, curriculum-embedded approach is flexible enough to be implemented at a range of institutions using a variety of research questions. By uniting evidence-based teaching methods with ongoing scientific research, the Pipeline CURE provides a new model for overcoming barriers to participation in undergraduate research.

The aim of this project is to help undergraduates understand the importance of making their research accessible to a wide audience and to practice this idea by deliberately designing a scientific poster that is accessible to a more inclusive audience. Students will complete an activity that helps them identify the main conclusion of their research and helps them identify the key supporting data for that conclusion. Then, students will use their main conclusion and figures to design a scientific poster. These activities are designed to be used with students that have already completed their research and have results figures.

This series of modules explores the complex world of polyploidy, including species formation, cell division, evolution, conservation, and economic importance. We focus on polyploidy across the plant and animal kingdoms using hands-on exercises and case studies.

This is cool!

Students explore how climate is changing from the recent record. Produced by Project EDDIE.

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.

The module was used in lab following lecture material on pairwise interactions in ecology (emphasizing consumption, competition, mutualism), and parallel to community ecology (emphasizing food web structure, succession, resistance and resilience).

Write-to-learn (WTL) assignments have been used in a variety of disciplines to encourage conceptual learning and critical thinking in undergraduate education. These assignments focus on facilitating rather than assessing learning. Conversely, write-to-communicate (WTC) assignments (e.g., lab reports and exams), often with the goal of assessing learning, are more commonly employed in foundation STEM courses. We developed a WTL assignment that focuses on promoting curiosity driven learning, critical thinking, and metacognition; skills that promote students’ scientific literacy through writing. We integrated theoretical frameworks for scientific literacy, that include the sub-constructs of third space, authenticity, and multiple discourse as well as science as a human endeavour, and metacognition and self-direction (1, 2) to develop this 3-part WTL assignment. In this assignment, students first select a topic of interest and write freely on their current understanding of the topic (Part 1). They then develop a research question based on their writing and seek answers to their question from published literature (Part 2). Finally, they reflect on their overall experience with the WTL process and propose further avenues of investigation for their research topic (Part 3). Student feedback suggests that they enjoyed the WTL process and their overall satisfaction with the structure of the assignment was high. As we continue to evolve the assignment based on student feedback, we are gratified that students reported high self-efficacy with regard to future writing as a result of participating in this assignment. We recommend use of this type of WTL assignment in large, introductory STEM courses, so as to facilitate rather than simply assess students’ learning.

Primary Image: Scientific literacy through writing. Schematic depicting a write-to-learn assignment format implemented in an introductory undergraduate biology course, along with corresponding science literacy constructs.

As biology becomes more data driven, teaching students data literacy skills has become central to biology curriculum. Despite a wealth of online resources that teach researchers how to use R, there are few that offer practical laboratory-based exercises, with teaching resources such as keys, learning objectives, and assessment materials. Here, we present a modular set of lessons and lab activities to help teach R through the platform of RStudio. Both software applications are free and open source making this curriculum highly accessible across various institutions. This curriculum was developed over several years of teaching a graduate level computational biology course. In response to the pandemic, the class was shifted to be completely online. These resources were then migrated to GitHub to make them broadly accessible to anyone wanting to learn R for the analysis of biological datasets. In the following year, these resources were used to teach the course in a flipped format, which is the lesson plan presented here. In general, students responded well to the flipped format, which used class time to conduct live coding demos and work through challenges with the instructor and teaching assistant. Overall, students were able to use these skills to practice analyzing and interpreting data, as well as producing publication quality graphics. While the modules presented range from very basic, doing simple summary statistics and plotting, to quite advanced, where R is integrated onto the command line, teachers should feel free to pick and choose which elements to incorporate into their own curriculum.

Primary Image: R‐Mini‐Course: An Introduction to R. The primary image was generated with BioRender to be a small representation of the applicability of R that we cover in our course.

How to determine physiochemical features of proteins using ExPasy Protpram, SOSUI server, and PSortB programs.

This case focuses on understanding how a mutation in a cell signalling protein (a kinase) can prevent insulin function and lead to diabetes.