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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...
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    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...
    Lesson
    4162

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    Using Bioinformatics and Molecular Visualization to Develop Student Hypotheses in a Malate Dehydrogenase Oriented CURE
    Developing student creativity and ability to develop a testable hypothesis represents a significant challenge in most laboratory courses. This lesson demonstrates how students use facets of molecular evolution and bioinformatics approaches...
    Teaching Tools and Strategies
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    A 360Ëš 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...
    Lesson
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    Using Raw Sequence Data to Analyze Tumor Suppressor Mutations
    Learning to identify DNA sequence variants from raw sequencing data (electropherograms) is a basic molecular biology skill with applications to basic research and clinical practice. Yet learning to map DNA sequence variants to functional regions...
    Lesson
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    An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure
    Gene structure, transcription, translation, and alternative splicing are challenging concepts for many undergraduates studying biology. These topics are typically covered in a traditional lecture environment, but students often fail to master and...
    Lesson
    7906

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    394

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    Investigating Cell Signaling with Gene Expression Datasets
    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)...
    Lesson
    4164

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    406

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    Discovering Prokaryotic Gene Regulation with Simulations of the trp Operon
    The trp operon exemplifies important biological concepts, including the central dogma of molecular biology, feedback inhibition, and gene regulation. For this reason, regulation of the trp operon is a common theme in introductory biology,...
    Lesson
    2092

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    656

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    Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses
    Introductory bioinformatics exercises often walk students through the use of computational tools, but often provide little understanding of what a computational tool does "under the hood." A solid understanding of how a bioinformatics...
    Lesson
    2256

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    276

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    Discovering Prokaryotic Gene Regulation by Building and Investigating a Computational Model of the lac Operon
    The ability to construct and reason through a biological system is an important skill to develop in science education. This level of understanding forces students to recognize the interrelatedness of components within a biological process and...
    Lesson
    3452

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    720

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    Homologous chromosomes? Exploring human sex chromosomes, sex determination and sex reversal using bioinformatics approaches
    Constructing a robust understanding of homologous chromosomes, sex chromosomes, and the particulate nature of genes is a notoriously difficult task for undergraduate biology students. In this lesson, students expand their knowledge of human...
    Lesson
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    676

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    A Hands-on Introduction to Hidden Markov Models
    In this Lesson, we describe a classroom activity that demonstrates how a Hidden Markov Model (HMM) is applied to predict a eukaryotic gene, focusing on predicting one exon-intron boundary. This HMM lesson is part of the BIOL/CS 370...
    Lesson
    4442

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    444

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    Teaching Advanced Concepts in Regulation of the Lac Operon With Modeling and Simulation
    Success in biochemistry and other life science courses requires that students understand important biological concepts. One of these concepts is how gene regulation ensures that homeostasis is maintained in an organism. The lac operon is a...
    Lesson
    3028

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    353

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    Discovering Cellular Respiration with Computational Modeling and Simulations
    Cellular respiration, a common topic among introductory and cellular biology curricula, is a complex biological process that exemplifies core biological concepts, including systems, pathways and transformation of energy, and structure and function...
    Essay
    1071

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    119

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    An Active Textbook Converts "Vision and Tweak" to Vision and Change
    Multiple reports over more than a century have documented the problems with the way introductory biology has been taught in most colleges and universities. An influential recent report, Vision and Change in Undergraduate Biology Education, has...
    Lesson
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    A CRISPR/Cas Guide RNA Design In Silico Activity
    CRISPR biotechnologies inspired by the Clustered Regularly Interspaced Short Palindromic Repeat RNA-guided nuclease adaptive bacterial immune system have revolutionized biology research and become ubiquitous tools for hypothesis and...
    Lesson
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    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...
    Lesson
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    Teaching the Photoelectric Effect Using an Open-Source Interactive Simulation
    The photoelectric effect is one of the fundamental experiments that established the basis of quantum mechanics. Students studying this experiment in modern physics courses struggle to understand what it actually measured and why it is significant....
    Lesson
    3054

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    452

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    Moths and Frogs and E. coli, Oh My!: Agent-based Modeling of Evolutionary Systems
    In evolution classrooms, introducing and reinforcing the idea of genetic drift and random selection can be challenging, as can be reinforcing appropriate mental models of evolution. Agent-based models offer students the opportunity to conduct a...
    Lesson
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    Marsh Madness: Using Video Games and a Case Study to Explore Food Webs and Ecosystem Services in Carpinteria Salt Marsh Reserve
    As the complexity and interconnectedness of our world increases, we are continually expected to be capable of complex, non-linear thinking in order to successfully tackle and solve the challenges we face in the 21st century. Tackling these...

    Courses: EcologyEcology