Inquiry-Based Genomics Lab Module Collection

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Title of Abstract: Inquiry-Based Genomics Lab Module Collection

Name of Author: Lois Banta
Author Company or Institution: Williams College
Author Title: Associate Professor
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Cell Biology, Ecology and Environmental Biology, Evolutionary Biology, General Biology, Genetics, Integrative Biology, Microbiology, Neuroscience, Organismal Biology, Physiology & Anatomy, Plant Biology & Botany, Virology
Course Levels: Across the Curriculum, Faculty Development, Introductory Course(s), Upper Division Course(s)
Approaches: Material Development
Keywords: inquiry-based integrative genomics bioinformatics faculty-development

Name, Title, and Institution of Author(s): Erica J. Crespi, Vassar College Ross H. Nehm, Ohio State University Jodi A. Schwarz, Vassar College Susan Singer, Carleton College Cathryn A. Manduca, Carleton College Eliot C. Bush, Harvey Mudd College Elizabeth Collins, Vassar College Cara M. Constance, Hiram College Derek Dean, Williams College David Esteban, Vassar College Sean Fox, Carleton College John McDaris, Carleton College Carol Ann Paul, Wellesley College Ginny Quinan, Wellesley College Kathleen M. Raley-Susman, Vassar College Marc L. Smith, Vassar College Christopher S. Wallace, Whitman College Ginger S. Withers, Whitman College Lynn Caporale, Consultant

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The integration of genomic and bioinformatic approaches into undergraduate curricula represents one response to the national calls for biology teaching that is more quantitative and that promotes deeper understanding of biological systems through interdisciplinary analyses. Yet relatively few of the faculty members who teach undergraduate biology have expertise in the fields of genomics or bioinformatics. For these instructors, designing new teaching labs in a field that is developing so rapidly can feel particularly daunting. Our genomics education initiative was designed to address the challenges of helping faculty members integrate genome-scale science into the undergraduate classroom.

Describe the methods and strategies that you are using: The project utilized a grassroots model for faculty development, by supporting a national consortium of faculty members from eight liberal arts colleges in 1) learning about genomics and bioinformatics; 2) developing curriculum and laboratory teaching materials that stem from their own research and/or teaching interests, and that are informed by research in the learning sciences; and 3) devising tools to evaluate the efficacy of their genomics curricular innovations. Three workshops over three years supported these goals through a combination of learning from expertise within the participating group and from outside expertise on specific topics. The workshops brought together a total of 34 faculty participants from 19 institutions to develop a set of lab modules containing a substantial genomics component. Building on a proven faculty development model formulated by the geoscience education community, we complemented the multi-workshop program with a web-based interactive information portal. The initiative was structured such that the iterative interactions resulting from our three-workshop series would allow participants to share the experience of curriculum development, from the inception of an idea for a curricular module to the assessment of the implementation of that module, thereby generating a community of genomics educators among undergraduate institutions in the process. In addition, by bringing together educators from different institutions and scientific backgrounds, we aimed to stimulate discussion of interdisciplinary approaches to teaching genomics and facilitate the establishment of collaborations with other colleges and universities.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Products include peer-reviewed, guided inquiry-based, integrated instructional units (I3Us) adaptable to a range of teaching settings, with a focus on both model and non-model systems. Each curricular module is built on vetted design principles: (1) they have clear pedagogical objectives; (2) they are integrated with lessons taught in the lecture; (3) they are designed to integrate the learning of science content with learning about the process of science; and (4) they require student reflection and discussion (National Research Council, America’s Lab Report, Committee on High School Science Laboratories: Role and Vision; 2005). Each I3U was peer reviewed by fellow participants, as well as by a professional project consultant who has extensive experience with web-based description of teaching materials using this format to ensure that the I3U met the design criteria articulated above, and to evaluate whether the Activity Sheet provided both an easily accessible overview of the content and enough detailed information for other instructors to adapt and implement the material and its associated assessment strategies.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Eleven I3Us were designed and implemented as multi-week modules within the context of an existing biology course (e.g., Microbiology, Comparative Anatomy, Introduction to Neurobiology); an additional three I3Us were incorporated into interdisciplinary Biology/Computer Science classes. Although these I3Us were designed for courses currently taught by the project participant within the specific institution’s curriculum, we propose that they can be inserted into other courses that encompass similar content and/or learning goals. We have received numerous communications from colleagues at other institutions who have adapted our I3Us for their courses.

Describe any unexpected challenges you encountered and your methods for dealing with them: Many participants lacked expertise needed to analyze sequence data or design wet labs and were overwhelmed by the array of possible tools, deciding which tools were useful in which scientific contexts, and the challenges of mastering their user interfaces. Some were concerned about teaching material with which they had little previous scientific experience. Most were isolated from colleagues who shared their interest or had the needed expertise to support their initial learning in this area. We provided hands-on training in three intensive days of short workshops, enabling participants to become familiar with bioinformatic tools for finding sequences, predicting the structure of proteins, visualizing and comparing genomes, and constructing phylogenetic trees. Participants who needed significantly more time to explore the tools and develop self-sufficiency maintained communication with at least one of the presenters over the course of the year, to obtain more training and to get ideas. For many, adapting bioinformatics tools into their modules was more easily accomplished by asking phylogenetic questions rather than adapting tools that could be used to explore genome-level questions of gene function or structure. The greatest challenge was that no robust assessment system, characterized by valid and reliable instruments evaluated by experts in education and psychometrics, existed to assess the efficacy of newly developed genomics and bioinformatics curricula. To help faculty build assessment tools, we provided: (1) A professional development session for faculty participants that reviewed the basics of educational assessment and the types of tools that could be employed in assessment efforts; (2) Individualized consultations to help participants build their assessments; and (3) Individualized consultations with faculty to assist in the interpretation of assessment data derived from point (2) above.

Describe your completed dissemination activities and your plans for continuing dissemination: All modules, together with extensive supporting material, are accessible on a dedicated website (https://serc.carleton.edu/genomics/activities.html) that also provides links to bioinformatics tools and on-line assessment and pedagogical resources, as well as all presentations from all three workshops, pre- and post-workshop content, and suggested readings provided by workshop leaders. The project website serves as a portal to Activity Sheets describing each I3U; these Activity Sheets include learning goals, teaching tips, and links to teaching materials, as well as downloadable assessment tools, that can be customized by any interested educator. Information about the collection of I3Us has been disseminated via publication.

Acknowledgements: This information has been published previously (Cell Biology Education-Life Science Education 11:203-208; 2012). The project was funded by the Teagle Foundation, with supplemental support from Williams College, Vassar College, and Schering-Plough.

Integrating Statistics into the Life Sciences Curriculum

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Title of Abstract: Integrating Statistics into the Life Sciences Curriculum

Name of Author: Edward Bartlett
Author Company or Institution: Purdue University
Author Title: Associate Professor
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Cell Biology, Ecology and Environmental Biology, Evolutionary Biology, General Biology, Integrative Biology, Microbiology, Neuroscience, Organismal Biology, Physiology & Anatomy, Virology
Course Levels: Across the Curriculum, Faculty Development, Introductory Course(s), Upper Division Course(s)
Approaches: Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: undergraduate research, modules, faculty learning community, secondary school teachers.

Name, Title, and Institution of Author(s): James Forney, Purdue University-West Lafayette Ann Rundell, Purdue University-West Lafayette Kari Clase, Purdue University-West Lafayette Stephanie Gardner, Purdue University-West Lafayette Omolola Adedokun, Purdue University-West Lafayette Dennis Minchella, Purdue University-West Lafayette

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Our program has 4 components: 1) Summer undergraduate research program 2) Faculty learning community 3) Curriculum development 4) Secondary school teacher development and research. The objective of our HHMI-funded summer research program is to bring together faculty and undergraduate students from an array of academic institutions and disciplines to provide a facilitated ‘hands-on’ experience focusing on experiment design and statistical analysis within the context of life science-related research projects. The objectives of the faculty learning community are twofold. First, it brings together interested faculty, graduate students and postdocs to discuss advances, innovations, and best practices in teaching and curriculum. Second, it facilitates the design of course modules that will be used for curricular development. The objective of the Curriculum Development component is to introduce experimental design, statistical and quantitative analysis, and critical evaluation of data throughout the life science curriculum through “plug and play” modules that are incorporated into existing courses. The objective of the teacher-scientist component is to provide secondary school teachers with research experiences as well as to provide training and ideas for incorporating statistical and data analysis into their life science courses.

Describe the methods and strategies that you are using: Eighteen undergraduate students (Purdue University WL, Purdue Calumet, Purdue University North Central, Indiana University-Purdue University Fort Wayne, Franklin College, Morehouse College, and Saint Mary’s College) were hosted within 18 different research laboratories on the West Lafayette Purdue University campus for an 8 week long research experience in 2011-2013. Our second Faculty Learning Community (FLC) began in September of 2011 with twelve members drawn from the departments of Statistics, Biological Sciences, Biochemistry, Biomedical Engineering, Industrial Technology, Horticulture, and Forestry. The group contained two postdoctoral researchers, seven tenure track faculty and two staff members (one from the Purdue Center for Instructional Excellence). Roughly half of the meetings were focused on statistics/learning module development and the other half on student learning (e.g. active learning, student development, learning and memory). During 2012, six new modules have been completed, bringing the total number of available modules to twelve. An additional five are being developed by the most recent cohort of FLC members (2013). Modules now cover a broad swath of the life sciences at Purdue, such as new modules in Forestry and in Speech, Language and Hearing Science. The new modules have covered statistical concepts such as the chi-squared test and Bayesian statistics and techniques in data analysis using confocal images of plant samples collected by the students. used STEMEdHub (https://stemedhub.org/groups/hhmibio). These are publicly available, and users may download the modules and provide feedback on them. In April 2012 the four teacher-scientists from the Summer Institute in 2011, presented a workshop at the Annual Meeting for the National Science Teachers Association in Indianapolis, IN, to approximately 30 teachers. The materials are available at: (https://www.nsta.org/conferences/schedule.aspx?id=2012ind).

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: For the summer research program, assessments were a combination of assessments of competency, such as portions of Garfield's Statistical Reasoning Assessments, as well as interviews. Assessment of the faculty learning community was mainly via interviews with participants. Assessments for curriculum development have largely been based on the individual modules themselves, taking the form of a written report by the students, a poster presentation, or exam questions for example. Assessments of the teacher-scientist program were mainly using interviews.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Summer research has resulted in at least 2 journal publications with students as co-authors. Students rated the summer research very highly, including the quantitative training sessions during each week as a group, as well as the students' interactions with their mentors. Over 12 faculty members, 4 postdocs, and 2 graduate students have participated as learning community members. They have rated the interactions within the community quite highly, and their participation has resulted in the bulk of the available modules. The 'plug and play' modules have been incorporated into many of the introductory and intermediate level courses in Biology, Biochemistry, and Biomedical Engineering. In addition, the modules are publicly available through a hosted site at Purdue. Over 6 teacher-scientists have been trained and have acted as role models within the community, holding larger outreach events.

Describe any unexpected challenges you encountered and your methods for dealing with them: For the summer research program, things we will improve for will be to continue to transform the quantitative training sessions towards effective problem based learning and to reinforce the link between the statistical analysis and the student research experience. For the faculty learning community, finding enough interested postdocs and willing advisors was difficult. We then permitted graduate students to join the faculty learning community, and they have been equally helpful in facilitating discussions of teaching and development of modules. For curriculum development, now that a large number of modules have been initially created and implemented in classes, but more or less piecemeal, it is important to make the modules more seamlessly integrated throughout the life sciences curricula. To do this, we have engaged new faculty of introductory courses and permitted them to attend a teaching workshop (SI Institute) as well as gathered syllabi to find common topics taught across courses. Following two summers of teacher-scientist training, the evaluation team recommended that the ?teachers receive focused training/instruction in very basic statistics?data representation, probability, etc from a plain spoken source. This instruction should be combined with pedagogical sessions wherein teachers brainstorm or work with each other to translate basic statistical concepts into classroom activities in life science contexts.? In order to address this recommendation the summer institute was revised to include two master math teachers that could provide: exemplar lessons from their classrooms, resources that would be appropriate to use with students, advice and insight during data analysis discussions and planning sessions for translating workshop topics into the classroom.

Describe your completed dissemination activities and your plans for continuing dissemination: Dissemination of summer student research has taken the forms of journal articles and posters at national meetings. Dissemination of the modules developed by faculty learning community members has taken the form of links to a website through Purdue's STEMEdHUB: STEMEdHub (https://stemedhub.org/groups/hhmibio/). Dissemination of findings and discussions of teachers is available at: https://hhmipurdue.wikispaces.com/ In addition, the first year research course has resulted in journal articles on the course design of such a course. Future dissemination will focus on publishing results from the various components of the program separately in journals, as well as a publication describing the overall program and its results and impact.

Acknowledgements: The authors gratefully acknowledge the Howard Hughes Medical Institute for providing funds for this project.

Learning Gains from Guided-Inquiry Labs with Bean Beetles

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Title of Abstract: Learning Gains from Guided-Inquiry Labs with Bean Beetles

Name of Author: Lawrence Blumer
Author Company or Institution: Morehouse College
Author Title: Professor
PULSE Fellow: No
Applicable Courses: Ecology and Environmental Biology, Evolutionary Biology, Genetics, Neuroscience, Organismal Biology, Physiology & Anatomy
Course Levels: Faculty Development, Introductory Course(s), Upper Division Course(s)
Approaches: Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: guided inquiry, assessment, bean beetles, Callosobruchus, faculty development

Name, Title, and Institution of Author(s): Christopher W. Beck, Emory University

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The aims of this project were increasing the use of guided-inquiry in undergraduate laboratory courses and to foster the development of new guided inquiry experiments with the bean beetle, Callosobruchus maculatus, model system in physiology, neurobiology, genetics, molecular biology, and developmental biology. Guided-inquiry is a student-centered inquiry method that aligns with the Vision and Change report recommendation that students learn science by doing science.

Describe the methods and strategies that you are using: We conducted four annual faculty development workshops that were attended by a total of 81 faculty from 40 different institutions. Participants were selected to represent a diversity of institution types including 12 minority-serving institutions (24 participants) and eight community colleges (16 participants). Participants, in teams of two from each institution, learned how to work with bean beetles, how guided-inquiry learning may be conducted, and developed a new laboratory activity with bean beetles that they class tested at their own institution.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: We conducted an Instructional Practices assessment on our workshop faculty participants both prior to our workshop and after implementing their new guided-inquiry laboratory activity. Students in the classes in which a new laboratory activity was implemented also were surveyed on their perceptions of their faculty Instructional Practices. These assessments were conducted to determine whether our workshops changed faculty instructional practices. Furthermore, students were assessed in a pre-test, post-test format on their confidence to conduct scientific research, their knowledge of the nature of science, and their problem solving skills. These student assessments were conducted to determine the effectiveness of guided-inquiry learning.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: In the first three years of the project, approximately 481 students at 11 institutions were directly affected. They conducted guided-inquiry bean beetle experiments in 37 different courses. The faculty development workshops we conducted were successful in changing teaching practices and those changes were reflected in student perceptions of how they were taught. Students participating in guided-inquiry activities experienced significant gains in confidence to conduct scientific research and these gains were greatest among students whose pre-test confidence was in the lowest quartile. Similarly, the greatest gains in knowledge of the nature of science and problem solving skills were among those students in the lowest pre-test quartiles. These findings indicate that guided inquiry laboratories provide the greatest benefits for students whose needs are the greatest. Our findings provide strong support for the transformation of undergraduate laboratory instructional methods recommended in the Vision and Change report.

Describe any unexpected challenges you encountered and your methods for dealing with them: Not all the faculty who attended our workshops successfully completed their development of a new laboratory activity. This challenge was not entirely unexpected and we withheld two-thirds of their stipend as an incentive for them to complete their work. This incentive was sufficient for the majority of our workshop participants.

Describe your completed dissemination activities and your plans for continuing dissemination: The new guided-inquiry laboratory activities that our workshop participants developed are being posted on the bean beetle website, www.beanbeetles.org. The open access content for these laboratory activities consists of a student handout, instructor notes, sample data, and image and data slides. This website will be maintained for a minimum of 10 years after the end of this project. We continue to collect data from faculty teams that are in the process of completing their work. The results of the Instructional Practices surveys of faculty and students, and the student pre-test, post-test student assessments of confidence to conduct scientific research, knowledge of the nature of science, and problem solving skills will be prepared as manuscripts for publication in peer reviewed journals.

Acknowledgements: We thank Dr. Tom McKlin of the Findings Group for his external evaluation of our project. We also thank the faculty and students of the participating colleges and universities. This project was supported by the National Science Foundation DUE-0815135 and DUE-0814373.