Cellular respiration game

Genome search

The relationship between protein structure and function is a foundational concept in undergraduate biochemistry. We find this theme is best presented with assignments that encourage exploration and analysis. Here, we share a series of four assignments that use open-source, online molecular visualization and bioinformatics tools to examine the interaction between the SARS-CoV-2 spike protein and the ACE2 receptor. The interaction between these two proteins initiates SARS-CoV-2 infection of human host cells and is the cause of COVID-19. In assignment I, students identify sequences with homology to the SARS-CoV-2 spike protein and use them to build a primary sequence alignment. Students make connections to a linked primary research article as an example of how scientists use molecular and phylogenetic analysis to explore the origins of a novel virus. Assignments II through IV teach students to use an online molecular visualization tool for analysis of secondary, tertiary, and quaternary structure. Emphasis is placed on identification of noncovalent interactions that stabilize the SARS-CoV-2 spike protein and mediate its interaction with ACE2. We assigned this project to upper-level undergraduate biochemistry students at a public university and liberal arts college. Students in our courses completed the project as individual homework assignments. However, we can easily envision implementation of this project during multiple in-class sessions or in a biochemistry laboratory using in-person or remote learning. We share this project as a resource for instructors who aim to teach protein structure and function using inquiry-based molecular visualization activities.

Primary image: Exploration of SARS-CoV-2 spike protein: student generated data from assignments I - IV. Includes examples of figures submitted by students, including a sequence alignment and representations of 3D protein structure generated using UCSF Chimera. The primary image includes student generated data and a cartoon from Pixabay, an online repository of copyright free art. 

Students will learn about infectious disease and the immune response to infection by investigating different types of tests (PCR, antigen, and antibody tests) to detect the SARS-CoV-2 viral genetic material, antigens, or anti-SARS-CoV-2 antibodies. In the activity, students will apply core concepts and competencies from Vision & Change (https://visionandchange.org/). The activity uses a jigsaw format, with students choosing one of three specialities (epidemiologist, infectious disease doctor, or immunologist) and completing an assignment, either in-class or as homework, based on their speciality. In groups, students first hold a conference by speciality, then teams with representatives from each speciality discuss possible conclusions using results from the three different tests for a hypothetical patient.

To complement AbleWeb BRCA1 activity

Most molecular biology and biological sciences students understand that the polymerase chain reaction (PCR) is used to amplify DNA. However, we have found that some students experience conceptual misunderstandings, a lack of detailed comprehension of the PCR process, or difficulties with troubleshooting and predicting the effects of alterations to the standard PCR process. We hypothesized that a problem-based learning approach that incorporates a kinesthetic modeling of the PCR process could address these problems. During this hands-on learning activity, students “amplified” a specific region of template DNA through three cycles of PCR using a “toolkit” composed of a) intertwined, supercoiled, and double-stranded yarn representing template DNA, b) short wax sticks representing primers, and c) long wax sticks representing the PCR products. Instructors can introduce a variety of assessments, including real-time image capture of the models, pre- and post-activity assessment quizzes, and homework assignment to gauge student learning. We administered identical four-question quizzes worth 12 points to 28 undergraduate students before and after the activity. The mean score on the post-quiz was three points higher than the pre-quiz score, demonstrating a 75% increase in score. Moreover, we found that students who began the activity with lower levels of understanding experienced the most significant learning gains. This hands-on, student-centered, kinesthetic activity allowed students to (i) visualize PCR processes, (ii) construct a model of the PCR process, (iii) correct common misconceptions and sources of confusion, and (iv) actively engage in the learning process.

Although genetics is an invaluable part of the undergraduate biology curriculum, it can be intimidating to students as well as instructors: Students must reduce their reliance on memorization and dive deep into quantitative analysis, and instructors must make a long, rich history of genetics experiments clear, coherent, and relevant for students. Our Lesson addresses these challenges by having students map an unknown mutation to its gene using a modern suite of genetic tools. Students receive a Drosophila melanogaster strain with a mutation that causes the normally flat wing to bend at distinct sites along its length. Although we recently mapped this mutation to its gene, here we have renamed it "crumpled wing" (cw), an example of a pseudonym that you could use in the classroom. Like many standard "fly labs" that are taught at undergraduate institutions, this Lesson reinforces classic genetics concepts: students selectively mate fly strains to determine mode of inheritance, test Mendel's Laws, and three-point map an unknown mutation relative to known markers. But here, we expand on this tradition to simulate a more modern primary research experience: we greatly increase mapping resolution with molecularly-defined transgene insertions, deletions, and duplications; then cross-examine our data with key bioinformatic resources to identify a short-list of candidate cw genes. After extensive data interpretation and integration, students have been able to map cw to a single gene. This Lesson has a flexible design to accommodate a wide range of course structures, staffing, budgets, facilities, and student experience levels.

Some concepts in genetics, such as genetic screens, are complex for students to visualize in a classroom and can be cumbersome to undertake in the laboratory. Typically, very large populations are needed, which can be addressed by using micro-organisms. However, students can struggle with phenotyping microbes. For macroscopic organisms, the number of offspring produced, and the generation time can be challenging. I developed this lesson as a small-scale genetic screen of Fast Plants^®. These plants are amenable to teaching labs as they have simple growth requirements, a short generation time, and produce numerous seeds that can be stored for years. Seeds used for this screen are purchased pre-treated with a DNA damaging agent, removing the need for in-house use of mutagens. Also, students can screen the phenotypes without specialized equipment. The initial lesson begins with an examination of the first generation of plants. Later their offspring are screened for altered phenotypes. Students responded well to having full-grown plants available on the first day of the lab project. This lesson fostered student collaboration, as they worked with class datasets. Differences in growth due to mutagenesis treatment in the first generation were clear to students who had not worked with plants before. Identifying plants with altered phenotypes in the next generation was more of a challenge. This lesson incorporates key concepts such as somatic and germline mutations, the impact of such mutations on phenotype, and the inheritance of mutation alleles, and provides a hands-on way to illustrate these concepts.

Primary Image: Fast Plant^® phenotype differences observed in the M2 generation. This pot contains three full-sibling M2 seedlings from a single M1 parent plant. The seed of their parent plant received 50 Krads of radiation. Plants 1 and 2 are of standard height, while plant 3 is greatly elongated. Image by AL Klocko.

Undergraduate education and long-term science literacy are enhanced by integrating data projects with public datasets and creating analysis summaries. Underutilized public datasets are often generated by community-based or citizen science projects to address conservation issues supported by local residents. The objectives of this course activity are for students to contribute to a community science project, observe local species diversity, develop biodiversity questions, and apply data science techniques. Engaging students in these local projects enhances their understanding of the scientific process and its broader impacts on their community. The City Nature Challenge (CNC) is an annual global community science event where students participate by documenting species observations with the iNaturalist application, similar to localized BioBlitz events. Students are guided through using the iNaturalist database to practice biodiversity calculations then data is collected through participation in CNC (or a BioBlitz event an instructor arranges for their class). Spreadsheet software is used by students to organize, analyze, and summarize their relevant data to their peers. Students join the iNaturalist community of observers, which includes professional and non-professional naturalists. Therefore, students can see the themselves as scientists by contributing locally relevant data to a global and digital community of scientists. Experience working with large datasets such as the CNC iNaturalist dataset is essential for STEM careers and building data literacy. Implementing these experiences in classrooms will provide students unique opportunities to learn more about local biodiversity, develop interdisciplinary skills and positively influence a global network of scientists.

Primary image: Students recording biodiversity observations in an open field. At the annual Macaulay Honors College BioBlitz, students are divided into teams to explore a specific NYC park and record the animal and plant life they observed, which they later used to generate biodiversity reports including the species richness and abundances for the park.

We have designed three laboratory modules for an introductory organismal biology course with an emphasis on quantitative reasoning and data analysis skills. Module 1 tests for dimorphism in crayfish chelae using a paired statistical design. Module 2 tests for allometric growth of tapeworm hook structures using a regression model. Module 3 tests for differences in stomatal densities between two groups of plants using a two-sample statistical approach. For all three modules, we emphasize the use of confidence intervals to draw statistical conclusions about hypotheses. Knowledge about the basic biology of animals and plants is required, including arthropods, platyhelminths, and vascular plants. Background reading on dimorphism, allometry, and transpiration provides the necessary foundation to develop questions and hypotheses. Some familiarity with R is necessary for both students and instructors, although the activities can be modified for analysis with Excel or another statistical package. These modules can be taught independently or together as a unit within a course. As stated in the AAAS document, Vision and Change: A Call to Action, the ability to use quantitative reasoning is a core competency that must be developed by all biology students. These modules address the call for instruction in quantitative reasoning and provide a hands-on active introduction to key tools that will be required to build students’ statistical repertoire in more advanced courses.

Primary Image: A highlight of the three modules used in our introductory organismal biology course, including the use of calipers to test for dimorphism in the size of crayfish chelae (upper right), a leaf impression (lower right) from a hydrangea plant (lower left) used to test hypotheses about stomata densities, and the image of an Echinococcus tapeworm (upper left) to test hypotheses about allometry.  

Cards to include on website

Laboratory experiences in large-enrollment introductory science courses often utilize “cookie-cutter style” laboratory experiences due to the relative simplicity of setting up the lab stations, as well as a need to teach students particular course content. These experiences rarely offer insights into the way science is done in the research setting, resulting in a lack of understanding of the scientific process. In addition, students enrolled in non-majors introductory science courses often fail to see the relevance between what they are doing in the lab and what they are learning in the lecture portion of their course. To address this gap, we developed a laboratory module for a non-majors Human Biology course that provides students with a hands-on, authentic research experience using the iWorx software and hardware for human physiology. Weekly modules were designed to guide students through the major steps of the research process, including reading current scientific literature, developing a testable hypothesis, designing and performing a physiology experiment, analyzing data and presenting their findings to their peers. The described course framework encouraged students to participate in the scientific process, providing them with the opportunity to engage in an authentic research experience. The model described here could be adapted for use with introductory or advanced students, and could be modified to fit any research model available to the instructor. Utilizing the multi-week format described is recommended for students to gain the full benefit from the research-design-revise process.

Without the use of real-life examples and models, actively instructing and engaging students in complex physiology topics related to bone biomechanics can be challenging. In our large-enrollment Human Physiology & Anatomy courses at the University of Connecticut, the skeletal system is the first organ system that we cover in depth, rendering even more important our establishment of (and emphasis on) how fascinating--and directly applicable to everyday life--the anatomical features and physiological properties of organs can be. Because our lecture courses are supplemented with 2 hours per week of anatomy-intensive laboratory investigations, we tend to focus heavily on physiology concepts during lecture. For the skeletal system, we consider stress-strain curves in the context of bone biomechanics, including the materials-science concepts of elasticity, plasticity, and viscoelasticity, and the more generalizable concepts of hysteresis and anisotropy. Hoping to provide a fun, entertaining, and real-world perspective on these topics, we used Silly Putty® as an inexpensive, familiar, and readily-available model of some of these bone properties. This lesson allows students to get engaged in, and familiarized with, biomechanical concepts through demonstration of this well-known play material's properties, as a concrete reference point. Coupling the lesson with active questioning and think-pair-share activities allows students to develop skills in data interpretation and to apply previously-acquired knowledge bases to a novel situation. In this lesson, we provide instructors with a template for re-creating this demonstration, which can be accompanied by active-learning strategies and resources that promote development of data-interpretation and problem-solving skills in students.

This article has an accompanying Science Behind the Lesson article: "A Short Bone Biomechanics Primer: Background for a Lesson on Bone Viscoelasticity."

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.