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Nextstrain adaptations for Understanding COVID-19

This resource introduces students to the use of Nextstrain and Nextclade to visualize the phylogeny of SARS-CoV-2 variants of concern and variants of interest. Terminology and an introduction to the Nextclade resource are provided in a 4-part worksheet.

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COVID-19: Molecular Basis of Infection-ADAPTATION

This case was written in Spring 2020 during the COVID-19 pandemic. It focuses on understanding the structure and interaction of the SARS-Cov-2 viral spike protein that facilitates infection in human cells.

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Digital Laboratory Framework via Canvas for LIFE courses at Colorado State University

The Life Lab Revisions team has piloted a Canvas-based approach to building scientific competencies in labs.

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A 360˚ View of COVID-19

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.

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"I Really Enjoy These Annotations:" Examining Primary Biological Literature Using Collaborative Annotation

Critically reading and evaluating claims made in the primary literature are vital skills for the future professional and personal lives of undergraduate students. However, the formal presentation of intricate content in primary research articles presents a challenge to inexperienced readers. During the fall 2020 semester, I introduced a Collaborative Annotation Project (CAP) into my online 400-level developmental neurobiology course to help students critically read eight research papers. During CAP, students used collaborative annotation software asynchronously to add clarifying comments, descriptions of and links to appropriate websites, and pose and answer questions on assigned papers. Student work was guided and assessed using a CAP grading rubric. Responses to anonymous surveys revealed students found CAP helpful for reading the primary literature and the rubric clarified expectations for the project. Here, I describe how I introduced, used, and assessed CAP in my online class, and I share the detailed CAP instructions and rubric.

Primary image: A moment of levity while annotating primary literature. Sample student annotations from the Collaborative Annotation Project. Student #1 compares immunofluorescence data to Christmas lights, an observation appreciated by student #2. Student names have been removed.

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Using Open-Source Bioinformatics and Visualization Tools to Explore the Structure and Function of SARS-CoV-2 Spike Protein

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. 

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General

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Electron Location, Location, Location: Understanding Biological Interactions

Introductory Biology courses typically introduce the structure and function of biomolecules such as proteins and nucleic acids. To understand biomolecules fully, students require knowledge of fundamental chemistry concepts such as covalent bonding, intermolecular interactions and hydrophilicity/hydrophobicity (1). Students enter our large (>400 student) course with a notoriously limited conceptual grasp of basic chemistry principles. Our lesson is an activity designed on the principles of POGIL (Process Oriented Guided Inquiry Learning). In 50 minutes, students build their own definitions of the following: polar vs. non-polar covalent bonds, hydrophilicity/hydrophobicity and the nature of hydrogen bonding based simply on the relative electronegativities of oxygen, nitrogen, carbon and hydrogen. We find that this exercise improves students’ understanding of these chemical concepts. Since adopting this activity, students have been better able to understand biomolecular structures and predict interactions between molecules.

Primary image: Hydrogen Bond. Possible hydrogen bond interaction that can form between two simple organic molecules.

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A How to Guide and Template for Designing a Puzzle Based Escape Room Game

Educational games are one active and effective way of engaging students with material while also providing additional motivation to tackle challenging concepts. A particularly popular game concept is the escape room, where students need to work in groups to solve a series of puzzles to prevent disaster from occurring in an imaginary universe, all within a specified amount of time. This paper presents a general guide to constructing an escape room for undergraduate classrooms. Unlike many recently published educational escape rooms, this template does not use any laboratory-based components, making it widely applicable to any class and any level, although it will be most easily adapted to classes that do include analytical components. The puzzles in the game escalate from remembering and understanding concepts to applying and evaluating techniques and data. Unlike many other games and puzzles, an escape room does not reveal the final answers until the allocated time is up, which forces students to work through challenging questions and find solutions within their group to advance in the game. The game provides students many instances for formative assessment and encourages helpful discussions surrounding misconceptions and core course content while they escalate through the challenges.

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A Classroom Intervention to Reduce Confirmation Bias

STEM students are often unable to recognize cognitive bias in their own disciplines, and simply describing cognitive bias to students has shown to be insufficient to improve critical thinking. However, habitual metacognitive techniques show promise for correcting cognitive biases, such as confirmation bias, a maladaptive cognitive strategy that specifically threatens the objectivity of scientists. As part of a course on metacognition in science, first-year STEM students were asked to give an oral presentation about a controversial socioscientific topic (e.g., GMO crops, de-extinction, or hydrofracking). The first year the course was offered, presentations exhibited confirmation bias at a high rate, despite instructions to examine multiple viewpoints about the scientific issue. In subsequent years, an intervention in the form of an interactive lecture/discussion/activity about confirmation bias and two specifically-designed homework assignments asked the students to reflect on evidence, search processes and potential biases. This intervention was jointly developed by faculty members in biology and philosophy to focus on habitual metacognitive techniques. Compared to no intervention, the resultant presentations had a higher percentage of reliable sources and a lower percentage of citations that only supported their conclusion. These results indicate that after the intervention exercise, students were discriminating among sources more carefully (Mann-Whitney p=0.009) and were using more sources from the other side of the argument, including presenting more reasons that refute their own ideas (Mann-Whitney p=0.003). We find that providing classroom instruction supported by deliberate practice to counteract confirmation bias improves students’ evaluation of scientific evidence.

Primary image: Venn diagram that illustrates the idea of confirmation bias.

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From Dirt to <em>Streptomyces</em> DNA

The purpose of this semester-long Lesson is to give students an authentic, course-based undergraduate research experience during which they learn basic and advanced microbiological and molecular biology techniques. This project begins with the isolation of a suspected Streptomyces bacterium from a soil sample and concludes with its identification. Students collect data, regarding colony and cell morphology, biochemical characteristics, the production of secondary metabolites, and employs the PCR using custom-designed primers to the Streptomyces 16s rRNA gene. The project culminates with the identification of their soil isolate using the National Center for Biotechnology Information (NCBI) web site to perform nucleotide blasts. The blastn program provides the final piece of evidence used to confirm, or not, the identification of their isolate as a Streptomyces from 16s rRNA gene sequence data, hence the title “From Dirt to Streptomyces DNA. In addition, the Lesson focuses on the Streptomyces bacteria to address several ASM aligned goals and objectives. These include prokaryotic growth phases and ways in which interactions of microorganisms among themselves and with their environment is determined by their metabolic abilities.  In addition, this Lesson illustrates how microbial metabolism is important to a relevant societal issue, the need for new antibiotic discovery particularly given the rise of antibiotic resistance strains of clinically relevant bacteria. It also illustrates the microbial diversity of soil and the developmental/physiological strategies employed in such a competitive environment. This Lesson hopes to impart both the thrill and challenges associated with scientific discovery.

Primary image: Photomicrograph of Streptomyces colonies growing on ISP 2 agar. The Streptomyces are student isolates showing stages of morphological development. Photomicrograph by Marc A. Brodkin.

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The Legacy of Redlining in Oakland, CA

The issues of redlining and environmental justice will be introduced and used as a framework for a number of topics in the third part of the semester in a non-majors Environmental Science course.

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Integrating Social Justice into your STEM Classroom: Redlining & Environmental Science

Materials for the workshop on social justice presented at the 2021 BIOME Institute.

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Integrating Social Justice into your STEM Classroom: Redlining & Health

Workshop about models for introducing social justice issues into classes developed in a Faculty Mentoring Network. Presented at the 2021 BIOME Institute.

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Exploring EnvironmenATL Justice with Data Analytics and Visualization

Basic data handling and data analysis skills are introduced to visualize and analyze ‘big data.’ Environmental justice is introduced to give students an understanding of tools and strategies to explore while developing advocacy and communication skills.

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Exploring Connections between Low Albedo, Urban Heat Islands and Social Justice

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

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Assessing Socioeconomic Trends in Tree Cover and Human Health in Urban Environments

In this exercise, students use a combination of publicly available data and tree cover data that they generate using iTree Canopy to test whether tree cover is equitably distributed within the city of Dallas.

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Water We Doing: A Deep Dive Into Sustainable Ocean Management & Blue Economies

Modules produced by students in the VCU ENVS graduate-level Environmental Methods course

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James R Vonesh onto VCU ENV METHODS

Learning Through Citizen Science: Enhancing Opportunities by Design

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Learning from the Trees: Using Project Budburst to Enhance Data Literacy and Scientific Writing Skills in an Introductory Biology Laboratory During Remote Learning

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Expanding the Scope of Citizen Science: Learning and Engagement of Undergraduate Students in a Citizen Science Chemistry Lab

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Leveraging Citizen Science in a College Classroom to Build Interest and Efficacy for Science and the Environment

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The Roles and Value of Citizen Science: Perceptions of Professional Educators Enrolled on a Postgraduate Course

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Creating Study-Specific Tools to Increase Community and Student Engagement

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Useful Biodiversity Data Were Obtained by Novice Observers Using iNaturalist During College Orientation Retreats

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