Science Process Skills

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.

• 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.  

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.

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)

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.

Week 1: CRISPR design

• Locate the coding sequence, flanking sequence, protein product, and characteristics of a given gene from the Saccharomyces Genome Database (https://www.yeastgenome.org/).
• Design and defend the design of guide RNA and single stranded template for DNA repair in CRISPR/Cas9 gene editing studies to generate Saccharomyces cerevisiae auxotrophic mutants.

Week 3-4: Cloning

• Describe the qualities of the vector, pML104, that allow replication and selection in bacteria and yeast as well as allow expression of necessary factors in CRISPR/Cas9 genome editing, including Cas9 and sgRNA.
• Describe the rationale of and perform procedures necessary for cloning a small cassette (i.e., sgRNA gene) into a vector (i.e., pML104) including; restriction digest, annealing of DNA strands, removal of 5’ phosphates, ligation, and transformation.
• Recognize and design appropriate controls for cloning procedures such as ligation and transformation.

Week 5: Screening clones

• Describe the method of polymerase chain reaction (PCR), including the rationale for essential components of a reaction mixture and thermal-cycling conditions.
• Locate the binding sites of and design primers for PCR, then report the expected size of the amplification product.
• Describe and perform isolation of plasmid DNA from E. coli.  

Week 6: Selection of clones and transformation of yeast

• Describe the rationale for and perform procedures to transform yeast, including the essential components of a transformation mixture and conditions necessary for transformation.
• Describe the basic conditions required for cultivating yeast.
• Describe the rationale for and perform agarose gel electrophoresis of a given size of DNA.
• Analyze DNA separated by agarose gel electrophoresis, including size estimation.
• Recognize and describe the qualities of a template for DNA repair that allows efficient DNA repair. 

Week 7: Phenotyping

• Design an experiment to determine auxotrophic phenotypes.
• Predict the outcome of multi-step experiments.

Multiweek

• Recognize and describe conditions necessary for growth of E. coli and S. cerevisiae.
• Qualitatively and quantitatively analyze scientific data from scientific experiments, including bacterial and yeast transformation, agarose gel electrophoresis, extraction of plasmid DNA from bacteria, PCR, and auxotroph phenotypic analysis.
• Communicate science to peers through maintenance of a laboratory notebook, verbal communication with group members, and writing of a formal laboratory report written in a format acceptable for journal publication.
• Troubleshoot scientific protocols by identifying procedures that are prone to error, comparing recommended protocols to actual procedure, and using positive and negative controls to narrow the location of a potential error.
• Communicate specific potential or actual uses of CRISPR/Cas9 in science and/or medicine.

Alignment with Society-Generated Learning Objectives - From Biochemistry and Molecular Biology, and Genetics Learning Frameworks

• Use various bioinformatics approaches to analyze macromolecular primary sequence and structure.
• Illustrate how DNA is replicated and genes are transmitted from one generation to the next in multiple types of organisms including bacteria, eukaryotes, viruses, and retroviruses.
• Define what a genome consists of and how the information in various genes and other sequence classes within each genome are used to store and express genetic information.
• Explain the meaning of ploidy (haploid, diploid, aneuploid etc.) and how it relates to the number of homologues of each chromosome. 
• Predict the effects of mutations on the activity, structure, or stability of a protein and design appropriate experiments to assess the effects of mutations.
• Predict the growth behavior of microbes based on their growth conditions, e.g., temperature, available nutrient, aeration level, etc.
• Discuss the benefits of specific tools of modern biotechnology that are derived from naturally occurring microbes (e.g. cloning vectors, restriction enzymes, Taq polymerase, etc.)
• Accurately prepare and use reagents and perform experiments.
• When presented with an observation, develop a testable and falsifiable hypothesis.
• When provided with a hypothesis, identify the appropriate experimental observations and controllable variables.

• Describe how cells can produce proteins at the right time and correct amount.
• Diagram how a repressor works to reduce transcription.
• Diagram how an activator works to increase transcription.
• Identify a new promoter from literature and design a method to clone it and test its function.
• Successfully and safely manipulate DNA and Escherichia coli for ligation and transformation experiments.
• Design an experiment to verify a new 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.

• Students will name and describe the salient features and cellular tasks for each stage of cell division.

• Students will predict the relative durations of the stages of cell division using prior knowledge and facts from assigned readings.

• Students will describe the relationship between duration of each stage of cell division and the frequency of cells present in each stage of cell division counted in a random sample of images of pluripotent stem cells.

• Students will identify the stages of cell division present in research-quality images of human pluripotent stem cells in various stages of cell division.

• Students will quantify, analyze and summarize data on the prevalence of cells at different stages of cell division in randomly sampled cell populations.

• Students will use data to reflect on and revise predictions.