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    Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?
    Commercial antibodies to the SARS-CoV-2 spike protein have been successfully used to treat people with COVID-19. Unfortunately, as the SARS-CoV-2 virus evolves, new variants have appeared that can...

    Keywords: course based undergraduate research experiencesBLASTmolecular modelingSARS-CoV-2antibodyNextstrainiCn3DSequence alignmentStructure alignment

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    SCIENCE/Fiction: Modular Template for Class Design
    We present a modular scaffold for designing an introductory seminar using speculative fiction and science papers to welcome university undergraduates to the biology major. A list of twelve possible...

    Keywords: geneticscell biologyneurosciencesystems biologyScience Fiction

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    2017-D_Goulet-Modeling, Simulating, and Parameter Fitting of Biochemical Kinetic Experiments
    In many chemical and biological applications, systems of differential equations containing unknown parameters are used to explain empirical observations and experimental data. The differential...

    Keywords: optimizationBiochemistrysensitivity analysischromatographymass actioncluster analysisconservation lawsdimerizationestrogen receptor protein

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    2015-G_Knott-Chemical Kinetics - Simple Binding F + G to and from B
    The study of this reaction, F + G goes to and from B, is common in chemistry and biochemistry. For example, F could be a hormone or drug and G the associated receptor sites.

    Keywords: bindingreactionchemical kineticsdeterministicBiochem Labsprobabilistickinetic reaction

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    2003-Richard-Carson-Tracer kinetic modeling in PET
    The use of radiopharmaceuticals and the imaging of their biodistribution and kinetics with modern instrumentation are key components to successful developments in PET.

    Keywords: Metabolismtomographyradiopharmaceuticalspositron emission

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    2006-Juska-Gedminiene-Ivanec-Growth of Microbial Populations-Mathematical Modeling-Laboratory Exercises-Model-Based Data Analysis
    The aim is to teach the students to use a fresh approach to the problems they are familiar with, to come up with an articulate verbal model after a mental effort, to express it in rigorous...

    Keywords: population growth ratelogistic equationVerhulst equationgeneration timelag time

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    Introducing Immunology Research Literature to Understand B-cell Receptor Gene Expression
    Immunology is relevant to our everyday lives, driving a need for more engaging and inclusive undergraduate immunology education. One way to engage a diverse group of learners is by teaching them...

    Keywords: recombinationantibodyV(D)J recombinationB-cell receptorlymphocyte receptor

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    Metastatic Mastery: A Case and Game-Based Approach to Learning About Cancer Mechanisms
    Mechanisms that contribute to the development of cancer are numerous and complicated, though most can be traced to a set of mutations in cell cycle regulatory genes that throw the process of cell...

    Keywords: mutationcancertranscriptioncell cycletranslationOncogenesTumor-suppressorp53Transcription factor

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    Mock Drug Activity Enhances Student Learning About the Challenges of HIV/AIDS Therapy
    While traditional didactic coursework is important for learning about the scientific aspects of HIV/AIDS, it is difficult to convey social aspects of the epidemic. Due to effective drug therapies,...

    Keywords: drug resistanceRetrovirusViral replication

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    Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?
    Commercial antibodies to the SARS-CoV-2 spike protein have been successfully used to treat people with COVID-19. Unfortunately, as the SARS-CoV-2 virus evolves, new variants have appeared that can...

    Keywords: course based undergraduate research experiencesBLASTmolecular modelingSARS-CoV-2antibodyNextstrainiCn3DSequence alignmentStructure alignment

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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...

    Keywords: bioinformaticsmolecular modelingCOVID19protein structure and functionUCSF ChimeraSARS-CoV-2 spike proteinACE2 receptor

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    Introduction to nucleotide sequence analysis and protein modeling in MEGA and PyMol using coronavirus SARS-CoV-2
    Introduction into computational approaches in phylogeny and protein modeling based on coronavirus SARS-CoV-2 (caused COVID-19 pandemic). Two self-guided tutorials for standard lab classes of 2.5...

    Keywords: phylogeneticsundergraduate educationbioinformaticsNCBICOVID19coronavirusMEGAPyMolvirtual labPDBprotein modelingSARSSARS-CoV

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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...

    Keywords: geneticsImmunologyBiochemistrybioinformaticsmolecular evolutionpublic healthvirusCOVID19

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    Exploring Miracle Fruit: An Undergraduate Laboratory Exercise on Experimental Design
    In recent years, undergraduate biology and biochemistry curricula have seen an increase in the use of course-based undergraduate research experiences (CUREs). CUREs maximize potential student gains...

    Keywords: sensory systemspHProtein shapeTaste

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    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...

    Keywords: diseasesignal transductionAcid SecretionAutonomic Nervous SystemEndocrineGastric PhysiologyGPCRHistology of Gastric Pit

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    Using Musical Instruments to Model Negative Feedback in the Hypothalamo-Pituitary-Target Gland Axes
    Homeostasis and negative feedback are crucial, yet difficult, concepts for undergraduates, particularly in the context of the hypothalamo-pituitary axes. This interactive activity was designed to...

    Keywords: cell-cell communicationhomeostasisnegative feedback

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    From Cre/LoxP to Fate Maps: Inclusive and Equitable Approaches for Engaging Developmental Biology Students in Experimental Design
    Engaging first generation underrepresented minority students in the process of inquiry in developmental biology is important to increase diversity in future graduate STEM education. One important...

    Keywords: experimental designC. elegansCre/LoxPFate mapheart developmentheart regenerationmousereporter constructzebrafish

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    Translating Co-Translational Translocation
    Understanding the process of proteins targeting to specific locations within a cell is a fundamental part of cell biology. Synthesis of proteins by co-translational translocation, which also...

    Keywords: Topologyco-translational translocationendoplasmic reticulumprotease protection assaysecretory proteinssignal sequencetransmembrane proteins

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    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...

    Keywords: geneticsbioinformaticsDNAgenotypephenotypegenegene annotation

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    The impact of diet and antibiotics on the gut microbiome
    The goal of this article is to describe an active learning exercise that can be used in a variety of advanced microbiology courses, including bacterial physiology, ecology, or systems biology. The...

    Keywords: microbiomeenvironmental controlhost responsemetabolites

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