CourseSource: Resources

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3785

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1246

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My Dog IS My Homework: Exploring Canine Genetics to Understand Genotype-Phenotype Relationships

To facilitate understanding of the fundamental genetic concept of the genotype-phenotype relationship in our introductory biology students, we designed an engaging multi-week series of related lessons about canine genetics in which students...

Courses: Bioinformatics Genetics Introductory Biology Science Process Skills

gel electrophoresissequence analysiscanine geneticsdeoxyribonucleic acid (DNA)dog coat morphologygenotype and phenotypemutationsPolymerase chain reaction (PCR)single nucleotide polymorphism (SNP)

Lesson

1840

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241

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0

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Bioinformatics is a BLAST: Engaging First-Year Biology Students on Campus Biodiversity Using DNA Barcoding

In order to introduce students to the concept of molecular diversity, we developed a short, engaging online lesson using basic bioinformatics techniques. Students were introduced to basic bioinformatics while learning about local on-campus species...

Courses: Bioinformatics Introductory Biology

geneticsorganismal biologybioinformaticstaxonomyDNA Barcodingspecies concepts

Lesson

4205

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286

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0

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Analysis of Microbiomes Using Free Web-Based Tools in Online and In-Person Undergraduate Science Courses

Our understanding of microbiomes, or the collection of microorganisms and their genes in a given environment, has been revolutionized by technological and computational advances. However, many undergraduate students do not get hands-on experiences...

Courses: Bioinformatics Ecology Ecology Microbiology

microbiomeDNA SubwayCyVerseCourse based undergraduate researchQIIME2ranacapa

Lesson

4839

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1206

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1

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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

1566

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300

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0

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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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3357

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1180

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0

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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

Lesson

6120

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1235

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0

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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

Lesson

3340

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275

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Application of a Bacterial Experimental Evolution System to Visualize and Teach Evolution in Action: A Course-Based Undergraduate Research Experience

Concepts of evolution are typically taught through examples of extremely long timescales, which do not always resonate broadly. Here, we describe a course-based undergraduate research experience tailored for junior and senior undergraduate biology...

Courses: Biochemistry and Molecular Biology Bioinformatics Cell Biology Evolution Genetics Microbiology

EvolutionmutationcompetitionNatural Selectionregulationstructure and functionreproductive fitnessgenotype to phenotypehomologs

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3671

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678

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0

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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...

Courses: Bioinformatics Genetics Science Process Skills

transcriptionexonintronsplicing

Lesson

2991

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549

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2

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A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

Radical innovations in DNA sequencing technology over the past decade have created an increased need for computational bioinformatics analyses in the 21st century STEM workforce. Recent evidence however demonstrates that there are significant...

Courses: Bioinformatics

bioinformaticsgenomicscodingJupyter notebookcommand lineCyVersescriptingnext generation sequencing analysis

Lesson

1793

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342

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0

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Cutthroat trout in Colorado: A case study connecting evolution and conservation

Evaluation of evidence is a key process skill for the core competencies of applying the process of science and using quantitative reasoning. This case study enables upper-division biology students to practice these skills by applying evolutionary...

Courses: Evolution Genetics Science Process Skills

population geneticsphylogeneticsSpeciationdivergencegene flow

Lesson

2113

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396

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0

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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

Lesson

2643

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459

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0

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Go Extinct! An Award-Winning Evolution Game That Teaches Tree-Thinking as Students Pursue the Winning Strategy

Evolutionary trees communicate both the diversity and unity of life, a central and important scientific concept, as highlighted by the Vision and Change undergraduate biology education movement. Evolutionary trees and cladograms are diagrams...

Courses: Evolution

phylogeneticsnatural historyBiodiversitycladogramCommon ancestorEvolutionary treeLand vertebratesMonophyletic cladeTetrapods

Lesson

5471

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2551

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0

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Exploring the Lytic and Lysogenic Life Cycles of Bacteriophages

The goal of this lesson is to introduce students to the lytic and lysogenic cycles of T4 and lambda bacteriophages, respectively, using student-centered pedagogies. Bacteriophages are viruses that infect bacteria and are either virulent or...

Courses: Microbiology

bacteriophagesLysogenic cycleLysogenyLytic cycle

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2875

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1007

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0

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Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeography

Teaching evolutionary theory is foundational for all biological sciences and a key aspect of overall science literacy. The conceptual framework for understanding evolution relies on thinking clearly about evolutionary trees (phylogenetics) and how...

Courses: Evolution Introductory Biology

EvolutionphylogeneticsTree thinkingbiogeography

Lesson

2270

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455

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A Short Laboratory Module to Help Infuse Metacognition during an Introductory Course-based Research Experience

A core competency identified in Vision and Change for undergraduate biology students is the Ability to Apply the Process of Science. Here, we describe a three-week laboratory module for students in an Introductory Cell and Molecular Biology...

Courses: Science Process Skills

metacognitiongene expressionScientific ProcessExperimenal DesignHypothesis Generationmodel organisms

Lesson

3406

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285

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Garden Variety Mutations: Using Primary Data to Understand the Central Dogma in Large-Lecture Introductory Biology

The ability to interpret and create an argument from data is a crucial skill for budding scientists, yet one that is seldom practiced in introductory courses. During this argumentation module, students in a large lecture class will work in groups...

Courses: Biochemistry and Molecular Biology Genetics Introductory Biology

mutationtranscriptiongene expressioncentral dogmatranslationgel electrophoresisGenotype/Phenotype

Lesson

2228

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445

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0

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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 division off balance. Communication of these...

Courses: Biochemistry and Molecular Biology Genetics Introductory Biology

mutationcancertranscriptioncell cycletranslationOncogenesTumor-suppressorp53Transcription factor

Teaching Tools and Strategies

1120

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140

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An Open Source, Collaborative Electronic Notebook for Undergraduate Laboratory Classes

To overcome many of the limitations of the paper laboratory notebook (PLN), we developed an electronic laboratory notebook (e-LN) for the Dynamic Genome course at the University of California. The Dynamic Genome course is an authentic research...

Courses: Science Process Skills

data collectionData annotationNotebook Skills

Lesson

2988

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346

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0

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A Muscular Dystrophy Case Study Illustrating the Phenotypic Effects of Mutation

Mutations in genes can lead to a variety of phenotypes, including various human diseases. Students often understand that a particular mutation in a single gene causes a disease phenotype, but it is more challenging to illustrate complex genetic...

Courses: Developmental Biology Genetics

mutationProtein Structureethicscentral dogmahuman disease

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My Dog IS My Homework: Exploring Canine Genetics to Understand Genotype-Phenotype Relationships

Bioinformatics is a BLAST: Engaging First-Year Biology Students on Campus Biodiversity Using DNA Barcoding

Analysis of Microbiomes Using Free Web-Based Tools in Online and In-Person Undergraduate Science Courses

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

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

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

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

Application of a Bacterial Experimental Evolution System to Visualize and Teach Evolution in Action: A Course-Based Undergraduate Research Experience

A Hands-on Introduction to Hidden Markov Models

A Fun Introductory Command Line Lesson: Next Generation Sequencing Quality Analysis with Emoji!

Cutthroat trout in Colorado: A case study connecting evolution and conservation

Integrating Manipulatives and Animations to Visualize Holliday Junctions

Go Extinct! An Award-Winning Evolution Game That Teaches Tree-Thinking as Students Pursue the Winning Strategy

Exploring the Lytic and Lysogenic Life Cycles of Bacteriophages

Building Trees: Introducing evolutionary concepts by exploring Crassulaceae phylogeny and biogeography

A Short Laboratory Module to Help Infuse Metacognition during an Introductory Course-based Research Experience

Garden Variety Mutations: Using Primary Data to Understand the Central Dogma in Large-Lecture Introductory Biology

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

An Open Source, Collaborative Electronic Notebook for Undergraduate Laboratory Classes

A Muscular Dystrophy Case Study Illustrating the Phenotypic Effects of Mutation

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