CourseSource: Resources

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Protein Import Into the ER: Understanding Experimental Methods for Old and New Cellular Discoveries

Process Oriented Guided Inquiry Learning (POGIL) is an effective approach for group work in STEM courses. POGIL-style lessons foster active learning because they require students to communicate and co-construct knowledge to solve problems. Here,...

Courses: Cell Biology Science Process Skills

Necessary and sufficientsignal sequenceProtein SynthesistrafficER importTranslocation

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Learning About Protein Localization: A Lesson for Analyzing Figures in a Scientific Publication

In order to function correctly, proteins must be localized to a specific subcellular location. We have designed this lesson to use data from the primary literature to teach students about the mechanisms cells use to direct proteins to the...

Courses: Cell Biology Science Process Skills

colocalizationimmunofluorescenceProtein localizationsignal sequencessubcellular fractionationwestern blotting

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4362

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402

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Distances in the Universe: An Inquiry Lab Sequence Taught in West Africa and North America

Astronomy evokes deep curiosity for many people, making it a beautiful topic for supporting students to learn scientific practices and develop as scientists. We present an inquiry-based lab sequence about distances in the Universe, which we have...

Courses: Astronomy

InquiryAstronomy labParallaxInverse-square law for lightCosmic distance ladderAsking investigable questions

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2141

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666

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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...

Courses: Biochemistry and Molecular Biology Bioinformatics Introductory Biology

BLASTmultiple sequence alignmentsequence similarityphylogramZika virusAlgorithmScoring Matrix

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4845

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1206

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Teaching the Central Dogma Using a Case Study of Genetic Variation in Cystic Fibrosis

The central dogma of biology is a foundational concept that is traditionally included in genetics curricula at all academic levels. Despite its ubiquitous presence throughout genetics education, students persistently struggle with both the...

Courses: Genetics

transcriptioncentral dogmatranslationsequence analysisDNA replicationgenetic variants

Lesson

5560

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2662

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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 series of short problem-based learning exercises...

Courses: Cell Biology Developmental Biology

signal transductiongene expressionCell communicationgenetic disordersregulation of enzyme activity

Teaching Tools and Strategies

2186

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356

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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 concepts. DNA Detective is a workshop we designed to...

Courses: Biochemistry and Molecular Biology Bioinformatics Genetics Plant Biology

geneticsbioinformaticsDNAgenotypephenotypegenegene annotation

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3345

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618

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Predicting and classifying effects of insertion and deletion mutations on protein coding regions

Mutations in genes can affect the encoded proteins in multiple ways, and some of these effects are counterintuitive. As for any other knowledge, students must create their own deep understanding of the Central Dogma. Students may not develop this...

Courses: Bioinformatics Genetics Science Process Skills

mutationcentral dogmatranslationframeshift

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914

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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...

Courses: Biochemistry and Molecular Biology Bioinformatics

bioinformaticsDNA sequenceRNAseqgene expression

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1566

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301

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Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course

Metagenomics is rapidly evolving due to advances in sequencing technologies and bioinformatics, but without proper training to interpret these datasets, student understanding remains limited. Aimed at undergraduate juniors and seniors and graduate...

Courses: Biochemistry and Molecular Biology Bioinformatics Ecology Ecology Microbiology Science Process Skills

microbiome

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4467

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448

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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...

Courses: Biochemistry and Molecular Biology

gene regulationinducible operonProkaryotic cellPhosphoenolpyruvate transferase system (PTS)

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415

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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...

Courses: Biochemistry and Molecular Biology Bioinformatics Science Process Skills

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

Lesson

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3321

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Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design

One of the challenges of inquiry-based research experiences is balancing the instruction on skills and techniques with data generation and analysis. This is especially true in technique heavy disciplines such as molecular biology, where emphasis...

Courses: Biochemistry and Molecular Biology

experimental designcrisprmolecular technique

Lesson

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405

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Integrating Manipulatives and Animations to Visualize Holliday Junctions

The complex molecular architecture of Holliday junctions is often challenging for undergraduate biochemistry students to conceptualize. In particular, they have difficulty translating from two-dimensional, linear representations shown in textbooks...

Courses: Biochemistry and Molecular Biology Genetics

dna structureDNA damageDNA recombinationGene crossoverHolliday junction

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CRISPR/Cas9 in yeast: a multi-week laboratory exercise for undergraduate students

Providing undergraduate life-science students with a course-based research experience that utilizes cutting-edge technology, is tractable for students, and is manageable as an instructor is a challenge. Here, I describe a multi-week lesson plan...

Courses: Biochemistry and Molecular Biology Bioinformatics Genetics Microbiology Science Process Skills

bioinformaticsPCRphenotypingCRISPR/Cas9gene editingcloningGenotypingRestriction enzyme

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A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics

Rapid advances in genomics and bioinformatics, the vast amount of data generated by next-generation sequencing, and the penetration of the ‘-omics’ into many areas of biology have created a need for students with hands-on experience with...

Courses: Biochemistry and Molecular Biology Bioinformatics Ecology Ecology Microbiology

epidemiologyresearchbioinformaticsgenomicspublic healthAntibiotic Resistant BacteriaSalmonellaDNA sequencingpathogenic bacteria

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Investigating the Function of a Transport Protein: Where is ABCB6 Located in Human Cells?

One of the challenges of teaching Cell Biology is helping students understand important research methods used to study cells. The goal of understanding cell biology methods is especially challenging in courses without a laboratory...

Courses: Cell Biology

ABC transporter familyDifferential centrifugationImmunoblottingImmunofluorescence assayProtein localizationPurifying organellesSDS-PAGE

Lesson

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A Laboratory Module That Explores RNA Interference and Codon Optimization Through Fluorescence Microscopy Using Caenorhabditis elegans

Scientific research experiences are beneficial to students allowing them to gain laboratory and problem-solving skills, as well as foundational research skills in a team-based setting. We designed a laboratory module to provide a guided research...

Courses: Bioinformatics Cell Biology Developmental Biology Genetics Science Process Skills

microscopyC. elegansquantitative analysisinquiry-based learninggene expressionRNA interferenceCodon UsageLaboratory Module

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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...

Courses: Biochemistry and Molecular Biology Bioinformatics Ecology Ecology Evolution Genetics Introductory Biology Science Process Skills

phylogeneticsbioinformaticsBiodiversityprocess of sciencetaxonomyPCRDNADNA sequencegel electrophoresis

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1282

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169

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Central Dogma, Dictionaries, and Functions: Using Programming Concepts to Simulate Biological Processes

Technologies like next-generation sequencing, proteomics, and high-throughput phenotyping have transformed the way we do biology. There is a continued need for scientists with computational skills to analyze biological data while understanding the...

Courses: Bioinformatics

computationpythonJupyter notebookFunctionscentral dogmaDictionaries

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Protein Import Into the ER: Understanding Experimental Methods for Old and New Cellular Discoveries

Learning About Protein Localization: A Lesson for Analyzing Figures in a Scientific Publication

Distances in the Universe: An Inquiry Lab Sequence Taught in West Africa and North America

Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence alignment in introductory undergraduate biology courses

Teaching the Central Dogma Using a Case Study of Genetic Variation in Cystic Fibrosis

Cell Signaling Pathways - a Case Study Approach

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

Predicting and classifying effects of insertion and deletion mutations on protein coding regions

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

Using QIIME to Interpret Environmental Microbial Communities in an Upper Level Metagenomics Course

Teaching Advanced Concepts in Regulation of the Lac Operon With Modeling and Simulation

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

Using CRISPR-Cas9 to teach the fundamentals of molecular biology and experimental design

Integrating Manipulatives and Animations to Visualize Holliday Junctions

CRISPR/Cas9 in yeast: a multi-week laboratory exercise for undergraduate students

A CURE for Salmonella: A Laboratory Course in Pathogen Microbiology and Genomics

Investigating the Function of a Transport Protein: Where is ABCB6 Located in Human Cells?

A Laboratory Module That Explores RNA Interference and Codon Optimization Through Fluorescence Microscopy Using Caenorhabditis elegans

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

Central Dogma, Dictionaries, and Functions: Using Programming Concepts to Simulate Biological Processes

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