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Introduction to Phylogenetic Trees for Comparative Genomic Analysis

In this activity, students are introduced to phylogenetic trees and networks as tools for analyzing evolutionary relationships.

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Cindy Trussell onto BIOL A273

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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Katie LaCommare onto Ecology Lab Ideas

How Many Squirrels Are in the Shrubs? A Lesson Plan for Comparing Methods for Population Estimation

Estimating the population sizes of animals is a key skill for any student interested in ecology, conservation, or management. However, counting animals in natural habitats is difficult, and the many techniques that exist each rely on assumptions that can bias results. Most wildlife courses teach one or two of these methods, but rarely are students given an opportunity to compare approaches and explore how underlying assumptions affect the accuracy of estimates. Here, we describe a hands-on activity in which students estimate the size of a single population of animals using multiple methods: strip censuses, scat counts, and camera traps. They then compare the estimates and evaluate how the assumptions of each model (e.g., random use of habitats and animal behavior) bias the results. Finally, students submit their data to a national database that aggregates observations across multiple institutions as part of Squirrel-Net (http://squirrel-net.org). They can then analyze the national dataset, permitting exploration of these questions across a broader variety of habitats and species than would be possible at any single institution. Extensions of this activity guide students to enumerate the advantages and disadvantages of each method in different contexts and to select the most appropriate method for a given scenario. This activity and the database focus on estimating population sizes of squirrels, which are diurnal, charismatic, easily identified, and present in a wide range of habitats (including many campuses), but the same methods could be broadly used for other terrestrial species, including birds, amphibians, reptiles, or invertebrates.

Primary image: Students estimate the population density of small mammals in a natural area near Grand Junction, CO.

Additional Squirrel-Net Articles:

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Katie LaCommare onto Ecology Lab Ideas

Discovery and Invention: A Reflection on Representation in Science

Despite increased awareness of the lack of equity and inclusion in the STEMM classroom, lessons on DEI topics are treated as separate to the scientific curriculum being taught. Rarely are intentional reflections and conversations on the lack of representation integrated into the lessons themselves. This lesson, titled “Discovery and Invention”, was developed to guide students through an exploration of the history of a topic—in this case, fermentation—followed by reflections and discussion on the culture of science and how it highlights certain individuals over others. Reflections allow students to explore and discuss their own scientific self-identity and sense of belonging in science. This fermentation lesson was designed to be integrated into a unit introducing students to microbial ecosystems, but it can be adapted for other topics as well, to suit the instructor’s needs.

Primary Image: Rosalind Franklin with microscope in 1955. MRC Laboratory of Molecular Biology. Creative Commons Attribution-Share Alike 4.0 Downloaded from commons.wikimedia.org on November 1, 2021 by authors.

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Katie Weglarz onto DEI seminar

Molecular CaseNet Biweekly meeting Mar. 31, 2023

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Shuchismita Dutta onto Meeting Recordings

NSF Final Outcomes Report: Using the Lived Experiences and Narratives of Black Heritage and African American Gullah/Geechee to Learn Science Concepts

First publication to mark launching of BRISCLab. The outcomes from the catalyst project will be shared first.

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Catherine Quinlan onto Dr. Catherine Quinlan's Work

Sexual Dimorphism CURE: Exploring Melanized Wing Patterns of Pieridae Butterflies

Teach a Course-based Undergraduate Research Experience (CURE) using digitized natural history collections data to test hypotheses on sexually dimorphic wing melanization patterns of Pieris rapae butterflies. This inclusive CURE can be implemented in in-person, online, and hybrid formats, synchronously or asynchronously, and requires only student access to a computer and the internet.

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Cindy Trussell onto BIOL A273

Measuring Size and Area of Digitized Specimens using ImageJ

Use ImageJ to analyze morphological characters in digital images of natural history specimens. Skills are transferable to many organisms and other morphological measurements.

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Cindy Trussell onto BIOL A273

Real World Scenarios in Non-Majors Biology

Students in non-majors’ biology courses may not choose careers that require biology content knowledge; however, all will encounter science in their lives. We redesigned a non-majors introductory biology course to support students in considering the importance of biology in their own lives. Our intent was to provide students with skills to engage in scientific reasoning, apply biological concepts, and increase their interest in the subject. One of the components we created to achieve these goals was a series of three Real World Scenarios (RWS). These RWSs consisted of existing case studies to which we added structured group discussion and individual reflection papers. These elements allowed students to grapple with a complex topic with peers, be exposed to viewpoints different from their own, and then have time to reflect and consider their own thoughts before they made an individual decision. We implemented these RWSs in both the face-to-face (F2F) and online sections. Students in both sections reported finding the assignments useful to help them connect the science to their own lives and appreciated the opportunity to interact with their peers and be exposed to differing viewpoints. We provide information on how we set up the assignment and provide suggestions for additional improvements.

Primary Image: The image depicts students engaged in a classroom discussion (obtained through Microsoft Word Stock Images).

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Kira Treibergs onto Scoping

An Original-Design Board Game to Increase Student Comprehension of Cellular Respiration Pathways

Cellular respiration is a daunting topic for many students in introductory biology courses. Students are challenged at conceptual and factual levels, since instruction covers multiple metabolic pathways occurring across different cellular compartments, involving abstract energy and electron transfers through diverse chemical reactions. Lecture-based instruction may clearly convey details of cellular respiration to students, but the complexity of this topic suggests alternative, active learning strategies may improve student comprehension and retention. I designed an original board game as a teaching tool for cellular respiration, targeted at improving learning outcomes for advanced high school, introductory undergraduate, and upper-level undergraduate biology students. “Aerobic Respiration: The Board Game” applies multiple learning strategies (quiz questions, student-completed study table, visual, tactile and quantitative learning, and game-play) with the goal that students are simultaneously entertained and invested in understanding this complex topic. Initial application in a small undergraduate introductory biology section (ca. 25–30 students) suggested improved student understanding of some aspects of cellular respiration. Use in a longer class or lab period and simplification of game board design and instructions should improve effectiveness of the game. Students had significantly favorable perceptions of the game as a learning tool. Included game board and game cards are provided to reflect multiple student academic levels, and are fully editable. Ordering information for materials and game pieces is also included.

Primary Image: Example setup for Aerobic Respiration: The Board Game.

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Kira Treibergs onto Scoping

A new approach to course-based research using a hermit crab-hydrozoan symbiosis

There are few feasible models for marine-focused inquiry laboratory activities, a notable shortcoming for instructors seeking to engage their students in meaningful, course-based research experiences (CUREs). We describe a multi-week CURE that investigates the symbiosis between hermit crabs and the hydrozoan Hydractinia spp. Although much is known about hermit crab biology, ecology, and behavior, little is known about Hydractinia, and less is known about the relationship between the two symbionts. Given their small size, low cost, and relative ease of maintenance, colonized hermit crabs may be useful subjects for student-driven research projects. We discuss our experiences with this system and offer adopters a suite of resources for in-lab implementation.

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Crystal Goldyn onto Ecology-symbiotic relationships

Integrating Community Ecology Into the Study of Parasites: Exploring the Effect of Host Behavior on Parasite Transmission Rates

Organismal life cycles are often presented as a set of facts to memorize in undergraduate biology courses. This approach is cognitively demanding for students and fails to convey how central life cycle diversity is in shaping ecological and evolutionary processes. Understanding the causes and consequences of life cycles is especially important when studying parasites with multiple life cycle stages for passing through diverse hosts. We designed a two-part lab activity to help our students gain a better understanding of the ecological interactions driven by parasite life cycles. Part I is a structured guide to reading a peer-reviewed journal article. Part II is a guided exercise in summarizing and interpreting mock experimental data involving a trematode parasite life cycle. These assignments helped students (1) understand how parasite life cycles shape ecological interactions with their hosts, (2) practice making predictions about species interactions using core ecological principles, and (3) practice quantitative reasoning and graph literacy skills by visualizing and interpreting data. We first used this activity as a self-guided lab exercise for an upper-division undergraduate parasitology class that switched from in-person to asynchronous-remote mid-semester. The stepwise structure of the activity allowed us to pinpoint the links in the chain of biological reasoning where students struggled most to guide target topic reviews in subsequent lectures. Here, we provide a summary of the activity, our experience with the activity, and suggestions for adapting the activity for a synchronous-remote or in-person class.

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Crystal Goldyn onto Science Literature

Molecular CaseNet Biweekly Meeting related (Mar 3, 2023)

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Shuchismita Dutta onto Meeting Recordings

Including Diverse Scientists for an Inclusive Class

Well, my friends, it's Black History Month, so I want to share with you some important Black scientist sites and several NSF-funded projects where you can learn about creating materials or using materials others have created....

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Molecular CaseNet Biweekly Meeting related (Feb. 17, 2023)

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Shuchismita Dutta onto Meeting Recordings

Black History Month Resource Collection 2023

In honor of Black History Month the BioQUEST team is putting together a collection of resources highlighting contributions from Black scientists, educators, and scholars. February should not be the only month where we honor the important contributions of Black STEM professionals, but we believe that BHM is the perfect time to capture some momentum and share some resources!

Anyone with a QUBESHub account can add to this resource so please share your favorite Black-centered resources here!

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Black History Month: 20 Black trailblazers in science and biotechnology that you need to know

The Biotechnology Innovation Organization brings us this resource of 20 Black trailblazers in science and biotechnology and includes a brief summary and external links to resources for each person. 

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Black History Month 2023 - Science and Medicine

List of Blackhistorymonth.org.uk articles that are relevant to science and medicine.

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What’s science got to do with Black History Month?

The Biotechnology Innovation Organization brings us this resource of 20 Black trailblazers in science and biotechnology and includes a brief summary and external links to resources for each person. 

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African American Scientists: Celebrating Black History Month

Promega Connections brings us a blog highlighting the contributions of 6 African American scientists

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35 Scientists from Black History Month

In honor of Black History Month, we highlight 35 African American scientists and engineers who made important contributions to science, technology, engineering, and math (STEM). There are many, many scientists who could be included on this list!

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100 inspiring Black scientists in America

Cell Mentor compiled a list of 100 inspiring Black scientists in America! 

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16 Black History Month STEM Activities

iD Tech shares 16 STEM teaching activities in honor of Black History Month. Geared towards K-12, but general enough to be easily adapted. 

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