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Freeman S, Mukerji J, Sievers M, Beltran IB, Dickinson K, Dy GEC, Gardiner A, Glenski EH, Hill MJ, Kerr B, Monet D, Reemts C, Theobald E, Tran ET, Velasco V, Wachtell L, Warfield L. A CURE on the Evolution of Antibiotic Resistance in Escherichia coli Improves Student Conceptual Understanding. CBE LIFE SCIENCES EDUCATION 2023; 22:ar7. [PMID: 36607289 PMCID: PMC10074268 DOI: 10.1187/cbe.21-12-0331] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 11/08/2022] [Accepted: 12/02/2022] [Indexed: 06/17/2023]
Abstract
We developed labs on the evolution of antibiotic resistance to assess the costs and benefits of replacing traditional laboratory exercises in an introductory biology course for majors with a course-based undergraduate research experience (CURE). To assess whether participating in the CURE imposed a cost in terms of exam performance, we implemented a quasi-experiment in which four lab sections in the same term of the same course did the CURE labs, while all other students did traditional labs. To assess whether participating in the CURE impacted other aspects of student learning, we implemented a second quasi-experiment in which all students either did traditional labs over a two-quarter sequence or did CURE labs over a two-quarter sequence. Data from the first experiment showed minimal impact on CURE students' exam scores, while data from the second experiment showed that CURE students demonstrated a better understanding of the culture of scientific research and a more expert-like understanding of evolution by natural selection. We did not find disproportionate costs or benefits for CURE students from groups that are minoritized in science, technology, engineering, and mathematics.
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Affiliation(s)
- Scott Freeman
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Joya Mukerji
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Matt Sievers
- Department of Biology, University of Washington, Seattle, WA 98195
| | | | - Katie Dickinson
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Grace E. C. Dy
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Amanda Gardiner
- Department of Biology, University of Washington, Seattle, WA 98195
| | | | - Mariah J. Hill
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Ben Kerr
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Deja Monet
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Connor Reemts
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Elli Theobald
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Elisa T. Tran
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Vicente Velasco
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Lexi Wachtell
- Department of Biology, University of Washington, Seattle, WA 98195
| | - Liz Warfield
- Department of Biology, University of Washington, Seattle, WA 98195
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Shoaf PT, French KS, Clifford NJ, McKenney EA, Ott LE. A gut microbiome tactile teaching tool and guided-inquiry activity promotes student learning. Front Microbiol 2022; 13:966289. [PMID: 36620056 PMCID: PMC9813521 DOI: 10.3389/fmicb.2022.966289] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 12/02/2022] [Indexed: 12/24/2022] Open
Abstract
The gut microbiome and its physiological impacts on human and animal health is an area of research emphasis. Microbes themselves are invisible and may therefore be abstract and challenging to understand. It is therefore important to infuse this topic into undergraduate curricula, including Anatomy and Physiology courses, ideally through an active learning approach. To accomplish this, we developed a novel tactile teaching tool with guided-inquiry (TTT-GI) activity where students explored how the gut microbiome ferments carbohydrates to produce short chain fatty acids (SCFAs). This activity was implemented in two sections of a large-enrollment Human Anatomy and Physiology course at a research intensive (R1) university in the Spring of 2022 that was taught using a hyflex format. Students who attended class in person used commonly available building toys to assemble representative carbohydrates of varying structural complexity, whereas students who attended class virtually made these carbohydrate structures using a digital learning tool. Students then predicted how microbes within the gut would ferment different carbohydrates into SCFAs, as well as the physiological implications of the SCFAs. We assessed this activity to address three research questions, with 182 students comprising our sample. First, we evaluated if the activity learning objectives were achieved through implementation of a pre-and post-assessment schema. Our results revealed that all three learning objectives of this activity were attained. Next, we evaluated if the format in which this TTT-GI activity was implemented impacted student learning. While we found minimal and nonsignificant differences in student learning between those who attended in-person and those who attended remotely, we did find significant differences between the two course sections, which differed in length and spacing of the activity. Finally, we evaluated if this TTT-GI approach was impactful for diverse students. We observed modest and nonsignificant positive learning gains for some populations of students traditionally underrepresented in STEM (first-generation students and students with one or more disabilities). That said, we found that the greatest learning gains associated with this TTT-GI activity were observed in students who had taken previous upper-level biology coursework.
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Affiliation(s)
- Parker T. Shoaf
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Katie S. French
- Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC, United States
| | - Noah J. Clifford
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States
| | - Erin A. McKenney
- Department of Applied Ecology, North Carolina State University, Raleigh, NC, United States
| | - Laura E. Ott
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,Carolina Biology Education Research Laboratory, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States,*Correspondence: Laura E. Ott, ✉
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3
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Abstract
Microbiome research projects are often interdisciplinary, involving fields such as microbiology, genetics, ecology, evolution, bioinformatics, and statistics. These research projects can be an excellent fit for undergraduate courses ranging from introductory biology labs to upper-level capstone courses. Microbiome research projects can attract the interest of students majoring in health and medical sciences, environmental sciences, and agriculture, and there are meaningful ties to real-world issues relating to human health, climate change, and environmental sustainability and resilience in pristine, fragile ecosystems to bustling urban centers. In this review, we will discuss the potential of microbiome research integrated into classes using a number of different modalities. Our experience scaling-up and implementing microbiome projects at a range of institutions across the US has provided us with insight and strategies for what works well and how to diminish common hurdles that are encountered when implementing undergraduate microbiome research projects. We will discuss how course-based microbiome research can be leveraged to help faculty make advances in their own research and professional development and the resources that are available to support faculty interested in integrating microbiome research into their courses.
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Affiliation(s)
- Theodore R Muth
- Department of Biology, Brooklyn College of The City University of New York, Brooklyn, NY, United States.,Molecular, Cellular, and Developmental Biology Department at The Graduate Center of The City University of New York, New York, NY, United States
| | - Avrom J Caplan
- Department of Biology, Dyson College of Arts and Sciences, Pace University, New York, NY, United States
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Kruchten AE. A Curricular Bioinformatics Approach to Teaching Undergraduates to Analyze Metagenomic Datasets Using R. Front Microbiol 2020; 11:578600. [PMID: 33013816 PMCID: PMC7511545 DOI: 10.3389/fmicb.2020.578600] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 08/12/2020] [Indexed: 01/06/2023] Open
Abstract
Biologists with bioinformatic skills will be better prepared for the job market, but relatively few biology programs require bioinformatics courses. Inclusion in the curriculum may be hindered by several barriers, including lack of faculty expertise, student resistance to computational work, and few examples in the pedagogical literature. An 8-week wet-lab and in silico research experience for undergraduates was implemented. Students performed DNA purification and metagenomics analysis to compare the diversity and abundance of microbes in two samples. Students sampled snow from sites in northern Minnesota and purified genomic DNA from the microbes, followed by metagenomic analysis. Students used an existing metagenomic dataset to practice analysis skills, including comparing the use of Excel versus R for analysis and visualization of a large dataset. Upon receipt of the snow data, students applied their recently acquired skills to their new dataset and reported their results via a poster. Several outcomes were achieved as a result of this module. First, YouTube videos demonstrating hands-on metagenomics and R techniques were used as professional development for faculty, leading to broadened research capabilities and comfort with bioinformatics. Second, students were introduced to computational skills in a manner that was intentional, with time for both introduction and reinforcement of skills. Finally, the module was effectively included in a biology curriculum because it could function as either a stand-alone course or a module within another course such as microbiology. This module, developed with Course-based Undergraduate Research Experience guidelines in mind, introduces students and faculty to bioinformatics in biology research.
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Affiliation(s)
- Anne E Kruchten
- Department of Biology, The College of St. Scholastica, Duluth, MN, United States
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Wernli D, Jørgensen PS, Harbarth S, Carroll SP, Laxminarayan R, Levrat N, Røttingen JA, Pittet D. Antimicrobial resistance: The complex challenge of measurement to inform policy and the public. PLoS Med 2017; 14:e1002378. [PMID: 28817562 PMCID: PMC5560527 DOI: 10.1371/journal.pmed.1002378] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Didier Wernli and colleagues discuss the role of monitoring in countering antimicrobial resistance.
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Affiliation(s)
- Didier Wernli
- Global Studies Institute, University of Geneva, Geneva, Switzerland
| | - Peter S. Jørgensen
- Global Economic Dynamics and the Biosphere, Royal Swedish Academy of Sciences, Stockholm, Sweden
- Stockholm Resilience Centre, Stockholm University, Stockholm, Sweden
| | - Stephan Harbarth
- Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
- WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
| | - Scott P. Carroll
- Department of Entomology and Nematology, University of California, Davis, Davis, California, United States of America
- Institute for Contemporary Evolution, Davis, California, United States of America
| | - Ramanan Laxminarayan
- Princeton Environmental Institute, Princeton, New Jersey, United States of America
- Center for Disease Dynamics, Economics & Policy, Washington, DC, United States of America
| | - Nicolas Levrat
- Global Studies Institute, University of Geneva, Geneva, Switzerland
- Faculty of Law, University of Geneva, Geneva, Switzerland
| | - John-Arne Røttingen
- Department of Global Health & Population, Harvard T.H. Chan School of Public Health, Harvard University, Boston, Massachusetts, United States of America
- Norwegian Institute of Public Health and University of Oslo, Oslo, Norway
| | - Didier Pittet
- Infection Control Program, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
- WHO Collaborating Centre on Patient Safety, University of Geneva Hospitals and Faculty of Medicine, Geneva, Switzerland
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