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Modeling the Research Process: Authentic human physiology research in a large non-majors course

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.

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Benjamin Wilhelm onto A&P

What do Bone and Silly Putty® have in Common?: A Lesson on Bone Viscoelasticity

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."

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Benjamin Wilhelm onto A&P

To Vaccinate or Not to Vaccinate

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.

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Benjamin Wilhelm onto Mammalian Physiology

Understanding Gastric Acid Secretion: An Active Learning Approach

The human digestive system is a diverse network of cells, tissues, and organs that is regulated by systemic (e.g., nervous and endocrine systems) and local factors (e.g., secretions, pH, and the microbiome). Given the volume of content and the dense physiology involved, this system is difficult for instructors to teach and equally challenging for students to understand. This is especially true in our two-semester Human Anatomy and Physiology course for pre-health students at the University of Connecticut. In the Spring 2017 semester, we developed and implemented an active-learning based approach when teaching the histology and regulation of gastric secretions—a physiology-intensive topic within the digestive system unit. Our lesson included a team-based case study on gastric ulcer formation and Helicobacter pylori, a guided drawing depicting the molecular mechanisms of HCl secretion, a concept map linking the cells with their secretions, a think-pair-share on pharmacological regulators, and a reflective assignment placing the content within a broader societal context. Consistent with the themes of active learning, the lesson is suitable for any physiology instructor seeking to create a more engaging classroom, and provide students with opportunities to problem solve, think critically, and build relationships between course content and real life.

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Benjamin Wilhelm onto Mammalian Physiology

A Quick and Simple Natural Selection Role Play

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.

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Benjamin Wilhelm onto BIOL 1004

One species, two species, red species, lead species? Phylogenetics and species concepts with Plethodon salamanders

This lab introduces students to species concepts and basic computer-based tree-building methods using published nuclear and mitochondrial sequence data for Plethodon salamanders.

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Katie M. Sandlin onto Bioinformatics

Yeti or not: Do they exist?

Through this 4-part bioinformatics case study, students will be led through the forensic analysis of putative Yeti artifacts based on published findings.

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Katie M. Sandlin onto Bioinformatics

Biodiversity Show and Tell: An Accessible Activity to Encourage Students to Explore the Tree of Life

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.

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Sarah MacLean onto Bio 1

Escape Zoom!: Reviewing Introductory Evolution Content Using an Escape Room Format

Reviewing and integrating key concepts and learning goals at the end of a biology course can be overwhelming to students and instructors alike. Often end-of-term review sessions in preparation for final exams are heavily based on memorization, and content coverage may be favored over students’ deeper understanding of fewer key ideas. We developed a final exam review for a virtual introductory evolution course using an “escape room” format, which consisted of unique activities—including puzzles, role-playing, and literature searches—aligned with course learning goals. Similar to a traditional escape room, students needed to collaboratively solve or complete each activity before moving on to the subsequent task. Our escape room activity was conducted virtually via Zoom and included both whole-class and smaller breakout room interactions. We recommend instructors utilize escape rooms as an engaging and effective way to review key concepts in their courses.

Primary image: Virtual Escape Room. In our activity, students virtually engage in activities related to evolutionary topics such as cichlid speciation, mRNA COVID-19 vaccines, and extinction, among others. All images used in this image are open source, and associated links for all images are listed here: https://unsplash.com/photos/smgTvepind4, https://unsplash.com/photos/4_hFxTsmaO4, https://unsplash.com/photos/_BJVJ4WcV1M, https://unsplash.com/photos/k0KRNtqcjfw, https://unsplash.com/photos/Pitb97HIn6Y

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Tamara Johnstone-Yellin onto Evolution

Interactive Video Vignettes (IVVs) to Help Students Learn Genetics Concepts

Many video resources exist to teach Mendelian genetics, but most consist of passive delivery of information rather than active construction of knowledge by users. We have created two interactive video vignettes (IVVs) that can be used together or separately to introduce students to core concepts of genetics, using principles of active learning (e.g., elicit-confront-resolve, directed feedback, reflection). These online resources are free and can be assigned as homework for students to complete outside of class. Each IVV features a realistic scenario of undergraduate students investigating genetic phenomena by collecting and analyzing data. During the IVVs, the user is integrated into the process, answers conceptual questions, receives feedback based on their answers, and reflects on the experience by comparing their original ideas to their new understandings. Marfamily is primarily designed to teach pedigree construction and analysis, while A Matter of Taste addresses common misconceptions about dominance. Both also demonstrate the scientific method. Users cannot advance without answering the questions, although they can review past scenes. Resources for both formative and summative assessment are provided. The IVV is easily integrated into any course where an introduction to or review of basic genetics is needed.

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Steven Krawczyk onto Genetics

BioVEDA Curriculum: An Approach to Link Conceptual and Quantitative Understanding of Variation During Experimental Design and Data Analysis

When performing a biological investigation, experts constantly cycle between conceptual and quantitative modes of thinking, integrating their understanding in both worlds to make decisions about their work. This cycling and mixing of conceptual and quantitative thinking in biology can be difficult for students. One way to help students integrate conceptual and quantitative thinking is by focusing on a single topic that has both conceptual and quantitative aspects. We have designed a curriculum that focuses on variation in experimental design and data analysis (The Biological Variation in Experimental Design and Analysis [BioVEDA] curriculum). We chose to focus on the idea of variation because it must be understood both conceptually and quantitatively at many points throughout a biological investigation. Additionally, this ability to apply quantitative thinking to biological concepts has been prioritized in national undergraduate education policy documents. Our curriculum consists of five activities that ask students to explore the idea of variation during the design of an experiment, and the representation and analysis of data. The activities are based on worksheets and incorporate Think-Pair-Share techniques with discussions facilitated by the instructor. We have implemented this curriculum twice in an introductory biology laboratory class for undergraduate students that is taught by graduate teaching assistants (TAs). So far, we have found that both TAs and students benefit from working through this curriculum. Students significantly improved in their understanding of variation in the context of biological investigations, and TAs gained more confidence in their ability to teach this content using active-learning techniques.

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Anne Cross onto Ecology Class

Molecular CaseNet Biweekly meeting related (Jan. 6, 2022)

Shuchi shares the Molecular CaseNet pipeline

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Shuchismita Dutta onto Meeting Recordings

UDL Resources shared by Pat

Discussed in meeting on Jan 20, 2023

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Shuchismita Dutta onto UDL Resources

Phylogenetic analysis using collections material: interpreting trait evolution by comparison of morphological and molecular genetic hypotheses

Exercise spans two weeks, includes homework, and involves some groups of animals as well as plants. Emphasizes re-interpretation of morphological trait evolution following molecular genetic phylogeny reconstruction

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Cindy Trussell onto BIOL A273

Testing hypotheses about the role of wildfire in structuring avian communities

This module assesses the role of wildfire in the eastern US and its impact on bird communities using NEON bird survey data from pre- and post- a major wildfire in the Great Smoky Mountains National Park (GRSM) in November 2016.

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Cindy Trussell onto BIOL A273

Passion-Driven Statistics

E-book in .pdf format and customizable .iba format

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Cindy Trussell onto BIOL A273

Data Management using National Ecological Observatory Network's (NEON) Small Mammal Data with Accompanying Lesson on Mark Recapture Analysis

Modules to learn big data management, analysis, and hypothesis testing.

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Cindy Trussell onto BIOL A273

Tackling "Big Data" with Biology Undergrads: A Simple RNA-seq Data Analysis Tutorial Using Galaxy

Analyzing high-throughput DNA sequence data is a fundamental skill in modern biology. However, real and perceived barriers such as massive file sizes, substantial computational requirements, and lack of instructor background knowledge can discourage faculty from incorporating high-throughput sequence data into their courses. We developed a straightforward and detailed tutorial that guides students through the analysis of RNA sequencing (RNA-seq) data using Galaxy, a public web-based bioinformatics platform. The tutorial stretches over three laboratory periods (~8 hours) and is appropriate for undergraduate molecular biology and genetics courses. Sequence files are imported into a student's Galaxy user account directly from the National Center for Biotechnology Information Sequence Read Archive (NCBI SRA), eliminating the need for on-site file storage. Using Galaxy's graphical user interface and a defined set of analysis tools, students perform sequence quality assessment and trimming, map individual sequence reads to a genome, generate a counts table, and carry out differential gene expression analysis. All of these steps are performed "in the cloud," using offsite computational infrastructure. The provided tutorial utilizes RNA-seq data from a published study focused on nematode infection of Arabidopsis thaliana. Based on their analysis of the data, students are challenged to develop new hypotheses about how plants respond to nematode parasitism. However, the workflow is flexible and can accommodate alternative data sets from NCBI SRA or the instructor. Overall, this resource provides a simple introduction to the analysis of "big data" in the undergraduate classroom, with limited prior background and infrastructure required for successful implementation.

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Carolyn Wetzel onto Genetics BIO243

DNA Detective: Genotype to Phenotype. A Bioinformatics Workshop for Middle School to College.

Advances in high-throughput techniques have resulted in a rising demand for scientists with basic bioinformatics skills as well as workshops and curricula that teach students bioinformatics concepts. DNA Detective is a workshop we designed to introduce students to big data and bioinformatics using CyVerse and the Dolan DNA Learning Center's online DNA Subway platform. DNA Subway is a user-friendly workspace for genome analysis and uses the metaphor of a network of subway lines to familiarize users with the steps involved in annotating and comparing DNA sequences. For DNA Detective, we use the DNA Subway Red Line to guide students through analyzing a "mystery" DNA sequence to distinguish its gene structure and name. During the workshop, students are assigned a unique Arabidopsis thaliana DNA sequence. Students "travel" the Red Line to computationally find and remove sequence repeats, use gene prediction software to identify structural elements of the sequence, search databases of known genes to determine the identity of their mystery sequence, and synthesize these results into a model of their gene. Next, students use The Arabidopsis Information Resource (TAIR) to identify their gene's function so they can hypothesize what a mutant plant lacking that gene might look like (its phenotype). Then, from a group of plants in the room, students select the plant they think is most likely defective for their gene. Through this workshop, students are acquainted to the flow of genetic information from genotype to phenotype and tackle complex genomics analyses in hopes of inspiring and empowering them towards continued science education.

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Carolyn Wetzel onto Genetics BIO243

Using computational molecular modeling software to demonstrate how DNA mutations cause phenotypes

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.

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Carolyn Wetzel onto Genetics BIO243

The Pipeline CURE: An Iterative Approach to Introduce All Students to Research Throughout a Biology Curriculum

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.

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Holly Bates onto CURE Resources

Student-Driven Design-and-Improve Modules to Explore the Effect of Plant Bioactive Compounds in Three Model Organisms

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).

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Holly Bates onto CURE Resources

Modeling the Research Process: Authentic human physiology research in a large non-majors course

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.

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Holly Bates onto Physiology Labs

Dynamic Daphnia: An inquiry-based research experience in ecology that teaches the scientific process to first-year biologists

This authentic research experience lesson teaches the core concept of systems and the competencies of quantitative reasoning, communication, and the ability to apply science. The research is student driven, the results are unknown, and the students engage in an iterative process to gather data, collaborating with classmates.  It is designed for first-year biology majors, in a class size of 15-30 students who can work in groups of three.  Students will learn to properly design an experiment, work as teams, analyze data, evaluate conclusions, and communicate findings to others. Additionally, this lesson also incorporates self-reflection and peer assessment when students produce a poster as a summative assessment. Over a five–week period, students will explore how an abiotic factor affects growth, reproduction, and survival of Daphnia.  Students are asked to compare their results to published literature. By the end, students should have a better understanding of science as an ongoing process where results are being updated and furthering the state of knowledge.

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Holly Bates onto CURE Resources

CURE-all: Large Scale Implementation of Authentic DNA Barcoding Research into First-Year Biology Curriculum

Growing calls in science education reform have emphasized wide-scale engagement of first-year undergraduate students in authentic research experiences; however, large course enrollments, inadequate student experience, limited resources and departmental inertia often create obstacles to reaching this goal. To help overcome these obstacles, the Department of Biology at James Madison University (JMU) has developed a cost-effective, scalable, and transferable semester-long (14-week) course-based undergraduate research experience (CURE) designed for large enrollment introductory biology labs. In this series of labs, first-year students use DNA barcoding to engage in authentic research practices drawn from the fields of ecology, molecular biology, and bioinformatics. These labs enable students to identify local species of plants, fungi, and invertebrates using student-generated DNA barcode sequences, which are then shared through a public database. Since their implementation at JMU in 2016, students in these labs have created and shared over 1,500 unique DNA barcode sequences and documented over 300 local species of plants, fungi, and invertebrates. These data are being used in an ongoing project comparing the biodiversity of forest edge versus forest interior habitats, but the labs are adaptable to almost any habitat or taxonomic group. In this article, we provide detailed descriptions of the content, logistics, and implementation of this 14-week series of labs. To our knowledge, this is among the largest-enrollment CUREs being offered to first-year undergraduates in the United States, and we hope that it can be useful to other institutions interested in documenting biodiversity and engaging introductory biology students in authentic research.

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Crystal Goldyn onto Dry Lab Activities-DNA Barcoding