QUBES - Resources

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...

Keywords: uniprotCOVID19SARS-CoV-2NextstrainNextcladeSpike glycoproteinVariants of Concern

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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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2004-Hill-Lozowski-Sampson-Experiments on ice spikes and a simple growth model

We observed ice-spike growth using time-lapse digital photography, using two water types in two different containers.

Keywords: iceice spikebulk heat transfermass conservation

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COVID-19: Molecular Basis of Infection

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...

Keywords: infectionvaccinemolecular visualization and analysisCOVID19PDBSARS-CoVMolecular Case Study

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COVID-19: Molecular Basis Infection Revisited One Year into the Pandemic

This adaptation was written in Spring 2021 exactly one year after the original case and includes explorations of the emerging mutations within the spike protein

Keywords: infectionvaccinemolecular visualization and analysisCOVID19PDBSARS-CoVMolecular Case Studyvariantsantibody

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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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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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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...

Keywords: infectionvaccinemolecular visualization and analysisCOVID19PDBSARS-CoVMolecular Case Study

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Understanding COVID-19 Biology to Design a Vaccine

This multi-part case study introduces the reader to the SARS-CoV-2 virus, replication, and treatment. Additional worksheets introduce students to bioinformatics tools of 3-D protein visualization...

Keywords: BLASTprotein structure modelingmolecular visualization and analysisCOVID19PDB

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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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Fitzhugh-Nagumo Model

The FitzHugh–Nagumo model describes a prototype of an excitable system (e.g., a neuron).

Keywords: differential equationsmathematical modeldifferential equation modelordinary differential equation modelneuroscienceexcitable

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Using Bioinformatics Activities to understand the Past and Present of SARS-CoV2

We have designed a Bioinformatics activity that uses tools to identify the origins and mutations in the novel SARS-CoV2 strains.

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COVID-19: On the way to a vaccine

This multi-part case study introduces the reader to the SARS-CoV-2 virus origins, the molecular basis of the infection, the development and severity of symptoms, and treatment.

Keywords: BLASTprotein structure modelingmolecular visualization and analysisCOVID19PDB

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Vaccine Development and Testing

Scientists have the tools and knowledge to develop safe, effective vaccines, from trials to vials. This resource addresses the process by which vaccines are designed, tested and regulated. Key...

Keywords: immunology educationvaccine literacyvaccine hesitancy

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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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The Leaky Neuron: Understanding synaptic integration using an analogy involving leaky cups

Students have difficulty understanding synaptic integration in neural circuits, and how spatial and temporal summation combine in a target neuron to reach threshold. This Lesson uses small...

Keywords: neuron physiologyspatial summationsynaptic integrationtemporal summationthreshold

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The Science Behind the ACTN3 Polymorphism

A common polymorphism in the alpha-actinin-3 (ACTN3) gene results in the lack of ACTN3 protein expression in fast twitch muscle fibers in ~16% of the human population (1). This genetic change has...

Keywords: protein structure and functionhuman genetic variationskeletal muscle physiology

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Ain't No Mountain Pine Enough: A Case Study of How Mountain Pine Beetles are Affecting Ecosystem Processes

This case study engages students in generating hypotheses and predictions, analyzing and interpreting data, critically evaluating contrasting results in science, and thinking about feedbacks...

Keywords: population biologycarbon cyclingSpecies-habitat interactions

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Fly Exercise: A Simple Experiment to Test the Physiological Effects of Exercise on a Model Organism

Model organisms are commonly used to study and experimentally explore biological processes in ways that are technically or ethically not possible in humans. For this reason, model organisms are an...

Keywords: exerciseenzyme kineticsmetabolite concentrationmodel speciesphysical activity

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Nextstrain adaptations for Understanding COVID-19

Introduction to nucleotide sequence analysis and protein modeling in MEGA and PyMol using coronavirus SARS-CoV-2

2004-Hill-Lozowski-Sampson-Experiments on ice spikes and a simple growth model

COVID-19: Molecular Basis of Infection

COVID-19: Molecular Basis Infection Revisited One Year into the Pandemic

Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?

Evaluating the potential for immune escape: how likely is an antibody to protect against a specific SARS-CoV-2 variant?

COVID-19: Molecular Basis of Infection-ADAPTATION

Understanding COVID-19 Biology to Design a Vaccine

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

Fitzhugh-Nagumo Model

Using Bioinformatics Activities to understand the Past and Present of SARS-CoV2

COVID-19: On the way to a vaccine

Vaccine Development and Testing

A 360˚ View of COVID-19

The Leaky Neuron: Understanding synaptic integration using an analogy involving leaky cups

The Science Behind the ACTN3 Polymorphism

Ain't No Mountain Pine Enough: A Case Study of How Mountain Pine Beetles are Affecting Ecosystem Processes

Fly Exercise: A Simple Experiment to Test the Physiological Effects of Exercise on a Model Organism

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