QUBES - Resources

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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Serotonin in the Pocket: Non-covalent interactions and neurotransmitter binding

This lesson introduces beginning biochemistry students to the concept of a biomolecule binding site, such as a neurotransmitter receptor site or an enzyme active site. A simple organic molecule,...

Keywords: active sitebindingbinding sitehydrogen bondinghydrophobic effectionic interactionsnon-covalent forces

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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...

Keywords: genomicstranscriptionsignaling

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Design Your Own Flow Cytometry Experiment: A Four-Week Inquiry Laboratory

Due to its importance to the field, flow cytometry should be one of the hallmark methods a student learns in the lab portion of an undergraduate immunology course. Flow cytometry is a classic lab...

Keywords: Immunologyexperimental designFlow cytometryMice

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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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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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Cell Signaling Pathways - a Case Study Approach

Signaling and gene expression are fundamental to cell biology and developmental biology. Although these topics are highly interrelated, they typically appear in separate units in a course. We use a...

Keywords: signal transductiongene expressionCell communicationgenetic disordersregulation of enzyme activity

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Using a Sequential Interpretation of Data in Envelopes (SIDE) approach to identify a mystery TRP channel

This lesson sought to engage students in data interpretation and to encourage critical thinking about neurophysiology in the context of temperature sensation. A family of receptors called Transient...

Keywords: Cell communicationChannel specificity and activationLimitations of tools of Cell BiologyNeuronal Signaling

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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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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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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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The Lecture-Free Classroom: Teaching students backward design and Bloom's Taxonomy to create their own learning environment

We describe Presentation Enhanced Learning (PEL), a flexible, lecture-free, field-tested teaching format to promote problem-based, active learning in upper-division or graduate biological sciences...

Keywords: active learningbackward designProblem based learningBloom's Taxonomy

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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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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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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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You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”

With limited time available for laboratory activities, introductory science courses for non-science majors typically use the laboratory period to reinforce material that was previously presented...

Keywords: bacteriamicrobiomeBLASTmicrobesDNA replicationPolymerase chain reaction (PCR)

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Open. Adaptable. Free.

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

Serotonin in the Pocket: Non-covalent interactions and neurotransmitter binding

Investigating Cell Signaling with Gene Expression Datasets

Design Your Own Flow Cytometry Experiment: A Four-Week Inquiry Laboratory

SCIENCE/Fiction: Modular Template for Class Design

From Cre/LoxP to Fate Maps: Inclusive and Equitable Approaches for Engaging Developmental Biology Students in Experimental Design

Cell Signaling Pathways - a Case Study Approach

Using a Sequential Interpretation of Data in Envelopes (SIDE) approach to identify a mystery TRP channel

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

Metastatic Mastery: A Case and Game-Based Approach to Learning About Cancer Mechanisms

Understanding Gastric Acid Secretion: An Active Learning Approach

The Lecture-Free Classroom: Teaching students backward design and Bloom's Taxonomy to create their own learning environment

Translating Co-Translational Translocation

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

The impact of diet and antibiotics on the gut microbiome

Mock Drug Activity Enhances Student Learning About the Challenges of HIV/AIDS Therapy

Using Musical Instruments to Model Negative Feedback in the Hypothalamo-Pituitary-Target Gland Axes

You and Your Oral Microflora: Introducing non-biology majors to their “forgotten organ”

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