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Martins A, Fonseca MJ, Lemos M, Lencastre L, Tavares F. Bioinformatics-Based Activities in High School: Fostering Students' Literacy, Interest, and Attitudes on Gene Regulation, Genomics, and Evolution. Front Microbiol 2020; 11:578099. [PMID: 33162959 PMCID: PMC7591593 DOI: 10.3389/fmicb.2020.578099] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/08/2020] [Indexed: 11/13/2022] Open
Abstract
The key role of bioinformatics in explaining biological phenomena calls for the need to rethink didactic approaches at high school aligned with a new scientific reality. Despite several initiatives to introduce bioinformatics in the classroom, there is still a lack of knowledge on their impact on students' learning gains, engagement, and motivation. In this study, we detail the effects of four bioinformatics laboratories tailored for high school biology classes named "Mining the Genome: Using Bioinformatics Tools in the Classroom to Support Student Discovery of Genes" on literacy, interest, and attitudes on 387 high school students. By exploring these laboratories, students get acquainted with bioinformatics and acknowledge that many bioinformatics tools can be intuitive for beginners. Furthermore, introducing comparative genomics in their learning practices contributed for a better understanding of curricular contents regarding the identification of genes, their regulation, and how to make evolutionary assumptions. Following the intervention, students were able to pinpoint bioinformatics tools required to identify genes in a genomics sequence, and most importantly, they were able to solve genomics-related misconceptions. Overall, students revealed a positive attitude regarding the integration of bioinformatics-based approaches in their learning practices, reinforcing their added value in educational approaches.
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Affiliation(s)
- Ana Martins
- Departamento de Biologia, FCUP-Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Vairão, Portugal
| | - Maria João Fonseca
- MHNC-UP-Museu de História Natural e da Ciência, Universidade do Porto, Porto, Portugal
| | - Marina Lemos
- FPCEUP-Faculdade de Psicologia e Ciências da Educação, Universidade do Porto, Porto, Portugal
| | - Leonor Lencastre
- FPCEUP-Faculdade de Psicologia e Ciências da Educação, Universidade do Porto, Porto, Portugal
| | - Fernando Tavares
- Departamento de Biologia, FCUP-Faculdade de Ciências, Universidade do Porto, Porto, Portugal.,CIBIO-Centro de Investigação em Biodiversidade e Recursos Genéticos, InBIO-Laboratório Associado, Universidade do Porto, Vairão, Portugal
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Wachira J, Hughes-Darden C, Nkwanta A. Investigating Cell Signaling with Gene Expression Datasets. COURSESOURCE 2019; 6:10.24918/cs.2019.1. [PMID: 32855998 PMCID: PMC7449260 DOI: 10.24918/cs.2019.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Modern molecular biology is a data- and computationally-intensive field with few instructional resources for introducing undergraduate students to the requisite skills and techniques for analyzing large data sets. This Lesson helps students: (i) build an understanding of the role of signal transduction in the control of gene expression; (ii) improve written scientific communication skills through engagement in literature searches, data analysis, and writing reports; and (iii) develop an awareness of the procedures and protocols for analyzing and making inferences from high-content quantitative molecular biology data. The Lesson is most suited to upper level biology courses because it requires foundational knowledge on cellular organization, protein structure and function, and the tenets of information flow from DNA to proteins. The first step lays the foundation for understanding cell signaling, which can be accomplished through assigned readings and presentations. In subsequent active learning sessions, data analysis is integrated with exercises that provide insight into the structure of scientific papers. The Lesson emphasizes the role of quantitative methods in research and helps students gain experience with functional genomics databases and data analysis, which are important skills for molecular biologists. Assessment is conducted through mini-reports designed to gauge students' perceptions of the purpose of each step, their awareness of the possible limitations of the methods utilized, and the ability to identify opportunities for further investigation. Summative assessment is conducted through a final report. The modules are suitable for complementing wet-laboratory experiments and can be adapted for different courses that use molecular biology data.
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Affiliation(s)
- James Wachira
- Department of Biology, Morgan State University, 1700 E. Cold Spring Lane, Baltimore, MD 21251
| | - Cleo Hughes-Darden
- Department of Biology, Morgan State University, 1700 E. Cold Spring Lane, Baltimore, MD 21251
| | - Asamoah Nkwanta
- Department of Mathematics, Morgan State University, 1700 E. Cold Spring Lane, Baltimore, MD 21251
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Moitra K. Releasing the "GENI": integrating authentic microbial genomics research into the classroom through GENI-ACT. FEMS Microbiol Lett 2018; 364:4443195. [PMID: 29040493 DOI: 10.1093/femsle/fnx215] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2017] [Accepted: 10/04/2017] [Indexed: 11/15/2022] Open
Abstract
The integration of genomics research into the undergraduate biology curriculum provides students with the opportunity to become familiar with bioinformatics tools and answer original research questions. Our purpose with this research project was to upscale the research experience through integration with classroom experience giving students access to authentic research projects. Students annotated 60 predicted ABC genes of Methanothermobacter thermautotrophicus and Methanobacterium sp. SWAN-1, and they were required to present a research poster to demonstrate their understanding of the project. During this research project a number of tests, assessments and surveys were conducted to assess familiarity with technical and conceptual understanding of genome annotation, satisfaction with annotation instruction, gain in bioinformatics research skills, scientific communications skills and increased student interest in research. We found that students gained significant skills in bioinformatics, specifically genome annotation skills and also gained confidence in their abilities to carry out scientific research. As a result of this authentic undergraduate research experience under-represented students were motivated to pursue future careers in STEM fields.
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Affiliation(s)
- Karobi Moitra
- Department of Biology, Trinity Washington University, College Of Arts and Sciences, 125 Michigan Avenue NE, Washington DC 20017, USA
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Wang JTH. Course-based undergraduate research experiences in molecular biosciences-patterns, trends, and faculty support. FEMS Microbiol Lett 2018; 364:4033031. [PMID: 28859321 DOI: 10.1093/femsle/fnx157] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2017] [Accepted: 07/21/2017] [Indexed: 12/20/2022] Open
Abstract
Inquiry-driven learning, research internships and course-based undergraduate research experiences all represent mechanisms through which educators can engage undergraduate students in scientific research. In life sciences education, the benefits of undergraduate research have been thoroughly evaluated, but limitations in infrastructure and training can prevent widespread uptake of these practices. It is not clear how faculty members can integrate complex laboratory techniques and equipment into their unique context, while finding the time and resources to implement undergraduate research according to best practice guidelines. This review will go through the trends and patterns in inquiry-based undergraduate life science projects with particular emphasis on molecular biosciences-the research-aligned disciplines of biochemistry, molecular cell biology, microbiology, and genomics and bioinformatics. This will provide instructors with an overview of the model organisms, laboratory techniques and research questions that are adaptable for semester-long projects, and serve as starting guidelines for course-based undergraduate research.
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Affiliation(s)
- Jack T H Wang
- School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD 4072, Australia
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Beck C, Butler A, da Silva KB. Promoting inquiry-based teaching in laboratory courses: are we meeting the grade? CBE LIFE SCIENCES EDUCATION 2014; 13:444-52. [PMID: 25185228 PMCID: PMC4152206 DOI: 10.1187/cbe.13-12-0245] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Over the past decade, repeated calls have been made to incorporate more active teaching and learning in undergraduate biology courses. The emphasis on inquiry-based teaching is especially important in laboratory courses, as these are the courses in which students are applying the process of science. To determine the current state of research on inquiry-based teaching in undergraduate biology laboratory courses, we reviewed the recent published literature on inquiry-based exercises. The majority of studies in our data set were in the subdisciplines of biochemistry, cell biology, developmental biology, genetics, and molecular biology. In addition, most exercises were guided inquiry, rather than open ended or research based. Almost 75% of the studies included assessment data, with two-thirds of these studies including multiple types of assessment data. However, few exercises were assessed in multiple courses or at multiple institutions. Furthermore, assessments were rarely based on published instruments. Although the results of the studies in our data set show a positive effect of inquiry-based teaching in biology laboratory courses on student learning gains, research that uses the same instrument across a range of courses and institutions is needed to determine whether these results can be generalized.
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Affiliation(s)
- Christopher Beck
- *Department of Biology, Emory University, Atlanta, GA 30322 School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Amy Butler
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
| | - Karen Burke da Silva
- School of Biological Sciences, Flinders University, Adelaide, SA 5001, Australia
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Abstract
A response to Maskiewicz and Lineback's essay in the September 2013 issue of CBE-Life Sciences Education.
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Affiliation(s)
| | - Rebecca M. Price
- School of Interdisciplinary Arts and Sciences, University of Washington–Bothell, Bothell, WA 98011-8246
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Beagley CT. Genome annotation in a community college cell biology lab. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:44-49. [PMID: 23382125 DOI: 10.1002/bmb.20669] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Indexed: 06/01/2023]
Abstract
The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning skills. Additionally, the project strengthens student understanding of the scientific method and contributes to student learning gains in curricular objectives centered around basic molecular biology, specifically, the Central Dogma. Importantly, inclusion of this project in the laboratory course provides students with a positive learning environment and allows for the use of cooperative learning strategies to increase overall student success.
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Affiliation(s)
- C Timothy Beagley
- Department of Biology, Salt Lake Community College, Salt Lake City, UT, USA.
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Brownell SE, Kloser MJ, Fukami T, Shavelson RJ. Context matters: volunteer bias, small sample size, and the value of comparison groups in the assessment of research-based undergraduate introductory biology lab courses. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2013; 14:176-82. [PMID: 24358380 PMCID: PMC3867754 DOI: 10.1128/jmbe.v14i2.609] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/06/2023]
Abstract
The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course.
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Affiliation(s)
- Sara E. Brownell
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
- Corresponding author. Mailing address: School of Life Sciences, PO Box 874501, Arizona State University, Tempe, AZ 85287-4501. Phone: 480-965-0803. Fax: 480-965-6899. E-mail:
| | - Matthew J. Kloser
- Institute for Educational Initiatives, University of Notre Dame, Notre Dame, IN 46556
| | - Tadashi Fukami
- Department of Biology, Stanford University, Stanford, CA 94305
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Brownell SE, Kloser MJ, Fukami T, Shavelson RJ. Context matters: volunteer bias, small sample size, and the value of comparison groups in the assessment of research-based undergraduate introductory biology lab courses. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2013. [PMID: 24358380 DOI: 10.1128/jmbe.v14i2.609barnes,] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The shift from cookbook to authentic research-based lab courses in undergraduate biology necessitates the need for evaluation and assessment of these novel courses. Although the biology education community has made progress in this area, it is important that we interpret the effectiveness of these courses with caution and remain mindful of inherent limitations to our study designs that may impact internal and external validity. The specific context of a research study can have a dramatic impact on the conclusions. We present a case study of our own three-year investigation of the impact of a research-based introductory lab course, highlighting how volunteer students, a lack of a comparison group, and small sample sizes can be limitations of a study design that can affect the interpretation of the effectiveness of a course.
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Affiliation(s)
- Sara E Brownell
- School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Matthew J Kloser
- Institute for Educational Initiatives, University of Notre Dame, Notre Dame, IN 46556
| | - Tadashi Fukami
- Department of Biology, Stanford University, Stanford, CA 94305
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Gasper BJ, Gardner SM. Engaging Students in Authentic Microbiology Research in an Introductory Biology Laboratory Course is Correlated with Gains in Student Understanding of the Nature of Authentic Research and Critical Thinking. JOURNAL OF MICROBIOLOGY & BIOLOGY EDUCATION 2013; 14:25-34. [PMID: 23858351 PMCID: PMC3706163 DOI: 10.1128/jmbe.v14i1.460] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
Recent recommendations for biology education highlight the role of authentic research experiences early in undergraduate education as a means of increasing the number and quality of biology majors. These experiences will inform students on the nature of science, increase their confidence in doing science, as well as foster critical thinking skills, an area that has been lacking despite it being one of the desired outcomes at undergraduate institutions and with future employers. With these things in mind, we have developed an introductory biology laboratory course where students design and execute an authentic microbiology research project. Students in this course are assimilated into the community of researchers by engaging in scholarly activities such as participating in inquiry, reading scientific literature, and communicating findings in written and oral formats. After three iterations of a semester-long laboratory course, we found that students who took the course showed a significant increase in their understanding of the nature of authentic research and their level of critical thinking skills.
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Affiliation(s)
- Brittany J. Gasper
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
- Department of Biology, Florida Southern College, Lakeland, FL 33801
| | - Stephanie M. Gardner
- Department of Biological Sciences, Purdue University, West Lafayette, IN 47907
- Corresponding author. Mailing address: Department of Biological Sciences, Purdue University, 915 West State Street, West Lafayette, IN 47907-2054. Phone: 765-496-2936. Fax: 765-494-0876. E-mail:
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Shapiro C, Ayon C, Moberg-Parker J, Levis-Fitzgerald M, Sanders ER. Strategies for using peer-assisted learning effectively in an undergraduate bioinformatics course. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION : A BIMONTHLY PUBLICATION OF THE INTERNATIONAL UNION OF BIOCHEMISTRY AND MOLECULAR BIOLOGY 2013; 41:24-33. [PMID: 23382123 DOI: 10.1002/bmb.20665] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Indexed: 05/14/2023]
Abstract
This study used a mixed methods approach to evaluate hybrid peer-assisted learning approaches incorporated into a bioinformatics tutorial for a genome annotation research project. Quantitative and qualitative data were collected from undergraduates who enrolled in a research-based laboratory course during two different academic terms at UCLA. Findings indicate that a critical feature of the peer-assisted learning approach is to have near-peer leaders with genome annotation experience, allowing them to communicate technical and conceptual aspects of the process in the context of a research project (a.k.a., the "big picture"). These characteristics are important for creating connections between the wet lab experiments and the computer lab activities, engendering excitement about the research project and fostering engagement in bioinformatics as a discipline. Likewise, it is essential to couple tutorial training in genome annotation with appropriate instructional materials, providing detailed, step-by-step instructions for database navigation. Finally, the assessment results support this hybrid peer-assisted learning approach as a model for undergraduates to successfully learn bioinformatics in a course setting.
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Affiliation(s)
- Casey Shapiro
- Center for Educational Assessment, Office of Instructional Development, University of California, Los Angeles, Los Angeles, CA 90095, USA
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Abstract
At the close of the Society for the Advancement of Biology Education Research conference in July 2012, one of the organizers made the comment: "Misconceptions are so yesterday." Within the community of learning sciences, misconceptions are yesterday's news, because the term has been aligned with eradication and/or replacement of conceptions, and our knowledge about how people learn has progressed past this idea. This essay provides an overview of the discussion within the learning sciences community surrounding the term "misconceptions" and how the education community's thinking has evolved with respect to students' conceptions. Using examples of students' incorrect ideas about evolution and ecology, we show that students' naïve ideas can provide the resources from which to build scientific understanding. We conclude by advocating that biology education researchers use one or more appropriate alternatives in place of the term misconception whenever possible.
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