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This text presents Saccharomyces cerevisiae (baker's yeast) as a model organism for teaching the basics or for independent student research. This text presents Saccharomyces cerevisiae (baker's yeast) as a model organism for teaching the basics or for independent student research. It gives technical and background information at a variety of levels to accommodate different objectives and user experience. An introductory section offers basic information about the Saccharomyces cerevisiae life cycle, genetics, metabolism, and response to ultraviolet (UV) irradiation. Later sections offer more in-depth information about understanding, analyzing, and setting up certain experiments; a glossary; and a reference section covering basic laboratory techniques. Experiments include a basic cross, a dihybrid cross, complementation, mitotic segregation, meiosis, the effects of nutrient availability and UV radiation on the organism, and more. About People Did you know. Contact Us Here, I describe a multi-week lesson plan for a laboratory-based course with the goal of editing the genome of budding yeast, Saccharomyces cerevisiae. The lesson requires students to master skills such as bioinformatics analysis, restriction enzyme digestion, ligation, basic microbiology skills, polymerase chain reaction, and plasmid purification. Instructors are led through the technical aspects of the protocols, as well as the teaching philosophy involved throughout the laboratory experience. As it stands, the laboratory lesson is appropriate for 6-8 weeks of an upper-level undergraduate laboratory course, but may be adapted for shorter stints and students with less experience. Students complete the lesson with a more realistic idea of life science research and report significant learning gains. I anticipate this lesson to provide instructors and students in undergraduate programs with a hands-on, discovery-based learning experience that allows students to cultivate skills essential for success in the life sciences. As student-scientists, they are required to prepare rationales and protocols (in the form of introduction, procedures, and expected results) ahead of individual experiments, giving time and framework to assemble their own questions and answers to problems. This strategy encourages active participation by students who are less likely to participate in discussion ( 24 ). The lesson and its structure also gives students the freedom to make decisions (and mistakes) regarding the process with minimal judgement or interference from instructor. Students are instead encouraged to utilize peer groups to validate or defend their own ideas. This provides a cooperative learning experience where the outcome of peer-discussions will determine students' performance in the lab ( 25 ). Weekly feedback on individual writing assignments provides another opportunity for inclusive teaching ( 24 ), but also can be used along with formative assessments to correct any misconceptions stemming from misguided student-led learning. Surveys were administered anonymously via Salgsite.org. Likert scale questions were offered with the following options: no gains, little gain, moderate gain, good gain, great gain, and not applicable. Separate prompts requested student comments. All study protocols were approved by institutional IRB (protocol identification number FY2018-784). Before the start of each laboratory exercise, students submit an introduction, materials and methods, and expected results portion of the lab notebook. The one page referenced introduction explicitly states the research goal and provides information necessary to the understanding of the goals and processes in the laboratory. Prompts are provided in the lab handout to direct students on some elements that should be included in this introduction. Students are encouraged to write the introduction after the materials and methods, addressing specific questions they had about the protocol in the introduction. The introduction is designed as practice in scientific writing, in addition to assessment of the content (accuracy and completeness of background). Extensive feedback is provided on elements of scientific writing, including sentence and paragraph structure, formatting of the references and in-text citations, third person narrative, etc. Formatting is determined by the required text, “A Short Guide to Writing in Biology” ( 22 ). However, there are often places where students need to provide additional details not provided in the handouts. For instance, the lab handout might say to “pour an agarose gel” whereas each student’s materials and methods section should explicitly write out the directions for this, including the amount of agarose and the volume of buffer. This is intended to provide a framework for experimental protocols but also provide an opportunity for students to solve problems and apply their skills and knowledge. The students in this setting have experience with basic lab techniques from at least four previous laboratory courses, as well as in the early weeks of this course, and therefore, are more than capable of transferring those skills to this laboratory. Students with less experience will likely need to be provided with more resources and guidance during and immediately before each exercise. I have recently began providing some content on the course website several days before the materials and methods are due to provide additional guidance through areas that are troublesome for students (Supporting File S1: CRISPR in Yeast - Lectures). Additional mini-lectures by the instructor at the start of each lab often help students complete or correct misconceptions or errors in the protocol. Students are also encouraged to consult with peers to address any inconsistencies in the materials and methods, prior to performing experiments. To minimize time spent grading the materials and methods, the instructor may grade for simple completion or choose 1-3 elements (e.g., reaction conditions, culture volumes) within the materials and methods to assess. Students are expected to develop a hypothesis, a critical element for an authentic research experience, but also, to be able to visualize the product(s) of the assay based on this hypothesis. A common mistake is to state the hypothesized conclusion, but not actually describe the evidence that will support or reject the hypothesis. I have had success limiting the expected results to a few sentences, and even encouraging students sketch their anticipated data. The results are checked for completion (and feedback provided) in the week following the lab, but are collected and stringently graded twice during the semester. The format of results is standardized as much as possible according to the required writing text ( 22 ). For example, all figures must have a figure number, descriptive title, legend and be fully labeled. The results should be described in text, and the meaning or interpretation of the results discussed. When experiments fail, students are asked to hypothesize reasons for this, and describe a potential solution for this problem.The topics included in this exam are discussed and practiced in the introductory laboratory exercises (i.e., sterile technique, DNA isolation, restriction enzyme digest, agarose gel electrophoresis, etc.) and, importantly, in the practical design of CRISPR-based experiments in yeast. The assessment is both practical and formal. For the practical portion, students are asked to describe how to do techniques, or to perform exercises parallel to those done in class. Students are assessed after the design of their CRISPR-based experiments, but before its application to allow the students and instructors to proceed confidently with the CRISPR experiments, but also to provide instructors with time to prepare and order materials necessary for the student-designed portion of the project. This exam takes place the same week that formal lab reports are also due, with the goal of assessing assimilation of knowledge that was compiled in the formal report (Supporting File S2: CRISPR in Yeast - Sample Assessments). These reports are modeled after a primary research article, with an introduction, materials and methods, results, and discussion. To encourage early writing, limited portions of the lab reports are turned into the instructor as early as week 2. The material assessed in these early drafts is limited (i.e., materials and methods from cloning week 1, or results from cloning lab 2), to limit load on the instructor and students. The drafts are low stakes (points awarded for completion) and feedback is designed to provide progressive guidance on scientific writing. Specific instruction in science writing is provided during portions of the laboratory with wait times (i.e., incubations). The lab report rubric (Supporting File S5: CRISPR in Yeast - Lab Report Rubric) is provided to the students during these discussions. Instructor feedback can be streamlined with the rubric. It is also possible to orchestrate peer-reviews of drafts during the laboratory section, or outside of class. This communication is a pillar of the authentic research experience ( 1 ). Indeed, students report significant gains in their ability to and comfort with scientific writing (Figure 3B). Moreover, the lab report is an opportunity to compile the separate pieces of the exercise, making connections between the content and skills gained through the weeks. Students report significant gains in the ability to make these connections (Figure 3A), likely due, in large part, to lab reports. One student commented, “The lab report forced me to understand the bigger picture of what we did throughout the entire course of the semester.” The benefits of research participation are clear: They include clarification of a career path and enhancement of conceptual learning, problem solving skills, laboratory skills, resilience, and independence. Both course-based undergraduate research experiences (CURE) and individual undergraduate research experiences (URE) can provide the opportunity to learn elements of the process of science. In practice, the scientific process starts with observations and inquiry, then proceeds to identification of a research question, design of experiments to answer the question, followed by collection and analysis of data. Then, rather than proceeding directly to drawing conclusions, the process typically diverts to a trouble-shooting stage before circling back to revisit the research question, requiring redesign of the experiments. The outcome, at times, is the generation of novel data for consumption by the scientific community. Some educational authentic research experiences include the creation of novel, publishable data of interest to the scientific community to be a defining characteristic. Programs with the goal of data product often do not accomplish that goal, but still show significant learning outcomes ( 1, 6 ). Altogether, the outcomes associated with product-centered research experiences may also be achieved with intentional design, even when they do not produce novel data ( 7 ). Students are instructed in the concepts underlying advanced laboratory skills including molecular cloning, bacterial transformation, yeast genetics, and PCR. Students are expected to analyze and integrate this knowledge by contributing to experimental design and trouble-shooting unsuccessful attempts. The concepts and skills are divided into mini-goals that connect across multiple exercises to have the ultimate outcome of site-specific editing of a eukaryotic genome. While there are multiple opportunities for student contributions, the choices are constrained to minimize the load on instructors. Clustered regularly interspaced short palindromic repeats (CRISPR) gene-editing technology is at the forefront of scientific inquiry. Several mentions of CRISPR in mainstream media have piqued the public curiosity. A large part of the excitement over CRISPR is its relative simplicity in design and use, which makes it an optimal tool for use in teaching. Overall, the laboratory experience is tractable to undergraduate students and can be performed with limited materials and expertise. CRISPR-associated (Cas) proteins are double-stranded endonucleases that are guided to cleave DNA at sites specified by an antisense base-paired CRISPR RNA (crRNA). Trans-acting crRNA (tracrRNA) binds both crRNA and Cas protein, linking the two so that the crRNA can guide Cas proteins to a complementary sequence of DNA. The only constraints for the ability of Cas (commonly Cas9) to cleave the DNA is that it has a region complementary to the 20 nucleotide crRNA that is immediately upstream of an NGG protospacer-adjacent-motif (PAM) ( 10, 11 ). Scientists have simplified the system even further by fusing tracrRNA and crRNA into a single guide RNA (sgRNA) ( 12 ). HR requires a homologous strand of DNA to serve as a template for repair. In a diploid organism, the opposing allele may be used as a template, generating two similar alleles. In S. cerevisiae, double stranded genome break repair is performed almost exclusively through HR ( 14 ). In order for the double stranded break to be repaired in haploid yeast strains, a homologous donor sequence must be incorporated into the cell to facilitate homologous repair. A synthetic single stranded oligonucleotide (ssODNA) is often used as a template for homologous repair after genome cleavage ( 15 ), directing HR to incorporate specified insertions, deletions, or mutations to the affected region of the genome (Figure 1 and Figure 2). I argue that the intentional design of the activity provides significant learning outcomes in its current, relatively simple format. Novel data could be generated with only slight modifications to the current exercise. Alternatively, instructors may adapt this protocol to disrupt any gene of interest in the yeast genome, and could then apply the produced yeast strain toward the production of novel data. The added activity of a comprehensive written report provides them with an opportunity to become more proficient and comfortable with scientific communication. Students report significant gains in the process of science, but also in their understanding of concepts related to this course and other life science courses. Overall, students come away with a more realistic understanding of the research and report significant learning outcomes (Figure 3). The course is a required for completion of the degree in Cell and Molecular Biology from the Department of Biomedical Sciences, but is also open to Agriculture and Biology terminal master's students at the University. The number of students in each course laboratory section varied between 14 and 22. However, the described learning activities are accomplished in 6-8 weeks of the course. The laboratory class period is 2 h 50 min long, one day a week. Some student out-of-class time is used for preparation or data collection. The course was first taught in the Spring of 2016 and was run in three semesters, with at least three sections each semester. Surveys were administered anonymously via Salgsite.org. Likert scale questions were offered with the following options: no gains, little gain, moderate gain, good gain, great gain, and not applicable. Extensive feedback is provided on elements of scientific writing, including sentence and paragraph structure, formatting of the references and in-text citations, third person narrative, etc.However, there are often places where students need to provide additional details not provided in the handouts. To minimize time spent grading the materials and methods, the instructor may grade for simple completion or choose 1-3 elements ( e.g., reaction conditions, culture volumes) within the materials and methods to assess. Students are expected to develop a hypothesis, a critical element for an authentic research experience, but also, to be able to visualize the product(s) of the assay based on this hypothesis. When experiments fail, students are asked to hypothesize reasons for this, and describe a potential solution for this problem.The topics included in this exam are discussed and practiced in the introductory laboratory exercises ( i.e., sterile technique, DNA isolation, restriction enzyme digest, agarose gel electrophoresis, etc.) and, importantly, in the practical design of CRISPR-based experiments in yeast. To encourage early writing, limited portions of the lab reports are turned into the instructor as early as week 2. The material assessed in these early drafts is limited ( i.e., materials and methods from cloning week 1, or results from cloning lab 2), to limit load on the instructor and students. Specific instruction in science writing is provided during portions of the laboratory with wait times ( i.e., incubations). The lab report rubric (Supporting File S5: CRISPR in Yeast - Lab Report Rubric) is provided to the students during these discussions. Students report significant gains in the ability to make these connections (Figure 3A), likely due, in large part, to lab reports.As student-scientists, they are required to prepare rationales and protocols (in the form of introduction, procedures, and expected results) ahead of individual experiments, giving time and framework to assemble their own questions and answers to problems. This strategy encourages active participation by students who are less likely to participate in discussion ( 24 ). Weekly feedback on individual writing assignments provides another opportunity for inclusive teaching ( 24 ), but also can be used, along with formative assessments, to correct any misconceptions stemming from misguided student-led learning. Each module takes place in 1-2 class periods (or weeks). Each class period begins with a brief instructional period to clarify common points of misconception and provide more explicit instruction ( i.e., where to find materials, how to operate equipment, etc.). The student laboratory manual (Supporting File S3: CRISPR in Yeast - Laboratory Manual) guides students through: 1. Obtaining the sequence of a yeast gene, 2. Designing sgRNA recognition sites in the gene that potentially disrupt the gene, and 3. Designing a template for repair of the gene after cleavage. The activity can be completed in groups (I limit groups to a maximum of three students per group).