Search

At the end of the activity, students will be able to:

• Explain the steps involved in genome assembly, annotation, and variant detection to other students and instructors.
• Create meaningful visualizations of their data using the integrated genome viewer.
• Use the Linux command line and web-based tools to answer research questions.
• Produce annotated genomes and call variants from raw sequencing reads in non-model species.

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)

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

At the end of this activity students will be able to:

• describe the use of two common research techniques for studying proteins: SDS-PAGE and immunoblot analysis.
• determine a protein’s subcellular location based on results from: 1) immunoblotting after differential centrifugation, and 2) immunofluorescence microscopy.
• analyze protein localization data based on the limitations of differential centrifugation and immunofluorescence microscopy.

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.

Each of these objectives are illustrated with a succinct slide presentation or other supplemental material available ahead of class time through the course administration system. Learners found it particularly helpful to have video clips that remind them of mathematical manipulations available (in the above example objective c). Students understand that foundational objectives tend to be the focus of the quiz (objectives a-d) and that others will be given more time to work on together in class (objectives e-g), but I don't specify this exactly to reduce temptation that 'gamers' take a shortcut that would impact their group work negatively later on. However, the assignment for a focused graded group activity is posted as well, so it is clear what we are working towards; if desired individuals could prepare ahead of the class.

• 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.

 

• Students will be able to distinguish between sex and gender, and apply each term appropriately.
• Students will be able to compare and contrast levels of sexual determination.
• Students will be able to critique societal misrepresentations surrounding sex, gender, and gender identity.

Students successfully completing this lesson will:

• Practice navigating an online bioinformatics resource and identify evidence relevant to solving investigation questions
• Contrast the array of genes expected on homologous autosomal chromosomes pairs with the array of genes expected on sex chromosome pairs
• Use bioinformatics evidence to defend the definition of homologous chromosomes
• Define chromosomal sex and defend the definition using experimental data
• Investigate the genetic basis of human chromosomal sex determination
• Identify at least two genetic mutations can lead to sex reversal

Students will be able to:

• Describe the reservoirs of infection in humans.
• Distinguish portals of entry and exit.
• Describe how each of the following contributes to bacterial virulence: adhesins, extracellular enzymes, toxins, and antiphagocytic factors.
• Define and distinguish etiology and epidemiology.
• Describe the five typical stages of infectious disease and depict the stages in graphical form.
• Contrast contact, vehicle and vector transmission, biological and mechanical vectors and identify the mode of transmission in a given scenario.
• Differentiate endemic, sporadic, epidemic, and pandemic disease.
• Distinguish descriptive, analytical, and experimental epidemiology.
• Compare and contrast social, economic, and cultural factors impacting health care in the early 1900s and today.

After completion of the lesson students will be able to:

1. Describe the differences between female and male meiosis.
2. Interpret graphical data to make decisions relevant to medical practices.
3. Develop a hypothesis that explains the difference in incidence of aneuploidy in gametes between males and females.

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.

• 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.

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

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)

• Describe how cells can produce proteins at the right time and correct amount. 
• Diagram a bacterial promoter with −35 and −10 elements and the transcription start site.
• Describe how mutational analysis can be used to study promoter sequence requirements.
• Develop a promoter mutation hypothesis and design an experiment to test it.
• Successfully and safely manipulate DNA and Escherichia coli for ligation and transformation experiments. 
• Design an experiment to verify a mutated promoter has been cloned into a destination vector. 
• Design an experiment to measure the strength of a promoter. 
• Analyze data showing reporter protein produced and use the data to assess promoter strength. 
• Define type IIs restriction enzymes.
• Distinguish between type II and type IIs restriction enzymes.
• Explain how Golden Gate Assembly (GGA) works.
• Measure the relative strength of a promoter compared to a standard promoter.  

At the end of this lesson, students will be able to:

• Describe the roles of light energy and carbon dioxide in photosynthetic organisms.
• Identify the effect of nutrients on the growth of photosynthetic organisms.
• Describe global cycles in atmospheric carbon dioxide levels and how they relate to photosynthetic organisms.