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• Students will be able to compare protein sequences and identify conserved regions and putative domains.
• Students will be able to obtain, examine, and compare structural models of protein domains.
• Students will be able to interpret data on protein interactions (in vitro pull-down and in vitro and in vivo functional assays)
• Students will be able to propose experiments to test protein interactions.

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:

• 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.

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.

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.

Students will be able to:

• Describe how changes in cellular homeostasis affect metabolic intermediates.
• Perturb and interpret a simulation of cellular respiration.
• Describe cellular mechanisms regulating cellular respiration.
• Describe how glucose, oxygen, and coenzymes affect cellular respiration.
• Describe the interconnectedness of cellular respiration.
• Identify and describe the inputs and outputs of cellular respiration, glycolysis, pyruvate processing, citric acid cycle, and the electron transport chain.
• Describe how different energy sources are used in cellular respiration.
• Trace carbon through cellular respiration from glucose to carbon dioxide.

• Students will be able to describe the three stages of cellular respiration.
• Students will be able to identify the reactants entering and the products formed during each stage of cellular respiration.
• Students will be able to explain how chemical energy in carbohydrates is transferred to ATP through the stages of cellular respiration.
• Students will be able to explain the effects of compartmentalization of cellular respiration reactions in different cellular spaces.
• Students will be able to predict biological outcomes when a specific stage(s) of cellular respiration is altered. 

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.

• Students will be able to simulate the movement of water and sodium at each region of the loop of Henle.
• Students will be able to associate osmosis and active transport with movement of water/solutes at each region of the loop of Henle.
• Students will be able to model how the descending and ascending limbs of the loop of Henle maintain a concentration gradient within the medulla.
• Students will be able to predict the effects of altering normal water and salt movement out of the loop of Henle on the salt concentration of the medulla, urine concentration, and urine volume.

Advanced Learning Objectives for Extensions

• Students will be able to predict the impact of the length of the loop of Henle on the magnitude of the concentration gradient within the medulla.
• Students will be able to predict the length of the loop of Henle in organisms from different habitats.

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 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 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.

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.

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

• use spot plating techniques to compare the growth of yeast strains on solid culture media.
• predict the ability of specific met deletion strains to grow on media containing various sulfur sources.
• predict how mutations in specific genes will affect the concentrations of metabolites in the pathways involved in methionine biosynthesis.

• Students will be able to identify and describe the steps of the scientific method.

• Students will be able to develop hypotheses and predictions.

• Students will be able to construct and interpret bar graphs based on data and predictions.

• Students will be able to draw conclusions from data presented in graphical form.

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 successfully completing this lesson will:

1. Practice basic molecular biology laboratory skills such as DNA isolation, PCR, and gel electrophoresis.
2. Gather and analyze quantitative and qualitative scientific data and present it in figures.
3. Use bioinformatics to analyze DNA sequences and obtain protein sequences for molecular modeling.
4. Make and analyze three-dimensional (3-D) protein models using molecular modeling software.
5. Write a laboratory report using the collected data to explain how mutations in the DNA cause changes in protein structure/function which lead to mutant phenotypes.

Students will be able to:

1. Characterize an aqueous environment as acidic or basic.
2. Explain that pKa is a measure of how easy it is to remove a proton from a molecule.
3. Predict ionization state of a molecule at a particular pH based on its pKa (qualitative use of the Henderson-Hasselbalch equation).
4. Calculate the ratio of protonated/unprotonated forms of ionizable groups depending on chemical characteristics and /or environment pH (quantitative use of the Henderson-Hasselbalch equation).
5. Apply this knowledge in a medical context.

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.

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)