Bacterial Diversity Studies Using the 16S rRNA Gene Provide a Powerful Research-Based Curriculum for Molecular Biology Laboratory

Boomer, Sarah M.; Lodge, Daniel P.; Dutton, Bryan E.

doi:10.1128/jmbe.v3.66

Cited by 10 publications

(12 citation statements)

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“…In addition to engaging students in their own learning, educators need to activate the sense of inquiry that drives scientists by facilitating original undergraduate research in and out of the classroom (17). Several recent publications describe increased learning, critical thinking skills, interest, and enthusiasm when original research and/or inquiry-based activities were incorporated into the undergraduate biology classroom (1,2,10,20).…”

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confidence: 99%

“…Several institutions have established genomics education modules and courses to teach undergraduates about highthroughput data-rich fi elds that integrate informatics with biology (3,9,18,19). There are impressive examples in the literature of modules and courses that integrate online data and web-based bioinformatic tools; original sequencing or functional genomics projects with the fl y, HIV mutant bioinformatics, phylogenetic analysis with 16S rRNA sequences, and comparative genomic exercises (1,4,6,12,30,32). Brad Goodner at Hiram College has made exceptional strides in integrating microbial genomics in undergraduate research and education by incorporating whole genome sequencing, comparative analysis, functional genomics, and annotation in undergraduate courses (13,15).…”

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confidence: 99%

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Whole Genome Sequencing in the Undergraduate Classroom: Outcomes and Lessons from a Pilot Course

Drew

Triplett

2008

J Microbiol Biol Educ.

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The BIO2010 report challenged undergraduate institutions to prepare the next generation of researchers for the changing direction of biology that increasingly integrates advanced technologies, digital information, and large-scale analyses. In response, the Microbiology and Cell Science Department at the University of Florida developed a research-based course, "Bacterial Genome Sequencing." The objectives were to teach undergraduates about genomics and original research by sequencing a bacterial genome, to develop scientifi c communication skills by writing and submitting the project results as a class effort, and to promote an interest in biological research, particularly genomics. The students worked together to sequence, assemble, and annotate the Enterobacter cloacae P101 genome. We assessed student learning, scientifi c communication skills, and student attitudes by a variety of methods including exams, writing assignments, oral presentations, pre-and postcourse surveys, and a fi nal exit survey. Assessment results demonstrate student learning gains and positive attitudes regarding the course.

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confidence: 99%

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Whole Genome Sequencing in the Undergraduate Classroom: Outcomes and Lessons from a Pilot Course

Drew

Triplett

2008

J Microbiol Biol Educ.

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“…Inquiry‐based courses have been designed that enable students to obtain a short research experience while learning laboratory techniques and pursuing open‐ended research questions. For example, Boomer et al [9, 10] developed a laboratory course in which students use 16S rRNA sequencing to characterize novel bacteria isolated from hot springs at Yellowstone National Park. Other approaches have ranged from reserving several laboratory periods for student‐designed experiments [11–14] to challenging students to implement their own semester‐long research projects [15–17].…”

Section: Facilitating Undergraduate Research Productivitymentioning

confidence: 99%

Outcomes of a research‐driven laboratory and literature course designed to enhance undergraduate contributions to original research

Rasche

2004

Biochem Molecular Bio Educ

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This work describes outcomes of a research-driven advanced microbiology laboratory and literature research course intended to enhance undergraduate preparation for and contributions to original research. The laboratory section was designed to teach fundamental biochemistry and molecular biology techniques in the context of an original research project. Site-directed mutants of a gene of interest were constructed, and the effects of mutations on the resulting enzymes were analyzed. Students were also introduced to the literature surrounding their project, electronic literature databases, and preparation of computer-generated slides for oral presentations. Student progress was evaluated through a laboratory report written as scientific manuscript, an oral presentation, a 10-page written review, and an essay examination. In the semester following the laboratory course, four of the 14 undergraduates joined the host laboratory to continue their projects as individual undergraduate researchers. Quantifiable outcomes of the course and subsequent undergraduate research included i) production of eight new site-directed mutants and preliminary characterization of the corresponding enzymes, ii) training of four individual undergraduate researchers prior to joining the laboratory, iii) publication of a manuscript with results from two undergraduate researchers, and iv) presentation of two posters with undergraduate co-authors at a national meeting. This research-driven approach may be applicable to enhance undergraduate contributions to other original research projects that have defined goals achievable within the timeframe of a single semester.Keywords: Microbiology, laboratory course, undergraduate research. FACILITATING UNDERGRADUATE RESEARCH PRODUCTIVITYActive participation in undergraduate research plays a valuable role in enhancing the educational experience of undergraduate science majors. In addition to providing training in practical laboratory techniques, undergraduate research can facilitate the development of higher thinking skills, expose students to the excitement of scientific discovery, and contribute to preparation for careers in scientific research [1][2][3][4]. Indeed, increased participation in discovery-driven research and literature colloquia comprise two of the specific recommendations made by the National Research Council to improve undergraduate training for future biological research scientists [5]. In addition, undergraduate research is strongly recommended as part of the core curriculum for a biochemistry and molecular biology major [6].Faculty at primarily undergraduate institutions and early career faculty have been noted as individuals with strong potential to provide research opportunities for undergraduates [5]. However, in these laboratories, conscientious promotion of undergraduate research can require considerable commitments of time, energy, and dedication, particularly if graduate students and postdoctoral associates are unavailable to assist in the mentoring process [7,8]. Because acqu...

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“…Students analyzed their own samples, gained molecular experience in the laboratory, and were instructed on computational tools to analyze the data. Similar to other microbiology modules described recently (27)(28)(29)(30)(31)(32)(33)(34)(35)(36)38), a goal of Fiber Force was for students to develop critical reasoning and problem-solving skills related to microbiology and microbiome research.…”

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confidence: 99%

Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course

Sewall

Oliver

Denaro

et al. 2020

J Microbiol Biol Educ.

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Course-based undergraduate research experiences (CUREs) are an effective way to introduce students to contemporary scientific research. Research experiences have been shown to promote critical thinking, improve understanding and proper use of the scientific method, and help students learn practical skills including writing and oral communication. We aimed to improve scientific training by engaging students enrolled in an upper division elective course in a human microbiome CURE. The "Fiber Force" course is aimed at studying the effect of a wholesome high-fiber diet (40 to 50 g/day for two weeks) on the students' gut microbiomes. Enrolled students participated in a noninvasive diet intervention, designed health surveys, tested hypotheses on the effect of a diet intervention on the gut microbiome, and analyzed their own samples (as anonymized aggregates). The course involved learning laboratory techniques (e.g., DNA extraction, PCR, and 16S sequencing) and the incorporation of computational techniques to analyze microbiome data with QIIME2 and within the R software environment. In addition, the learning objectives focused on effective student performance in writing, data analysis, and oral communication. Enrolled students showed high performance grades on writing, data analysis and oral communication assignments. Pre-and post-course surveys indicate that the students found the experience favorable, increased their interest in science, and heightened awareness of their diet habits. Fiber Force constitutes a validated case of a research experience on microbiology with the capacity to improve research training and promote healthy dietary habits.

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Bacterial Diversity Studies Using the 16S rRNA Gene Provide a Powerful Research-Based Curriculum for Molecular Biology Laboratory

Cited by 10 publications

References 0 publications

Whole Genome Sequencing in the Undergraduate Classroom: Outcomes and Lessons from a Pilot Course

Whole Genome Sequencing in the Undergraduate Classroom: Outcomes and Lessons from a Pilot Course

Outcomes of a research‐driven laboratory and literature course designed to enhance undergraduate contributions to original research

Fiber Force: A Fiber Diet Intervention in an Advanced Course-Based Undergraduate Research Experience (CURE) Course

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