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.