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  • Image from http://www.epa.gov/airdata/ad_maps.html

    Air Quality Data Mining: Mining the US EPA AirData website for student-led evaluation of air quality issues

    Learning Objectives
    Students will be able to:
    • Describe various parameters of air quality that can negatively impact human health, list priority air pollutants, and interpret the EPA Air Quality Index as it relates to human health.
    • Identify an air quality problem that varies on spatial and/or temporal scales that can be addressed using publicly available U.S. EPA air data.
    • Collect appropriate U.S. EPA Airdata information needed to answer that/those questions, using the U.S. EPA Airdata website data mining tools.
    • Analyze the data as needed to address or answer their question(s).
    • Interpret data and draw conclusions regarding air quality levels and/or impacts on human and public health.
    • Communicate results in the form of a scientific paper.
  • Photograph by Marilyn Chung, The Desert Sun
  • Hydrozoan polyps on a hermit-crab shell (photo by Tiffany Galush)

    A new approach to course-based research using a hermit crab-hydrozoan symbiosis

    Learning Objectives
    Students will be able to:
    • define different types of symbiotic interactions, with specific examples.
    • summarize and critically evaluate contemporary primary literature relevant to ecological symbioses, in particular that between hermit crabs and Hydractinia spp.
    • articulate a question, based on observations of a natural phenomenon (in this example, the hermit crab-Hydractinia interaction).
    • articulate a testable hypothesis, based on their own observations and read of the literature.
    • design appropriate experimental or observational studies to address their hypotheses.
    • collect and interpret data in light of their hypotheses.
    • problem-solve and troubleshoot issues that arise during their experiment.
    • communicate scientific results, both orally and in written form.
  • Madhumathi S V (2013) This image is license under a Creative Commons Atrribution-Share Alike 4.0 International.  https://commons.wikimedia.org/wiki/File:Business_ethics.jpg

    Priority Setting in Public Health: A lesson in ethics and hard choices

    Learning Objectives
    At the end of this unit, students will be able to:
    • Define the central distinction between public health and medicine
    • Apply objectives of public health and individual medical care in a particular situation to identify potential areas of conflict in priority setting
    • Apply moral theories of utilitarianism and deontology to a particular situation to identify the course of action proponents of each theory would see as morally justified
    • Identify the range of morally justifiable actions that might be available to a health professional in a particular setting
    • Choose from among a range of possible actions in a particular health situation and articulate the ethical principles that would justify that choice.
  • A A student assists Colorado Parks & Wildlife employees spawning greenback cutthroat trout at the Leadville National Fish Hatchery; B greenback cutthroat trout adults in a hatchery raceway; C tissue samples collected by students to be used for genetic analysis (images taken by S. Love Stowell)

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

    Learning Objectives
    Students will be able to:
    • interpret figures such as maps, phylogenies, STRUCTURE plots, and networks for species delimitation
    • identify sources of uncertainty and disagreement in real data sets
    • propose research to address or remedy uncertainty
    • construct an evidence-based argument for the management of a rare taxon
  • Students participating in the peer review process. Practicing the writing of scientific manuscripts prepares students to understand and engage in the primary literature they encounter.
  • DNA

    Why do Some People Inherit a Predisposition to Cancer? A small group activity on cancer genetics

    Learning Objectives
    At the end of this activity, we expect students will be able to:
    1. Use family pedigrees and additional genetic information to determine inheritance patterns for hereditary forms of cancer
    2. Explain why a person with or without cancer can pass on a mutant allele to the next generation and how that impacts probability calculations
    3. Distinguish between proto-oncogenes and tumor suppressor genes
  • Wikipedia in the Science Classroom. In this primary image, students are sharing their Wikipedia article evaluations and evaluation process with their peers.
  • Many colorful hand prints
  • Image of tick from US Department of Agriculture_ARS photo by Scott Bauer

    Mice, Acorns, and Lyme Disease: a Case Study to Teach the Ecology of Emerging Infectious Diseases.

    Learning Objectives
    Students will be able to...
    • outline the life cycle of ticks and explain the transmission cycle of Lyme disease.
    • describe factors that make mice a competent reservoir for Borrelia burgdorferi.
    • analyze and interpret line and bar graphs of data on the effects of changes to ecological communities on the risk of human exposure to Lyme disease.
    • explain how the incidence of Lyme disease is determined by interactions between bacteria, animals, humans and the environment.
    • predict how changes in the ecosystem affect Borrelia burgdorferi transmission.
    • explain how human activities affect biodiversity and the consequences of those actions on disease outbreaks.
  • Plant ecology students surveying vegetation at Red Hills, CA, spring 2012.  From left to right are G.L, F.D, A.M., and R.P.  Photo used with permission from all students.

    Out of Your Seat and on Your Feet! An adaptable course-based research project in plant ecology for advanced students

    Learning Objectives
    Students will:
    • Articulate testable hypotheses. (Lab 8, final presentation/paper, in-class exercises)
    • Analyze data to determine the level of support for articulated hypotheses. (Labs 4-7, final presentation/paper)
    • Identify multiple species of plants in the field quickly and accurately. (Labs 2-3, field trip)
    • Measure environmental variables and sample vegetation in the field. (Labs 2-3, field trip)
    • Analyze soil samples using a variety of low-tech lab techniques. (Open labs after field trip)
    • Use multiple statistical techniques to analyze data for patterns. (Labs 4-8, final presentation/paper)
    • Interpret statistical analyses to distinguish between strong and weak interactions in a biological system. (Labs 4-7, final presentation/paper)
    • Develop and present a conference-style presentation in a public forum. (Lab 8, final presentation/paper)
    • Write a publication-ready research paper communicating findings and displaying data. (Lab 8, final presentation/paper)
  • Sliced vegan no-knead whole what bread loaf” by Veganbaking.net is licensed under CC BY-SA 2.0
  • How Silly Putty® is like bone

    What do Bone and Silly Putty® have in Common?: A Lesson on Bone Viscoelasticity

    Learning Objectives
    • Students will be able to explain how the anatomical structure of long bones relates to their function.
    • Students will be able to define viscoelasticity, hysteresis, anisotropy, stiffness, strength, ductility, and toughness.
    • Students will be able to identify the elastic and plastic regions of a stress-strain curve. They will be able to correlate each phase of the stress-strain curve with physical changes to bone.
    • Students will be able to predict how a bone would respond to changes in the magnitude of an applied force, and to variations in the speed or angle at which a force is applied.
    • Students will be able to determine the reason(s) why bone injuries occur more frequently during athletic events than during normal everyday use.
  • An active-learning lesson that targets student understanding of population growth in ecology

    Learning Objectives
    Students will be able to:
    • Calculate and compare population density and abundance.
    • Identify whether a growth curve describes exponential, linear, and/or logistic growth.
    • Describe and calculate a population's growth rate using linear, exponential, and logistic models.
    • Explain the influence of carrying capacity and population density on growth rate.
  • Figure 2. ICB-Students come to class prepared to discuss the text
  • A photo of grizzly bears fishing in the McNeil Falls in Alaska, taken using BearCam by Lawrence Griffing.

    Authentic Ecological Inquiries Using BearCam Archives

    Learning Objectives
    Students will be able to:
    • conduct an authentic ecological inquiry including
      • generate a testable hypothesis based on observations,
      • design investigation with appropriate sampling selection and variables,
      • collect and analyze data following the design, and
      • interpret results and draw conclusions based on the evidence.
    • write a research report with appropriate structure and style.
    • evaluate the quality of inquiry reports using a rubric.
    • conduct peer review to evaluate and provide feedback to others' work.
    • revise the inquiry report based on peer feedback and self-assessment.
  • Train tracks, image author: Mitya Ilyinov

    BioMap Degree Plan: A project to guide students in exploring, defining, and building a plan to achieve career goals

    Learning Objectives
    Students will be able to...
    • Identify their values and interests.
    • Identify careers that align with their values and interests.
    • Identify academic programs and co-curricular experiences that will prepare them for a career.
    • Create the first draft of a BioMap Degree Plan to support achievement of their career goals.
    • Articulate how their undergraduate academic experience will prepare them for their future career.
    • Use professional communication skills
  • Dilution and Pipetting Lesson Using Food Dyes

    Learning Objectives
    • Students can use the formula c1v1=c2v2 to calculate dilutions.
    • Students can accurately set and use a micropipette.
    • Students are able to prepare complex solutions such as enzyme reactions.
  • Evaluating the Quick Fix: Weight Loss Drugs and Cellular Respiration Image File: QuickFixPrimImage.tiff Sources for images: Balance: Public Domain CCO http://www.pd4pic.com/scales-justice-scale-libra-balance-weighbridge.html Mitochondria: https://thumb7.shutterstock.com/thumb_large/1503584/235472731/stock-vector-mitochondrion-235472731.jpg Pills: https://pixabay.com/static/uploads/photo/2014/07/05/15/16/pills-384846_960_720.jpg

    Evaluating the Quick Fix: Weight Loss Drugs and Cellular Respiration

    Learning Objectives
    • Students will be able to explain how the energy from sugars is transformed into ATP via cellular respiration.
    • Students will be able to predict an outcome if there is a perturbation in the cellular respiration pathway.
    • Students will be able to state and evaluate a hypothesis.
    • Students will be able to interpret data from a graph, and use that data to make inferences about the action of a drug.
  • This collage contains original images taken by the course instructor. The images show a microscopic view of stomata on the underside of a Brassica rapa leaf (A), B. rapa plants in their growth trays (B), a flowering B. rapa plant (C), and different concentrations of foliar protein (D). Photos edited via Microsoft Windows Photo Editor and Phototastic Collage Maker.

    A flexible, multi-week approach to plant biology - How will plants respond to higher levels of CO2?

    Learning Objectives
    Students will be able to:
    • Apply findings from each week's lesson to make predictions and informed hypotheses about the next week's lesson.
    • Keep a detailed laboratory notebook.
    • Write and peer-edit the sections of a scientific paper, and collaboratively write an entire lab report in the form of a scientific research paper.
    • Search for, find, and read scientific research papers.
    • Work together as a team to conduct experiments.
    • Connect findings and ideas from each week's lesson to get a broader understanding of how plants will respond to higher levels of CO2 (e.g., stomatal density, photosynthetic/respiratory rates, foliar protein concentrations, growth, and resource allocation).
    Note: Additional, more specific objectives are included with each of the four lessons (Supporting Files S1-S4)
  • Pipets - photo by Magnus Manske

    Learning to Pipet Correctly by Pipetting Incorrectly?

    Learning Objectives
    • Students will be able to use analytical balances and micropipettes.
    • Students will be able to calculate averages and standard deviations.
    • Students will be able to use t-tests to compare two independent samples.
    • Students will be able to justify accepting or rejecting a null hypothesis based on an interpretation of p-values.
    • Students will learn to use spreadsheet software such as Microsoft Excel and/or Google Sheets
    • Students will be able to explain how pipetting incorrectly leads to errors.
  • Sodium-Potassium pump

    Lights, Camera, Acting Transport! Using role-play to teach membrane transport

    Learning Objectives
    At the end of this activity, students should be able to:
    • Compare and contrast the mechanisms of simple diffusion, facilitated diffusion, and active transport (both primary and secondary).
    • Identify, and provide a rationale for, the mechanism(s) by which various substances cross the plasma membrane.
    • Describe the steps involved in the transport of ions by the Na+/K+ pump, and explain the importance of electrogenic pumps to the generation and maintenance of membrane potentials.
    • Explain the function of electrochemical gradients as potential energy sources specifically used in secondary active transport.
    • Relate each molecule or ion transported by the Na+/glucose cotransporter (SGLT1) to its own concentration or electrochemical gradient, and describe which molecules travel with and against these gradients.
  • Two cells stained

    Bad Cell Reception? Using a cell part activity to help students appreciate cell biology, with an improved data plan and...

    Learning Objectives
    • Identify cell parts and explain their function
    • Explain how defects in a cell part can result in human disease
    • Generate thought-provoking questions that expand upon existing knowledge
    • Create a hypothesis and plan an experiment to answer a cell part question
    • Find and reference relevant cell biology journal articles
  • Your Tax Dollars at Work: A mock grant writing experience centered on scientific process skills

    Learning Objectives
    Students will be able to:
    • Propose a testable, novel question contributing to a biological field of study.
    • Formulate a study rationale.
    • Describe relevant background information on a topic using the primary literature.
    • Choose appropriate scientific, mathematical, and statistical methods to analyze a research question.
    • Determine the financial costs of a research project.
    • Present a proposal for peer review and compose a constructive peer review.
    • Collaborate as a member of a scientific team.
    • Articulate the review criteria and process used in NSF-style proposal review.
  • Results formula questions. Shows the five questions that comprise the formula for writing a scientific Results section.
  • DNA barcoding research in first-year biology curriculum

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

    Learning Objectives
    Students will be able to: Week 1-4: Fundamentals of Science and Biology
    • List the major processes involved in scientific discovery
    • List the different types of scientific studies and which types can establish causation
    • Design experiments with appropriate controls
    • Create and evaluate phylogenetic trees
    • Define taxonomy and phylogeny and explain their relationship to each other
    • Explain DNA sequence divergence and how it applies to evolutionary relationships and DNA barcoding
    Week 5-6: Ecology
    • Define and measure biodiversity and explain its importance
    • Catalog organisms using the morphospecies concept
    • Geographically map organisms using smartphones and an online mapping program
    • Calculate metrics of species diversity using spreadsheet software
    • Use spreadsheet software to quantify and graph biodiversity at forest edges vs. interiors
    • Write a formal lab report
    Week 7-11: Cellular and Molecular Biology
    • Extract, amplify, visualize and sequence DNA using standard molecular techniques (PCR, gel electrophoresis, Sanger sequencing)
    • Explain how DNA extraction, PCR, gel electrophoresis, and Sanger sequencing work at the molecular level
    Week 12-13: Bioinformatics
    • Trim and assemble raw DNA sequence data
    • Taxonomically identify DNA sequences isolated from unknown organisms using BLAST
    • Visualize sequence data relationships using sequence alignments and gene-based phylogenetic trees
    • Map and report data in a publicly available online database
    • Share data in a formal scientific poster
  • Image from a clicker-based case study on muscular dystrophy and the effect of mutations on the processes in the central dogma.

    A clicker-based case study that untangles student thinking about the processes in the central dogma

    Learning Objectives
    Students will be able to:
    • explain the differences between silent (no change in the resulting amino acid sequence), missense (a change in the amino acid sequence), and nonsense (a change resulting in a premature stop codon) mutations.
    • differentiate between how information is encoded during DNA replication, transcription, and translation.
    • evaluate how different types of mutations (silent, missense, and nonsense) and the location of those mutations (intron, exon, and promoter) differentially affect the processes in the central dogma.
    • predict the molecular (DNA size, mRNA length, mRNA abundance, and protein length) and/or phenotypic consequences of mutations.
  • The Roc is a mythical giant bird of prey, first conceived during the Islamic Golden Age (~8th to 13th centuries CE), popularized in folk tales gathered in One Thousand One Nights. Rocs figured prominently in tales of Sinbad the Sailor. In this 1898 illustration by René Bull, the Roc is harassing two of Sinbad’s small fleet of ships. Illustration by René Bull is licensed under CC BY 2.0. (Source: https://en.wikipedia.org/wiki/Roc_(mythology)#mediaviewer/File:Rocweb.jpg)

    A first lesson in mathematical modeling for biologists: Rocs

    Learning Objectives
    • Systematically develop a functioning, discrete, single-species model of an exponentially-growing or -declining population.
    • Use the model to recommend appropriate action for population management.
    • Communicate model output and recommendations to non-expert audiences.
    • Generate a collaborative work product that most individuals could not generate on their own, given time and resource constraints.
  • Students at Century College use gel electrophoresis to analyze PCR samples in order to detect a group of ampicillin-resistance genes.

    Antibiotic Resistance Genes Detection in Environmental Samples

    Learning Objectives
    After completing this laboratory series, students will be able to:
    • apply the scientific method in formulating a hypothesis, designing a controlled experiment using appropriate molecular biology techniques, and analyzing experimental results;
    • conduct a molecular biology experiment and explain the principles behind methodologies, such as accurate use of micropipettes, PCR (polymerase chain reaction), and gel electrophoresis;
    • determine the presence of antibiotic-resistance genes in environmental samples by analyzing PCR products using gel electrophoresis;
    • explain mechanisms of microbial antibiotic resistance;
    • contribute data to the Antibiotic Resistance Genes Network;
    • define and apply key concepts of antibiotic resistance and gene identification via PCR fragment size.
  • Memory Helper is an illustration of a made up dietary supplement. Because the supplement is named Memory Helper, and because a picture of a brain is placed on the label, consumers might believe that the supplement is a memory aid. We add the footnote “tested?” to suggest that consumers should take a closer look.

    Bad Science: Exploring the unethical research behind a putative memory supplement

    Learning Objectives
    Students will be able to:
    • create criteria for evaluating information that is touted as scientific.
    • apply those criteria to evaluate the claim that Prevagen® enhances memory.
    • identify the misleading tactics used on the Prevagen® website and in their self-published reporting.
    • decide whether to recommend taking Prevagen® and explain their decisions.
  • Building a Model of Tumorigenesis: A small group activity for a cancer biology/cell biology course

    Learning Objectives
    At the end of the activity, students will be able to:
    • Analyze data from a retrospective clinical study uncovering genetic alterations in colorectal cancer.
    • Draw conclusions about human tumorigenesis using data from a retrospective clinical study.
    • Present scientific data in an appropriate and accurate way.
    • Discuss why modeling is an important practice of science.
    • Create a simple model of the genetic changes associated with a particular human cancer.
  • SNP model by David Eccles (gringer) [GFDL (http://www.gnu.org/copyleft/fdl.html) or CC BY 4.0 (http://creativecommons.org/licenses/by/4.0)], via Wikimedia Commons

    Exploration of the Human Genome by Investigation of Personalized SNPs

    Learning Objectives
    Students successfully completing this lesson will be able to:
    • Effectively use the bioinformatics databases (SNPedia, the UCSC Genome Browser, and NCBI) to explore SNPs of interest within the human genome.
    • Identify three health-related SNPs of personal interest and use the UCSC Genome Browser to define their precise chromosomal locations and determine whether they lie within a gene or are intergenic.
    • Establish a list of all genome-wide association studies correlated with a particular health-related SNP.
    • Predict which model organism would be most appropriate for conducting further research on a human disease.
  • Playon Words Title Screen

    Using Gamification to Teach Undergraduate Students about Scientific Writing

    Learning Objectives
    Topics within Playon Words are grouped into “mini-games.” The Learning Objectives for each mini-game are as follows: Sentence Sensei
    • Identify the best sentence variant from a list of options
    • Identify and eliminate needless words
    • Identify where and when to use different types of punctuation marks
    • Identify and correct common grammar mistakes
    Organization Optimizer
    • Organize sentences in a logical order
    • Describe the components of different sections of a scientific paper
    • Identify the section of a scientific paper where a given sentence belongs
    • Eliminate sentences which do not belong in a given writing sample
    Science Officer Training
    • Classify statements as scientific or non-scientific
    • Identify which statements support a particular hypothesis or position
    • Classify provided sentences (e.g. hypotheses vs. predictions, problems vs. experiments, results vs. discussion)
    Reference Referee
    • Compare and contrast different types (e.g. primary literature, review articles, popular literature etc.) and sources (PubMed, Web of Science, Google Scholar etc.) of scientific information
    • Identify locations in texts where citations are needed
    • Identify citations and/or references that are incorrect or missing key information
    • Identify information that does not belong in the reference list (e.g. vendor information)
  • Simplified Representation of the Global Carbon Cycle, https://earthobservatory.nasa.gov/Features/CarbonCycle/images/carbon_cycle.jpg

    Promoting Climate Change Literacy for Non-majors: Implementation of an atmospheric carbon dioxide modeling activity as...

    Learning Objectives
    • Students will be able to manipulate and produce data and graphs.
    • Students will be able to design a simple mathematical model of atmospheric CO2 that can be used to make predictions.
    • Students will be able to conduct simulations, analyze, interpret, and draw conclusions about atmospheric CO2 levels from their own computer generated simulated data.
     
  • A pair of homologous chromosomes.

    Meiosis: A Play in Three Acts, Starring DNA Sequence

    Learning Objectives
    • Students will be able to identify sister chromatids and homologous chromosomes at different stages of meiosis.
    • Students will be able to identify haploid and diploid cells, whether or not the chromosomes are replicated.
    • Students will be able to explain why homologous chromosomes must pair during meiosis.
    • Students will be able to relate DNA sequence similarity to chromosomal structures.
    • Students will be able to identify crossing over as the key to proper pairing of homologous chromosomes during meiosis.
    • Students will be able to predict the outcomes of meiosis for a particular individual or cell.
  • Students using the Understanding Eukaryotic Genes curriculum to construct a gene model. Students are working as a pair to complete each Module using classroom computers.

    An undergraduate bioinformatics curriculum that teaches eukaryotic gene structure

    Learning Objectives
    Module 1
    • Demonstrate basic skills in using the UCSC Genome Browser to navigate to a genomic region and to control the display settings for different evidence tracks.
    • Explain the relationships among DNA, pre-mRNA, mRNA, and protein.
    Module 2
    • Describe how a primary transcript (pre-mRNA) can be synthesized using a DNA molecule as the template.
    • Explain the importance of the 5' and 3' regions of the gene for initiation and termination of transcription by RNA polymerase II.
    • Identify the beginning and the end of a transcript using the capabilities of the genome browser.
    Module 3
    • Explain how the primary transcript generated by RNA polymerase II is processed to become a mature mRNA, using the sequence signals identified in Module 2.
    • Use the genome browser to analyze the relationships among:
    • pre-mRNA
    • 5' capping
    • 3' polyadenylation
    • splicing
    • mRNA
    Module 4
    • Identify splice donor and acceptor sites that are best supported by RNA-Seq data and TopHat splice junction predictions.
    • Utilize the canonical splice donor and splice acceptor sequences to identify intron-exon boundaries.
    Module 5
    • Determine the codons for specific amino acids and identify reading frames by examining the Base Position track in the genome browser.
    • Assemble exons to maintain the open reading frame (ORF) for a given gene.
    • Define the phases of the splice donor and acceptor sites and describe how they impact the maintenance of the ORF.
    • Identify the start and stop codons of an assembled ORF.
    Module 6
    • Demonstrate how alternative splicing of a gene can lead to different mRNAs.
    • Show how alternative splicing can lead to the production of different polypeptides and result in drastic changes in phenotype.
  • Using the Cell Engineer/Detective Approach to Explore Cell Structure and Function

    Learning Objectives
    Students will be able to:
    • Identify the major cell organelles
    • List the major functions of the organelles
    • Predict how changes in organelle/cell structure could alter cellular function
    • Explain how overall cellular function is dependent upon organelles/cell structure
    • Relate cell structure to everyday contexts
  • Double-stranded, supercoiled yarn. Intertwined, supercoiled, and double-stranded yarn, representing chromosomal template DNA, with a section marked with black stripes to represent the DNA fragment for modeling PCR fundamentals.

    A Kinesthetic Modeling Activity to Teach PCR Fundamentals

    Learning Objectives
    Students will be able to:
    • Draw or model the first three cycles of PCR, including the correct directionality (5’- and 3’-ends) of the primers and single-stranded PCR products.
    • Diagram how single-stranded products from the first cycle of PCR are used as templates for subsequent PCR cycles.
    • Demonstrate which parts of the primers will anneal to the original DNA template and subsequent PCR products.
    • Model and demonstrate when the primer restriction enzyme sites are incorporated into double-stranded PCR products.
    • Calculate the number of desired-length PCR products and long PCR products for each amplification cycle.
    • Demonstrate how the incorporation of primer restriction enzyme sites into PCR products is a useful tool for subsequent cloning of the product into a vector.
  • Students engaged in building the PCR model

    A Close-Up Look at PCR

    Learning Objectives
    At the end of this lesson students will be able to...
    • Describe the role of a primer in PCR
    • Predict sequence and length of PCR product based on primer sequences
    • Recognize that primers are incorporated into the final PCR products and explain why
    • Identify covalent and hydrogen bonds formed and broken during PCR
    • Predict the structure of PCR products after each cycle of the reaction
    • Explain why amplification proceeds exponentially
  • MA plot of RNA-seq data. An MA plot is a visual summary of gene expression data which identifies genes showing differential expression between two treatments.

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

    Learning Objectives
    • Students will locate and download high-throughput sequence data and genome annotation files from publically available data repositories.
    • Students will use Galaxy to create an automated computational workflow that performs sequence quality assessment, trimming, and mapping of RNA-seq data.
    • Students will analyze and interpret the outputs of RNA-seq analysis programs.
    • Students will identify a group of genes that is differentially expressed between treatment and control samples, and interpret the biological significance of this list of differentially expressed genes.
  • Student-generated targeting construct from the construct ribbon parts

    Make It Stick: Teaching Gene Targeting with Ribbons and Fasteners

    Learning Objectives
    • Students will be able to design targeting constructs.
    • Students will be able to predict changes to the gene locus after homologous recombination.
    • Students will be able to design experiments to answer a biological question (e.g., "Design an experiment to test if the expression of gene X is necessary for limb development").
  • Multiple sequence alignment of homologous cytochrome C protein sequences using Jalview viewer.

    Sequence Similarity: An inquiry based and "under the hood" approach for incorporating molecular sequence...

    Learning Objectives
    At the end of this lesson, students will be able to:
    • Define similarity in a non-biological and biological sense when provided with two strings of letters.
    • Quantify the similarity between two gene/protein sequences.
    • Explain how a substitution matrix is used to quantify similarity.
    • Calculate amino acid similarity scores using a scoring matrix.
    • Demonstrate how to access genomic data (e.g., from NCBI nucleotide and protein databases).
    • Demonstrate how to use bioinformatics tools to analyze genomic data (e.g., BLASTP), explain a simplified BLAST search algorithm including how similarity is used to perform a BLAST search, and how to evaluate the results of a BLAST search.
    • Create a nearest-neighbor distance matrix.
    • Create a multiple sequence alignment using a nearest-neighbor distance matrix and a phylogram based on similarity of amino acid sequences.
    • Use appropriate bioinformatics sequence alignment tools to investigate a biological question.
  • Using Undergraduate Molecular Biology Labs to Discover Targets of miRNAs in Humans

    Learning Objectives
    • Use biological databases to generate and compare lists of predicted miR targets, and obtain the mRNA sequence of their selected candidate gene
    • Use bioinformatics tools to design and optimize primer sets for qPCR
  • Using phylogenetics to make inferences about historical biogeographic patterns of evolution.

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

    Learning Objectives
    Students will be able to:
    • Estimate phylogenetic trees using diverse data types and phylogenetic models.
    • Correctly make inferences about evolutionary history and relatedness from the tree diagrams obtained.
    • Use selected computer programs for phylogenetic analysis.
    • Use bootstrapping to assess the statistical support for a phylogeny.
    • Use phylogenetic data to construct, compare, and evaluate the role of geologic processes in shaping the historical and current geographic distributions of a group of organisms.
  • Medical students at a fair. Credit: Danieladelrio

    Casting a Wide Net via Case Studies: Educating across the undergraduate to medical school continuum in the biological...

    Learning Objectives
    At the end of this lesson, the student should be able to:
    • Consider the potential advantages and disadvantages of widespread use of whole genome sequencing and direct-to-consumer genetic testing.
    • Explore the critical need to maintain privacy of individual genetic test results to protect patient interests.
    • Dissect the nuances of reporting whole genome sequencing results.
    • Recognize the economic ramifications of precision medicine strategies.
    • Formulate a deeper understanding of the ethical dimensions of emerging genetic testing technologies.
  • “The outcome of the Central Dogma is not always intuitive” Variation in gene size does not necessarily correlate with variation in protein size. Here, two related genes differ in length due to a deletion mutation that removes four nucleotides. Many students do not predict that the smaller gene, after transcription and translation, would produce a larger protein.

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

    Learning Objectives
    Students will be able to:
    • accurately predict effects of frameshift mutations in protein coding regions
    • conduct statistical analysis to compare expected and observed values
    • become familiar with accessing and using DNA sequence databases and analysis tools

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