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Rowe L. Comparing Learning Outcomes and Student and Instructor Perceptions of a Simultaneous Online versus In-Person Biochemistry Laboratory Course. JOURNAL OF CHEMICAL EDUCATION 2024; 101:882-891. [PMID: 38495613 PMCID: PMC10938634 DOI: 10.1021/acs.jchemed.3c00571] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 01/12/2024] [Accepted: 01/16/2024] [Indexed: 03/19/2024]
Abstract
This article compares the learning outcomes and student perceptions of a one semester undergraduate biochemistry laboratory course that was taught using either a fully online or a fully in-person teaching modality. The semester long biochemistry laboratory mimicked the work sequence a researcher would encounter when transforming a plasmid containing a gene for a recombinant protein (superfolder green fluorescent protein, sf-GFP) and then purifying, identifying, and characterizing that protein. The two modalities of the course were completed in the same semester, by the same instructor, in which students self-selected into which modality they preferred at the beginning of the semester. Students in the in-person section reported enjoying the laboratory course more than the online cohort of students and found it to be less time-consuming. Additionally, a survey of biochemistry laboratory instructors from across the United States, who had experience teaching both online and in-person biochemistry laboratories, indicated that the majority of instructors that responded to the survey preferred the in-person modality: believing them to be more effective and engaging for the students, more enjoyable, and less time-consuming for the instructor. Statistical analysis of formative and summative assessments indicated no significant difference in non-hands-on student learning objective and learning goal scores between the two groups, but the small number of students and instructors in this study limits the generalizability of these results.
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Affiliation(s)
- Laura Rowe
- Department of Chemistry, Eastern
Kentucky University, Richmond, Kentucky 40475, United States
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2
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Mayta ML, Dotto M, Orellano EG, Krapp AR. An experimental protocol for teaching CRISPR/Cas9 in a post-graduate plant laboratory course: An analysis of mutant-edited plants without sequencing. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2022; 50:537-546. [PMID: 35894125 DOI: 10.1002/bmb.21659] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Revised: 02/08/2022] [Accepted: 07/08/2022] [Indexed: 06/15/2023]
Abstract
The CRISPR/Cas9 system is widely used for editing genes in various organisms and is a very useful tool due to its versatility, simplicity, and efficiency. To teach its principles to post-graduate students we designed a laboratory activity to obtain and analyze PDS3 mutants in Arabidopsis thaliana plants consisting of: 1) Design of guide RNAs using bioinformatics tools; 2) plant transformation (which is optional depending on the length of the course); 3) observation and evaluation of the mutant's phenotypes in the Phytoene desaturase (PDS3) gene, which exhibit an albino phenotype and different degrees of mosaicism in the editing events we evaluated; 4) PCR amplification of a fragment that includes the mutated region followed by analysis of single-stranded DNA conformation polymorphisms (SSCP) using native polyacrylamide gel electrophoresis and silver nitrate staining to detect changes in the amplicon sequence due to gene editing. Through SSCP, the students were able to distinguish between homozygous and heterozygous edited plants. A highlight feature of this protocol is the visualization and detection of the mutation/edition without sequencing the edited fragment.
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Affiliation(s)
- Martín L Mayta
- Área Biología Molecular, Departamento Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Centro para la Investigación en Ciencias de la Salud, Facultad de Ciencias de la Salud, Universidad Adventista del Plata, Entre Ríos, Argentina
| | - Marcela Dotto
- Área Biología Molecular, Departamento Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Instituto de Ciencias Agropecuarias del Litoral (ICiAgro L.), Facultad de Ciencias Agrarias, Universidad Nacional del Litoral, Esperanza, Argentina
| | - Elena G Orellano
- Área Biología Molecular, Departamento Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Adriana R Krapp
- Área Biología Molecular, Departamento Ciencias Biológicas, Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
- Instituto de Biología Molecular y Celular de Rosario (IBR-CONICET), Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
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Baidya S, Choudhury S, De RK. A Novel CRISPR-MultiTargeter Multi-agent Reinforcement learning (CMT-MARL) algorithm to identify editable target regions using a Hybrid scoring from multiple similar sequences. APPL INTELL 2022. [DOI: 10.1007/s10489-022-03871-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Juríková K, Sepšiová R, Ševčovičová A, Tomáška Ľ, Džugasová V. Implementing CRISPR-Cas9 Yeast Practicals into Biology Curricula. CRISPR J 2022; 5:181-186. [PMID: 35333620 DOI: 10.1089/crispr.2021.0125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
CRISPR-Cas9 is a genome-editing technique that has been widely adopted thanks to its simplicity, efficiency, and broad application potential. Due to its advantages and pervasive use, there have been attempts to include this method in the existing curricula for students majoring in various disciplines of biology. In this perspective, we summarize the existing CRISPR-Cas courses that harness a well-established model organism: baker's yeast, Saccharomyces cerevisiae. As an example, we present a detailed description of a fully hands-on, flexible, robust, and cost-efficient practical CRISPR-Cas9 course, where students participate in yeast genome editing at every stage-from the bioinformatic design of single-guide RNA, through molecular cloning and yeast transformation, to the final confirmation of the introduced mutation. Finally, we emphasize that in addition to providing experimental skills and theoretical knowledge, the practical courses on CRISPR-Cas represent ideal platforms for discussing the ethical implications of the democratization of biology.
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Affiliation(s)
- Katarína Juríková
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia; Computational and Integrative Biology, University of Trento, Trento, Italy
- CIBIO-Department of Cellular, Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Regina Sepšiová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia; Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Andrea Ševčovičová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia; Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Ľubomír Tomáška
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia; Computational and Integrative Biology, University of Trento, Trento, Italy
| | - Vladimíra Džugasová
- Department of Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia; Computational and Integrative Biology, University of Trento, Trento, Italy
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Peyton BM, Skorupa DJ. Integrating CUREs in Ongoing Research: Undergraduates as Active Participants in the Discovery of Biodegrading Thermophiles. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2021; 22:jmbe00102-21. [PMID: 34594470 PMCID: PMC8457424 DOI: 10.1128/jmbe.00102-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 03/16/2021] [Indexed: 05/24/2023]
Abstract
Research-based courses are a powerful way to engage undergraduates in the scientific process while simultaneously teaching participants relevant laboratory, analysis, and scientific communication skills. In most programs, students conduct a simulated project which effectively improves student conceptions of scientific thinking but does not produce research-quality data. The course described here delivered an authentic research experience by assigning undergraduates an objective from an active grant-funded project. Participants contributed to research aimed at culturing biodegrading thermophiles from hot springs in Yellowstone National Park. Students participated in a backcountry field experience, collecting environmental samples of their choosing and determining appropriate culturing conditions. Following high-temperature incubations, 16S rRNA gene sequencing identified enriched microbial populations, with analytical and microscopy methods tracking degradation and growth. Importantly, several teams successfully cultivated thermophilic plastic-degrading consortia. Student learning was assessed using several methods, including grade distributions on assignments and statistical comparisons of pre- and posttests. A consistent and, in most cases, statistically significant increase was observed in the students' posttest scores. The grade distribution on summative assessments also suggests that students achieved the desired learning outcomes. Student perceptions of their learning and experience gains were high, with participants reporting improvements in components emphasized in the research activities. Overall, the findings highlight how involving undergraduates in real-world research projects can enhance student interest and ownership of scientific research, along with contributing quality data that inform active studies.
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Affiliation(s)
- Brent M. Peyton
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
| | - Dana J. Skorupa
- Department of Chemical and Biological Engineering, Montana State University, Bozeman, Montana, USA
- Thermal Biology Institute, Montana State University, Bozeman, Montana, USA
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Genome Editing in Bacteria: CRISPR-Cas and Beyond. Microorganisms 2021; 9:microorganisms9040844. [PMID: 33920749 PMCID: PMC8071187 DOI: 10.3390/microorganisms9040844] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2021] [Revised: 02/05/2021] [Accepted: 02/07/2021] [Indexed: 12/11/2022] Open
Abstract
Genome editing in bacteria encompasses a wide array of laborious and multi-step methods such as suicide plasmids. The discovery and applications of clustered regularly interspaced short palindromic repeats (CRISPR)-Cas based technologies have revolutionized genome editing in eukaryotic organisms due to its simplicity and programmability. Nevertheless, this system has not been as widely favored for bacterial genome editing. In this review, we summarize the main approaches and difficulties associated with CRISPR-Cas-mediated genome editing in bacteria and present some alternatives to circumvent these issues, including CRISPR nickases, Cas12a, base editors, CRISPR-associated transposases, prime-editing, endogenous CRISPR systems, and the use of pre-made ribonucleoprotein complexes of Cas proteins and guide RNAs. Finally, we also address fluorescent-protein-based methods to evaluate the efficacy of CRISPR-based systems for genome editing in bacteria. CRISPR-Cas still holds promise as a generalized genome-editing tool in bacteria and is developing further optimization for an expanded application in these organisms. This review provides a rarely offered comprehensive view of genome editing. It also aims to familiarize the microbiology community with an ever-growing genome-editing toolbox for bacteria.
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Pieczynski JN, Kee HL. "Designer babies?!" A CRISPR-based learning module for undergraduates built around the CCR5 gene. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2021; 49:80-93. [PMID: 32777177 PMCID: PMC7891609 DOI: 10.1002/bmb.21395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2020] [Revised: 05/12/2020] [Accepted: 05/26/2020] [Indexed: 05/11/2023]
Abstract
CRISPR-cas technology is being incorporated into undergraduate biology curriculum through lab experiences to immerse students in modern technology that is rapidly changing the landscape of science, medicine and agriculture. We developed and implemented an educational module that introduces students to CRISPR-cas technology in a Genetic course and an Advanced Genetics course. Our primary teaching objective was to immerse students in the design, strategy, conceptual modeling, and application of CRISPR-cas technology using the current research claim of the modification of the CCR5 gene in twin girls. This also allowed us to engage students in an open conversation about the bioethical implications of heritable germline and non-heritable somatic genomic editing. We assessed student-learning outcomes and conclude that this learning module is an effective strategy for teaching undergraduates the fundamentals and application of CRISPR-cas gene editing technology and can be adapted to other genes and diseases that are currently being treated with CRISPR-cas technology.
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Affiliation(s)
- Jay N Pieczynski
- Department of Biology, Rollins College, Winter Park, Florida, USA
| | - Hooi Lynn Kee
- Department of Biology, Stetson University, DeLand, Florida, USA
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Challenges of in vitro genome editing with CRISPR/Cas9 and possible solutions: A review. Gene 2020; 753:144813. [DOI: 10.1016/j.gene.2020.144813] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Revised: 04/26/2020] [Accepted: 05/23/2020] [Indexed: 12/20/2022]
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Martin A, Wolcott NS, O'Connell LA. Bringing immersive science to undergraduate laboratory courses using CRISPR gene knockouts in frogs and butterflies. ACTA ACUST UNITED AC 2020; 223:223/Suppl_1/jeb208793. [PMID: 32034043 DOI: 10.1242/jeb.208793] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The use of CRISPR/Cas9 for gene editing offers new opportunities for biology students to perform genuine research exploring the gene-to-phenotype relationship. It is important to introduce the next generation of scientists, health practitioners and other members of society to the technical and ethical aspects of gene editing. Here, we share our experience leading hands-on undergraduate laboratory classes, where students formulate hypotheses regarding the roles of candidate genes involved in development, perform loss-of-function experiments using programmable nucleases and analyze the phenotypic effects of mosaic mutant animals. This is enabled by the use of the amphibian Xenopus laevis and the butterfly Vanessa cardui, two organisms that reliably yield hundreds of large and freshly fertilized eggs in a scalable manner. Frogs and butterflies also present opportunities to teach key biological concepts about gene regulation and development. To complement these practical aspects, we describe learning activities aimed at equipping students with a broad understanding of genome editing techniques, their application in fundamental and translational research, and the bioethical challenges they raise. Overall, our work supports the introduction of CRISPR technology into undergraduate classrooms and, when coupled with classroom undergraduate research experiences, enables hypothesis-driven research by undergraduates.
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Affiliation(s)
- Arnaud Martin
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
| | - Nora S Wolcott
- Department of Biological Sciences, The George Washington University, Washington, DC 20052, USA
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Hastie E, Sellers R, Valan B, Sherwood DR. A Scalable CURE Using a CRISPR/Cas9 Fluorescent Protein Knock-In Strategy in Caenorhabditis elegans. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2019; 20:jmbe-20-60. [PMID: 31890079 PMCID: PMC6914349 DOI: 10.1128/jmbe.v20i3.1847] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/16/2019] [Indexed: 06/07/2023]
Abstract
Genome editing with CRISPR/Cas9 technology has advanced from the lab bench to clinical application with multiple trials underway. This article introduces a course-based undergraduate experience (CURE) combining CRISPR/Cas9 genome editing (using a modified two-plasmid system) and the animal model Caenorhabditis elegans. This CURE is designed to be a scalable, semester-long laboratory that will introduce the students to literature searches, molecular biology, experiment planning, microscopy, CRISPR bioethics discussion, and scientific writing. Here, students challenged themselves to endogenously tag the C. elegans gene zmp-4, a matrix metalloproteinase enzyme, with a fluorescent protein marker and successfully generated a new worm strain. The knock-in was confirmed with genotyping and imaging and will be available for use by the entire worm community.
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Affiliation(s)
- Eric Hastie
- Department of Biology, Duke University, Durham, NC 27708
| | - Ryan Sellers
- Department of Biology, Duke University, Durham, NC 27708
| | - Bruno Valan
- Department of Biology, Duke University, Durham, NC 27708
| | - David R. Sherwood
- Department of Biology, Duke University, Durham, NC 27708
- Regeneration Next, Duke University, Durham, NC 27708
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