Microbes, Metagenomes and Marine Mammals: Enabling the Next

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Title of Abstract: Microbes, Metagenomes and Marine Mammals: Enabling the Next

Name of Author: elizabeth dinsdale
Author Company or Institution: San Diego State University
Author Title: Dr
PULSE Fellow: No
Applicable Courses: Bioinformatics, Microbiology, Virology
Course Levels: Upper Division Course(s)
Approaches: Mixed Approach
Keywords: DNA sequencing, practical research experience

Name, Title, and Institution of Author(s): Robert A. Edwards, San Diego State University Meredith Houle Vaughn, San Diego State University

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The revolution in DNA sequencing technology continues unabated, and is impacting all aspects of the biological and medical sciences. The training and recruitment of the next generation of researchers who are able to use and exploit the new technology is severely lacking and potentially negatively impacting research and development efforts to advance genomics. Here we present a cross-disciplinary course which has three goals: 1) Inspiring student learning by allowing students to use the latest technology and generate new data; 2) Engaging students by integrating teaching and research; 3) Enabling students to integrate genomics in areas of biology and ecology. Many labs across world are installing next generation sequencing technology and we show that the undergraduate students produce quality sequence data and were excited to participate in cutting edge research.

Describe the methods and strategies that you are using: A practical course in DNA sequencing and annotating novel genomes from start to finish with a next-generation sequencer was offered to upper division undergraduates and graduate students as a lecture and laboratory course and was open to students across biology and computer sciences.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: The first evaluation of the course was to assess the quality of the DNA sequencing data that the students produced. They sequenced 40 microbes, 60 metagenomes, and a marine mammal, the Californian sea lion, Zalophus californianus. The students met sequencing quality controls, had no detectable contamination in the targeted DNA sequences, provided publication quality data, and became part of an international collaboration to investigate carcinomas in carnivores. Evaluation of the course where conducted using pre and post formative and summative tests that assess student learning, in scientific conduct, genomic analysis, biology and computer science. Overall, the students perceived ability to conduct scientific research increased from 3.3 to 3.8 (t = -6.08; p = 0.001). The students show an increased confidence in conducting projects where 1) no one knows the outcome, 2) they have input into the process, 3) they need to work as a whole class and 4) they have responsibility for part of the process. The students increased in their ability to interpret primary literature, present data and keep a lab book. Skills required in becoming a successful scientist. In addition, students’ overall self-confidence in their ability to conduct genomic sequencing and analysis increased from 3.0 to 3.9 (t = -3.21; p = 0.01). All students would recommend the course to other students and had extremely positive comments about the course, and recognized that it would provide benefits for their future careers.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Outputs to date include involving 130 students in research, 5 publications, 33 student presentation, and 5 papers in review all of which include student co-authors. We have been involved in four education forums, 1) CSUPERB genomic education workshop, 2) HHMI Bioinformatics workshop, 3) RABLE San Diego meeting to help develop laboratory training and 4) NSF TUES- Course Curriculum, Laboratory Improvement Conference. Developing and teaching this course have trained undergraduate students the newest technology, developed their scientific processing skills, helped many students obtain employment, and developed sequencing capabilities in Brazil and Chile.

Describe any unexpected challenges you encountered and your methods for dealing with them: Logistics to conduct the hands-on sequencing course was difficult because there is a high potential for contamination of the environmental DNA with the linker DNA, following the samples through the process and manipulation of large datasets. These logistical problems were overcome by teaching the course across multiple rooms and in a rotation fashion, so that every student gets to complete all the processes. Last a web site was set up to follow the samples and manipulate the data.

Describe your completed dissemination activities and your plans for continuing dissemination: The course is in its fourth year and other Faculty are providing samples and support to run the course. The Faculty receives publication quality data and the students get the practice at sequencing and annotation. Teaching undergraduates to use the latest technology to sequence genomic DNA ensures they are ready to meet the challenges of the genomic era and allows them to participate in annotating the tree of life. We are helping other universities set up similar courses and have visited Earlham College and the University of Puerto Rico. We are developing a faculty workshop to enable faculty to conduct and teach next generation sequencing and annotation.

Acknowledgements: We acknowledge Roche 454 Lifesciences for providing the backing to conduct the course. The course and EAD was supported by a NSF for Transforming Undergraduate Education in Science: 1044453 from the Division of Undergraduate Training grant. RAE is supported by NSF grants DBI: 0850356 from the Division of Biological Infrastructure and DEB: 1046413 from the Division of Environmental Biology.

Assessing a Year-Long, Research Lab in a Core Biology Course

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Title of Abstract: Assessing a Year-Long, Research Lab in a Core Biology Course

Name of Author: Marcy Kelly
Author Company or Institution: Pace University
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Cell Biology, Genetics
Course Levels: Introductory Course(s), Upper Division Course(s)
Approaches: Material Development, Research projects in the teaching laboratory
Keywords: microarray, nextgen RNA sequencing, year-long core biology course, novel research

Name, Title, and Institution of Author(s): David S. Zuzga, LaSalle University

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: It is anticipated that enrollment in this year-long laboratory program will yield the following outcomes for the students: 1. Develop a strong foundation in the following core concepts associated with biological literacy: (a) Structure and function at the cellular and molecular level; (b) Information flow, exchange and storage through genes and proteins; (c) Pathways and transformations of energy and matter involved in cellular communication and responses to the environment 2. Become proficient in the following biological core competencies and disciplinary practices: (a) Realize the steps involved in the process of science including the examination and critique of scientific literature, hypothesis generation, experimental design, data interpretation, trouble-shooting and experimental revision and, the generation of biologically relevant datasets; (b) Development of quantitative reasoning skills to interrogate large datasets; (c) Appreciate the interdisciplinary nature of science by navigating biological data repositories and Bioinformatics to obtain information pertaining to specific genes and gene families; (d) Communicate and collaborate with other scientists in graphic form, written form, and verbally.

Describe the methods and strategies that you are using: The year-long program is completed by all biology majors and is spread over two courses: Genetics (BIO231) and Introduction to Cellular and Molecular Biology (BIO335). During the first semester (BIO231), students examine global changes in gene expression in response to osmotic stress in S. cerevisiae. Students perform an osmotic stress experiment, isolate RNA and prepare samples for analysis by either microarray or nextgen RNA sequencing, apply bioinformatics to examine differential expression in a large data set, and, importantly, interrogate the dataset with Gene Ontology tools to identify candidate genes not previously described as functional regulators of the osmotic stress response. Linking the two semesters, students write proposals for conducting functional studies of candidate genes and engage in peer review sessions to rank proposals and select candidate genes for investigation in the subsequent semester. In BIO335, students develop a cloning strategy for a selected candidate gene and design experiments to characterize the function of the gene products in osmotic stress. Thus, students are provided with an authentic research experience and the opportunity to identify novel roles for genes in the stress response.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: The two outcomes for the year-long laboratory course can be simplified for the means of describing the assessment plan. The first outcome, develop a strong foundation in the core concepts associated with biological literacy, focuses on the acquisition of biological content knowledge by the students participating in the year-long laboratory program. The second outcome, become proficient in biological core competencies and disciplinary practices, focuses on the enhancement of the critical thinking skills of the students participating in the year-long laboratory program. Several quantitative and qualitative assessment tools will be utilized to assess whether or not the students participating in the year-long laboratory program made gains in biological content knowledge and critical thinking skills: (a) Writing assignments required for the BIO231 and BIO335 laboratory courses; (b) Pre- and post- program open ended questions; (c) BIO231 and BIO335 final course grades; (d) Performance on the Department of Biology and Health Sciences-NYC major assessment exam; (e) Participation in the Classroom Undergraduate Research Experience (CURE) survey.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: The implementation of the laboratory program has yielded significant impacts at the student, faculty, and institutional level. Student Impact: The year-long lab course is integrated into core courses, ensuring that all biology majors will obtain authentic research experiences. At Pace, these courses have an enrollment of approximately 60-80 students per year. It is anticipated that participation in the lab program will enhance students’ potential to conduct scientific research. Projects initiated during the year-long laboratory program may be pursued in faculty mentored, independent research courses. Indeed, four students are continuing their investigations. Faculty and Institutional Impact: A Phase I TUES grant from the NSF was recently awarded to support the expansion of the program to peer institutions. Two participating faculty members (from Pace and La Salle University) recently attended an NSF and HHMI funded GCAT-SEEK workshop to develop RNA sequencing laboratory protocols to broaden the methodological framework of the program. Indeed, the laboratory program itself is modular and scalar - the framework of the program, generation and analysis of a transcriptome database, selection of candidate genes, cloning, and design of an experiment to test the functional role of the candidate gene can be readily adopted by Biology Departments at other institutions. The core courses in which the proposed laboratory program are integrated are ubiquitous offerings in the undergraduate setting, negating the need for partner institutions to develop courses de novo. Moreover, the program can also accommodate a breadth of faculty research questions, providing the opportunity for faculty to integrate their own research into the lab program, thus leveraging faculty expertise in the course. Indeed, the program will be adopted at La Salle University and further efforts will be made to recruit partner institutes in anticipation of a Phase II TUES proposal.

Describe any unexpected challenges you encountered and your methods for dealing with them: Hurricane Sandy struck the New York City metropolitan area in October 2012. The students enrolled in the BIO231 course at that time had isolated their RNA and were getting ready to send it out for analysis. Unfortunately, due to power loss from the storm, all of the student RNA samples were lost. The students were provided with the data sets obtained by the students enrolled in BIO231 the year before. This enabled us to continue with the work as planned without any interruption to our schedule. As we continue to implement this program, the datasets we employ will become increasingly robust and can be interrogated by the students in the advent of challenges - whether they are experimental or otherwise.

Describe your completed dissemination activities and your plans for continuing dissemination: To reach as broad and audience as possible, the program outline and accompanying assessment data will be presented at the major annual meetings of faculty associated with this program and reported in journals with a pedagogical foci. Furthermore, faculty involved in this program have diverse research interests which allows for the program to be introduced at major meetings for societies that include pedagogical sessions. These include the annual meetings of the, the American Society of Microbiology (ASM) and the American Association for Cancer Research. Finally, assessment data and the program structure will be disseminated among faculty with interests in novel pedagogical ideas via ASM’s Biology Scholars Program Listserv and GCAT SEEK’s Listserv. In each of these venues, emphasis will be placed upon 1) the success of the program in enhancing student learning and 2) the adaptability of this program by any institution.

Acknowledgements: We would like to thank and acknowledge GCAT-SEEK for the nextgen sequencing training and analyses and Dr. David Lopatto for allowing us to participate in the CURE survey (https://www.grinnell.edu/academic/csla/assessment/cure). MPK would like to acknowledge the American Society of Microbiology’s Biology Scholars Program (NSF Award # 0715777) for helping her develop the research ideas for this assessment study. Support for the development and assessment of this year long laboratory program is from an NSF Type 1 TUES grant to MPK (NSF Award # 1246000).

Research Projects in Biochemistry and Molecular Biology

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Title of Abstract: Research Projects in Biochemistry and Molecular Biology

Name of Author: Emina Stojkovic
Author Company or Institution: Northeastern Illinois University
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Biophysics
Course Levels: Upper Division Course(s)
Approaches: Assessment, Material Development
Keywords: Biochemistry, Molecular Biology, Research, Peer-led Team Learning,

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The overall goal is to develop confident and collaborative scientists comfortable with the conduct of authentic research including data analysis and discussion of conclusions and future directions. Intended outcomes of this project are student-centered and listed below: a) Functioning as a member of a team, the student will design and present experimental procedure to address a scientific question. b) The student will be able to apply the principles underpinning protein structure and function to illustrate data analysis and conclusions through computer-based presentation.

Describe the methods and strategies that you are using: The methods used are based on the semester-long research projects integrating regular course curriculum with weekly laboratory exercises in upper-level Biochemistry and Molecular Biology. Lecture material and laboratory exercises are not independent of each other and regular student attendance and participation is important for student success. Weekly laboratories are developed to specifically encourage team learning through experimental design. Students appreciate potential impact of their research through dissemination at undergraduate research symposia and publications in appropriate journals. In Biochemistry, students complete experiments involving protein expression and purification, analysis of purified protein using SDS-PAGE, UV-vis absorption spectroscopy, protein crystallization, and X-ray diffraction experiments. In Molecular Biology, students focus on site-directed mutagenesis including design of primers for PCR reactions that would introduce single amino acid mutations in the protein of interest. They complete PCR reactions, select for possible mutants, submit DNA samples for sequencing, and analyze and interpret DNA sequencing chromatograms. To support student learning and success, we use Peer-Led Team Learning (PLTL) as a method of integrating student-centered learning through power of peer-group communication.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: The evaluation is based on the assessment data collected through a questionnaire administered to students at the beginning and at the end of each semester. In addition, students are required to fill out course evaluation form that involves essay-based questions involving curriculum design and research. Example of assessment: On scale 1-5 (with 1-strongly disagree and 5-strongly agree) students’ average response is 4.5 to following statements: I. Laboratory exercises helped me learn and understand the basic experimental techniques used in protein biochemistry. II. Overall, I think that experiments conducted in BIO-362 laboratory setting were a positive learning experience.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Students have been able to reference research experiences from Biochemistry and Molecular Biology courses during their job and/or graduate school interviews. This is in particular helpful to students who have not been able to get a summer research internship during their undergraduate education. My colleagues, encouraged by positive comments that I have received from students, are starting to incorporate smaller research projects (4-6 weeks) in their courses. In particular, we started to incorporate smaller research projects in our General Biology Courses for majors.

Describe any unexpected challenges you encountered and your methods for dealing with them: Students show resistance to reading primary literature relevant to their research project in the lab. To solve this problem, I assigned research articles at the beginning of the semester and asked students to work in pairs. We would finish the semester with student presentations where each pair of students would present their assigned research article to other students in the class.

Describe your completed dissemination activities and your plans for continuing dissemination: Students are encouraged to present their research projects at Northeastern Illinois Annual Undergraduate Research Symposium. In addition, students want to continue being involved in research once the semester is over. Depending on their availability, students are asked to develop future directions and/or continue data analysis. Several of them are asked to come back as Peer Leaders the following academic year. We are also finalizing a manuscript for Education Journal where we plan to report on methodologies used to ensure success of research projects and their design in upper level Biochemistry. Manuscript was prepared and written by students who took the course in the past.

Acknowledgements: I would like to thank my colleagues and my department chair, Dr. John Kasmer, for continued support and constructive feedback in developing research-based curriculum.

Preparing the next Generation of Bioengineers

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Title of Abstract: Preparing the next Generation of Bioengineers

Name of Author: Rebecca Reiss
Author Company or Institution: New Mexico Tech
Author Title: Associate Professor
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Cell Biology, General Biology, Genetics
Course Levels: Introductory Course(s)
Approaches: Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: Bioinformatics, Bioengineering, Nanotechnology, Biomaterials,

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: “How do we prepare students for careers that don’t yet exist?” This perplexing question was posed at the 2009 Vision and Change Conference. Bioengineering is a rapidly evolving discipline that has captured the interest many of our engineering students, who are searching for ways to apply engineering skills and concepts to medical and environmental issues. This requires a multidisciplinary approach to problem solving, but the ‘after Google’ generation has access to an exponentially increasing amount of information that can facilitate this type of critical thinking. But the Internet is a double-edged sword, since the availability of so much information can contribute to a common attitude among students: “I can look up anything, why do I need to learn this material?” This project is focused on the first undergraduate general biology course, Biology (Biol) 111, which serves both majors and non-majors. Recent changes in engineering requirements encourage engineering students to take Biol 111, which is now included in assessment protocols for engineering accreditation. Since students envision careers in bioengineering, our focus is to change Biol 111 with the goal to make the course relevant to engineering majors while continuing to address the needs of biology majors. The outcomes of this project include an increased understanding of both students and faculty of the rapidly changing interface between biology and engineering, and preparing students for upper division biology courses that include increased exposure to research projects.

Describe the methods and strategies that you are using: The strategy involves the identification of research projects on campus that require engineering and biology expertise, then preparing activities that include information on these projects. Discussions with faculty involved in the development of a Bioengineering program revealed numerous topics that can be emphasized in Biol 111. These efforts began with the Spring 2013 course by merging descriptions of biological macromolecules with the perspective of biomaterials engineers. To a biologist a liposome is a self-assembling bilayer of phospholipid molecules, but to a bioengineer, the same structure is a nanoparticle. A faculty member in Chemical Engineering is working on targeting methods for drug delivery, so the topic has relevance to pre-medical students. This lesson is intended to interface with the Cell Biology course. For students who lean toward environmental issues, the results of a high-throughput DNA sequencing project focused on a microbial community capable of remediating toxic volatile organic carbon compounds provides an example of the application of bioinformatics to an environmental engineering problem. This was used to introduce lessons on information flow in cells and on bioinformatics. Efforts to change Biol 111 are linked to efforts to establish a minor in Biomaterials Engineering as well as a larger, inter-disciplinary Bioengineering program.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Students taking Biol 111 in the Spring 2013 semester were asked to complete Student Assessment of Learning Gains (SALG) surveys three times during the course of the semester that included questions about their attitudes towards biology and if the inter-disciplinary made it easier for them to make connections between other classes. The results of these surveys were not conclusive, there were only 30 students in the class and only 22 responded to all survey questions. Overall, students felt they already know how to integrate their learning with other classes in the baseline survey and this increased only slightly as a result of the course. Clickers were considered to be an effective teaching tool and the discussions of research projects were well received. But the connection between these discussions, the associated clicker questions, and the concepts included on the tests was not clear to many students, as evidenced by their test scores. The main problem with the course that students noted were the tests, which include true/false, fill in the blank, multiple choice, and short essay questions. Additional research is necessary to identify the reasons for this disconnect.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Majors in disciplines other than biology are becoming increasingly interested in biological research projects and often query regarding the availability of research jobs. Interactions between faculty in Biology and Materials Science regarding the development of a biomaterials minor resulted in a research proposal to the National Institutes of Health that if funded, will include undergraduate research assistants. As the pipeline between biology and other disciplines increases, further collaborations are anticipated.

Describe any unexpected challenges you encountered and your methods for dealing with them: Students had difficulty with the connections between the research projects and the concepts taught in the course. Although concepts were emphasized during lectures and with clickers, the student’s understanding was not necessary obvious from test scores. This is likely to be related to the student’s attitudes about the availability of knowledge on the Internet. Two strategies are under consideration, first is to redesign the activities, the second is to change the traditional testing method used to evaluate student learning.

Describe your completed dissemination activities and your plans for continuing dissemination: Currently the information is disseminated informally among faculty involved in the development of bioengineering programs. As discussions of research projects for Biol 111 are revised and new ones develop, they may be turned into case studies and submitted to the Bioscience Educators Network (BEN) and the National Center for Case Study Teaching in Science.

Acknowledgements: The research projects described above were partially funded by the National Institute of Health through grants from the National Center for Research Resources (5P20RR016480-12) and the National Institute of General Medical Sciences (8P20GM103451-12).

Fostering Student-Centered Inter-Investigator Collaborations

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Title of Abstract: Fostering Student-Centered Inter-Investigator Collaborations

Name of Author: Catherine Reinke
Author Company or Institution: Linfield College
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Cell Biology, Genetics
Course Levels: Across the Curriculum
Approaches: Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: molecular biology, independent research, collaboration

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: In the context of extracurricular, course-based, and laboratory projects, students carried out novel research to participate in key aspects of the contemporary practice of science often absent from traditional undergraduate science curriculum, namely inter-investigator and inter-institutional collaboration. Students enrolled in the Linfield College iFOCUS program or BIOL400 Molecular Cell Biology performed 1) wet bench (in collaboration with the Reinke lab), 2) writing (in collaboration with 11 research labs at various institutions), or 3) bioinformatics exercises (in collaboration with the Genomics Education Partnership and Washington University). Student projects were designed such that students generated 1) gene mapping data, 2) testable hypotheses and tractable experimental approaches, or 3) genome annotation information, all of suitable relevance and quality to be used in ongoing academic research. The goal of these efforts was to demystify the practice of science for undergraduate students by facilitating their authentic contributions to the scientific community.

Describe the methods and strategies that you are using: 1) In the inaugural year of iFOCUS, a one-week camp aimed toward fostering an interdisciplinary science community, one project was designed to have students identify the genetic basis of traits and the relationship between genes, traits, and chromosomes through a bona fide gene-mapping project using Drosophila melanogaster. Students were charged with contributing to the identification of a novel gene required for microRNA-mediated gene silencing. 2) One Molecular Cell Biology (BIOL400) project was designed to have students author feasible research proposals addressing a student-generated research question that would be of interest to an active research laboratory. Students were encouraged to research and/or contact relevant investigators as they developed their proposals. Students were charged with crafting their research proposal through an iterative process of reading, oral presentations, and writing, and guided peer and instructor review of oral presentations and written drafts. 3) The Genomics Education Partnership (GEP) facilitates undergraduate participation in authentic genomics research through the student-led annotation of genes on the Dot chromosome of various Drosophila species, to better understand the evolution of this unique genomic region. BIOL400 laboratory students claimed a GEP project and annotated a novel sequence of genomic DNA. Subsequently, students generated a yeast genomic library and analyzed representative clones via enzyme digest, DNA sequencing, and BLAST to identify a gene required for normal organelle morphology by complementation of a temperature-sensitive phenotype in Saccharomyces cerevisiae. Taken together, these complementary laboratory modules required students to generate genome annotation data de novo and then use similar extant genome annotation data to address an authentic cell biological research question.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Thus far, student participation in two of three projects has furthered subsequent research by active laboratories as measured by the incorporation of student-generated information into ongoing projects. Students consequently have a heightened sense of ownership and thus a higher level of commitment to their work. Students were provided with the opportunity to provide evaluations (both institutionally standardized evaluations and instructor-authored evaluations) to allow for the evaluation of the project's ability to achieve the desired learning outcomes. For all projects, student learning gains were measured by pre- and post-project assessment, indicating attainment of learning objectives.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: 1) Interested students (8/10) returned once the semester began to determine which genomic region contained the mutation of interest based on their data collection and complementation analysis. In addition, data generated by iFOCUS students directed the course of the independent research projects for two fourth-year students in Fall ‘12, and 4/10 iFOCUS students subsequently elected to enroll in BIOL220 Research Methods in Spring ‘13, to carry out further independent research on this topic. 2) Two students spontaneously demonstrated palpable investment in their proposals, further revising or summarizing their work after the course for communication with investigators at other institutions, achieving the goal of inter-investigator and inter-institutional scientific collaboration. 3) Additional Linfield College student TAs and faculty members have committed to or are exploring participation in the GEP. Subsequent students and researchers will use student-generated data and reagents in Spring ‘13, achieving the goal of inter-investigator and inter-institutional scientific collaboration.

Describe any unexpected challenges you encountered and your methods for dealing with them: Students are often surprised by the fact that they can contribute directly to ongoing research even at the undergraduate level. Descriptions of the various projects thus needed to include direct examples of how student work contributes to the whole and furthers the overall project.

Describe your completed dissemination activities and your plans for continuing dissemination: 1) Formal and informal student and faculty reviews of iFOCUS were provided to faculty and administrators to generate support for future iterations of iFOCUS. 2) Peer review of final oral presentations of research proposals led to recommendations for funding. In addition, two students spontaneously demonstrated palpable investment in their proposals, further revising or summarizing their work after the course for communication with investigators at other institutions, achieving the goal of inter-investigator and inter-institutional scientific collaboration. 3) Data analyzed will be submitted to the Genomics Education Partnership.

Acknowledgements: Tom Hellie; presenident of Linfield College, Susan Agre-Kippenhan, Dean of Faculty, and the members of the Linfield College Biology Department.

Visual Analytics in Biology Curriculum Network

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Title of Abstract: Visual Analytics in Biology Curriculum Network

Name of Author: Raphael Isokpehi
Author Company or Institution: Jackson State University
PULSE Fellow: No
Applicable Courses: Bioinformatics, Biotechnology, Evolutionary Biology, General Biology
Course Levels: Across the Curriculum, Faculty Development, Introductory Course(s), Upper Division Course(s)
Approaches: Adding to the literature on how people learn, Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: Visual Analytics, Data-Rich Biology, Teaching with Data, Data Visualization

Name, Title, and Institution of Author(s): Shaneka S. Simmons, Jackson State Universtiy Jian Chen, University of Maryland, Baltimore County Edu Suarez-Martine, University of Puerto Rico at Ponce Robert Dottin, Hunter College of the City University of New York

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The Biology of the 21st Century (the New Biology) already generates massive amounts of data on biological systems from cellular molecules to ecosystems. It demands new skills and knowledge for teachers and learners of biology to make biological inferences from large datasets (such as genome sequences and long-term ecological measurements) that are now essential for evidence-based learning. The primary mission of the Visual Analytics in Biology Curriculum Network (VABCN; www.vabcn.org) is to contribute to the national efforts to change the way the core concepts for biology literacy and practice are taught and learned. According to the Final Report of the July 2009 National Conference titled “VISION AND CHANGE IN UNDERGRADUATE BIOLOGY EDUCATION: A CALL TO ACTION”, the core concepts for biological literacy and practice are (i) evolution; (ii) structure and function; (iii) information flow, exchange, and storage; and (iv) systems. To transform undergraduate biology education these concepts need to be mastered using a set of core competencies. Incorporating visual analytics, the science of analytical reasoning facilitated by interactive visual interfaces, in the biology curriculum will improve the ability of biology learners to develop competencies to understand (master) the core concepts for biological literacy. The overall goal of the Visual Analytics in Biology Curriculum Network (VABCN) is to facilitate and promote the collaboration of researchers, educators, and students who are developing approaches for incorporating visual analytics into biology undergraduate education. The intended outcomes of the VABCN are to (1) Develop and expand a network of scholars for improvement in undergraduate biology education; (2) Produce, assess and disseminate course resources designed to improve biological literacy; (3) Promote a globally engaged network of faculty and students; and (4) Provide effective communications and collaboration tools.

Describe the methods and strategies that you are using: Many interactive visual interfaces that are key to teaching, learning and assessment are now available through diverse computing devices including desktop computers, laptops, notebooks, tablets and smartphones. The three main strategies for implementing the Visual Analytics in Biology Curriculum Network (VABCN) are: (1) Web Portal to Visual Analytics for Undergraduate Biology Education; (2) Development of Visual Analytics Enhanced Biology Course Resources; and (3) Webinars and Classroom Guest Speakers. A visual analytics enhanced biology course resource incorporates the use of interactive visual interfaces and software that facilitate visual analytics tasks on the selected biological datasets. The course resources will be mapped to the categories that are aligned to the core concepts and core competencies as described in the 2011 Vision and Change Report. Other categories are student audience, scientific domain and nature of research.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: The planning phase (April 2011 to March 2012) of the VABCN enabled us to develop frameworks for the design of evaluation studies: e.g. pre- and post-assessment materials; comparisons between implementations at different sites; and comparative assessments of course resource implementation with and without the visual analytic component. Additional frameworks are students’ pre and post knowledge and skills in different aspects of scientific inquiry. The proposed project will allow members to further develop these assessment strategies and share them.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: The Preparing Faculty Working Group (Theme III: Ways to Bring About Change: Change Agents) during the 2009 Vision and Change meeting recognized the need “To develop and grow communities of scholars (students, postdocs, faculty, and administrators) who are committed to creating, using, assessing, and disseminating effective practices in teaching and learning” (https://live-visionandchange.pantheonsite.io/working-group-descriptions/). The planning phase of the VABCN enabled the formation of a Steering Committee consisting of 33 scholars from 13 diverse institutions. The full implementation of the VABCN will provide activities to improve and expand a network of scholars interested in improving the approaches to teaching and learning biology in a data intensive world. Our measurable aim is to reach at least 100 unique participants per year in the VABCN activities. Integrated analysis and visualization can allow learners and teachers of biology to analyze data of interest, display relevant parts, and concurrent ways to interact with the data for deeper understanding. Science education research suggests that activities are most effective when they are designed to interactively engage students.

Describe any unexpected challenges you encountered and your methods for dealing with them: In the planning (incubator) phase of the VABCN we identified that heterogeneous virtual communities take time to develop the bonds, sharing of expertise, shared understanding and vocabulary needed for productive development of visual analytic course materials. More time than a year is needed to develop at once solid collaborative dynamics, high quality instructional materials integrating innovative visual analytics, implementation of the materials, and assessment instruments. It is likely that investment in these longer start-up times for a first module will make it possible for a group to produce additional instructional materials very efficiently and effectively. Thus efforts are in progress to secure grant funding and other funding sources to continue the activities of the VABCN.

Describe your completed dissemination activities and your plans for continuing dissemination: The principal product from the network activities will be a system of course resources on visual analytics for mastering core concepts for biological literacy. The VABCN will facilitate the production, assessment and dissemination of biology course resources that incorporate visual analytics. During the planning phase, members of the network produced, assessed and disseminated prototype course resources on diversity of life targeted at biology courses offered to freshmen and sophomores (https://www.vabcn.org/). We will promote, encourage and support the use of best practices for student-centered course resource development as recommended by the Vision and Change Report. Therefore, an expected outcome of this VABCN activity is that the developed course resources will have well-articulated learning outcomes to align assessments with learning activities. As an international network with participants in different geographical locations, the VABCN will maximize the use of cyber-based collaboration strategies and promote the use of videoconferencing to accomplish collaborations. As part of our international public dissemination of the results of the planning activities of the VABCN, we have worked with International Innovation Magazine to prepare an article on the importance of visual analytics in biology curriculum in language accessible to the public. The full digital edition of the May 2012 International Innovation can be found at: https://www.research-europe.com/. Since the VABCN is responsive to the Vision and Change effort, we will establish a VABCN group on the PULSE (Partnership for Undergraduate Life Sciences Education) website (https://www.pulsecommunity.org/). In particular, we will provide VABCN information materials to the PULSE Vision and Change Ambassadors, a group dedicated to meeting with biology and life science departments to encourage them to adopt the principles and recommendations of the “Vision and Change” report.

Acknowledgements: The incubator phase of the Visual Analytics in Biology Curriculum Network was jointly funded by the Directorate for Biological Sciences, Division of Biological Infrastructure and the Directorate for Education and Human Resources, Division of Undergraduate Education of the National Science Foundation as part of their Vision and Change in Undergraduate Biology Education efforts. Award: NSF-DBI-1062057

Group Research: Experiment in Efficiency of Delivery

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Title of Abstract: Group Research: Experiment in Efficiency of Delivery

Name of Author: Louise Temple
Author Company or Institution: James Madison University
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Evolutionary Biology, Genetics
Course Levels: Upper Division Course(s)
Approaches: Mixed Approach
Keywords: Undergraduate research Efficient delivery Multiple students Single mentor

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: With the overwhelming documentation of undergraduate research as a transformative experience, biology educators are being challenged to offer research to more students. The goal of this project is to offer original research opportunities to more undergraduates by developing experimental questions that can be addressed by small groups of students mentored by one faculty. Since 2008, we have offered a research class to freshman involving bacteriophage discovery and genomics, originally sponsored by HHMI and now continuing with institutional support. This program has been extremely successful, so much so that there is enormous pressure on faculty to host more upper-level students in their research labs. One solution to this fortuitous problem is to continue a more advanced research project with groups of 6 to12 students mentored by one faculty member. We have dubbed this class 'Superphage'. The intended outcomes of the project are twofold: (1) students will derive the benefits of an undergraduate research experience similar to that offered by a one-on-one mentoring situation, and (2) different models will reveal the best possible way to offer this opportunity to more students.

Describe the methods and strategies that you are using: The SuperPhage course has been offered for four semesters and involved 25 students. Half of these enrolled for two semesters, which is the limit, and the other half for one semester. Four different models have been tried: (1) 16 students working in groups trained and supervised by the faculty mentor, (2) 12 students working in small groups of 3-4 with an assigned student leaders, (3) 11 students working at designated times all together for several hours a week, and (4) 5 students working somewhat independently on the same project. In every case, the research questions have derived from the freshman Viral Discovery course, building directly on biological discoveries and data generated by the first year students, as well as an additional project that utilizes the skills learned in the course and applied to a different question. Regardless of the model, the groups have met more or less regularly for journal club, which has consisted of primary data literature reading and discussions, as well as reports on individual results and issues.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Every semester, the students have answered questionnaires and been involved in discussions about the effectiveness of the course for them, what they would change about how the course is run, and what they would change about their own behavior. In addition a recent survey was given which included the attitude assessment questions from the Classroom Undergraduate Research Experiences (CURE) survey. It is our intention to track the students for the next few years, as closely as possible, in their career tracks.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: The major question, 'Do students benefit from group (as opposed to individual) research experiences'? seems clear from the early outcomes. All student report that they strongly benefited from this experience. There are several other measurable outcomes, including that all these students have continued beyond the group experience into individual, independent projects, and high numbers of them obtain summer research opportunities outside our school. One additional, explicit goal of this project is to address the challenge of publication of undergraduate research results. In this regard, a second outcome has been the preparation of two manuscripts that are student driven, one accepted for publication in the journal, Virology, and the other likely to be ready for submission by the end of the summer. The strategies used in designing research with the expressed goal of publication have been documented and student feedback recorded. Our initial observation with regard to the different models described above is that different groups of students will be differently successful due not only to the model but also to their personalities, motivation, and preparation. One incontrovertible conclusion is that regular journal clubs are extremely valuable, giving students a strong background for the particular project and the skills needed to read primary literature, and fostering ideas that directly impact their approaches to their research. An additional outcome is new collaborations within our institution and with another university, which have already resulted in external funding and promise higher success rate in dissemination of the work.

Describe any unexpected challenges you encountered and your methods for dealing with them: The challenge of this model is to ensure that the members of the group receive the benefits that have been shown so profoundly in the one-on-one, mentor - mentee model. The CURE attitudinal question results are not completely analyzed at this writing, but initial observations indicate this model provides equal or better self-evaluation than other high research classes, including intense summer experiences. A second challenge for the model is faculty effort. Regardless of which of the four models is used, a large effort is required of a single faculty mentor. Because the students are signed up for academic credit under a single rubric, the faculty member receives teaching credit for this 'course'. Financial support for the projects is also a challenge, which in our case has been met largely by departmental support and some external funding from the state of Virginia.

Describe your completed dissemination activities and your plans for continuing dissemination: The science produced by the students has been disseminated in several regional and national meetings. This write-up is the first effort to disseminate what we have learned from the faculty and educational standpoints, about this model.

Acknowledgements: Several faculty members in the Viral Discovery and Biotechnology programs have assisted in this project, either by helping students directly or by teaching coverage to allow a single professor to mentor students using this model. These include Drs. Steve Cresawn, Stephanie Stockwell, Ron Raab, Crystal Scott, and Bob McKown. The Department of Integrated Science & Technology and Dr. George Coffman have been very supportive from financial and lab support perspectives.

Ciliate Genomics Consortium: Teaching-Research Integration

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Title of Abstract: Ciliate Genomics Consortium: Teaching-Research Integration

Name of Author: Emily Wiley
Author Company or Institution: Claremont McKenna, Pitzer, and Scripps Colleges
Author Title: Associate Professor
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Cell Biology, General Biology, Plant Biology & Botany
Course Levels: Faculty Development, Introductory Course(s), Upper Division Course(s)
Approaches: Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Material Development
Keywords: class-based research learning community collaborative research molecular biology functional genomics

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: To improve biological literacy and student-centered education, V&C action items include integrating science process, and introducing research experiences, into all undergraduate biology courses. Developing a model for integrating undergraduate research, with a particular eye to making class-based authentic experiences more sustainable for faculty, was a central goal. The Ciliate Genomics Consortium (CGC) was aimed to 1) improve feasibility/sustainability of undergraduate research in the classroom through melding faculty research goals with student research efforts in a professional learning community model; 2) increase student (early) participation in authentic research by integrating opportunities into a variety of commonly-taught biology courses at different levels and types of institutions; 3) enrich classroom undergraduate research experiences through immediate web publication of students' original findings to an appropriate 'user' group; and 4) expand science leadership opportunities for students.

Describe the methods and strategies that you are using: A learning consortium of faculty and students based on functional annotation of Tetrahymena genes was developed. Scalable research modules for integration into existing courses serve to engage students in making new and highly valued contributions to the larger community of ciliate biologists. Student discoveries are directly disseminated to this community through a database for unpublished results that is hyperlinked to the official genome database, a highly visible and well-utilized community resource. Faculty at any institution can engage their students, in class, in explorations of genes in families related to the faculty member's research program, and results are used to progress their research agenda. Opportunities for collaboration between consortium faculty across institutions and disciplines that create new research possibilities, are provided through workshops run as part of, or separate from, regular scientific meetings. Resulting collaborations allow students to feed into larger projects of interest to multiple faculty members.

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: Changes in student attitudes and motivation to engage science that correlate with using consortium research modules and other consortium activities, such as dissemination of student discoveries and inclusion in a broader learning community, were assessed. Pre/post attitudinal and confidence surveys were administered; voluntary student time spent on the project outside of class was tracked, as were student efforts to seek additional research opportunities in the following year. Comparisons were made with control groups that did not participate in the consortium. Student learning gains from engaging research in class guided by the modules was assessed using the CURE and SALG instruments. To assess sustainability for faculty, the number of course repeats using the research modules was tracked, and the number of faculty publications using student-generated data, and the number of new collaborations between consortium faculty were used as measures of impact to faculty research programs. Impact on the larger ciliate research community was measured by tracking numbers of new gene function annotation entries resulting from the class-based research made on the Tetrahymena Genome Database (TGD) Wiki, or through the database for unpublished results linked to TGD.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Nine faculty at 11 different schools (private colleges, universities, and state universities) have integrated the research modules into 12 courses (cell bio, molecular, and intro) taught multiple times, plus bridge programs - over 500 students have contributed toward understanding function of ~300 Tetrahymena genes. Repeated use of modules in courses was 95%. Some courses were designed around this experience (a research course for sophomores, and others) and modules were successfully established in intro biology courses at Claremont and Missouri State U. Through CGC, 10 faculty and 6 students have received technical cross-training through workshops; 52 students have presented their research at conferences (including intro bio students); 23 are authors on peer-reviewed publications. Learning and behavioral outcomes from the research modules include significant gains in students' understanding of research process, how scientists approach real world problems, data analysis, readiness for more demanding research, and gains in student confidence in experimental design and execution, data presentation, scientific writing, oral presentation of results, and scientific record-keeping. Tracking and self-reports showed 25% increase in upper division students, and 6-fold increase in first year students, who pursued additional research within one year after module experience. Adding web publication opportunity produced large gains in motivation to 'do science', measured by tracking voluntary student hours spent on the research project outside of class time, and beyond the end of the course. Faculty research programs benefitted from the class-based research, shown by number of publications (6) with student authors from classes (20) and 5 new multi-year faculty collaborations.

Describe any unexpected challenges you encountered and your methods for dealing with them: Challenge #1: Time/effort to adopt and implement the research modules in a given classroom. Faculty can bring UG students to workshop training sessions - students serve as TAs at the home institution, aiding module implementation and reducing faculty time/effort required. Challenge #2: Faculty reluctance to adopt modules using unfamiliar experimental systems. Instead of only recruiting faculty into work with Tetrahymena, we are also disseminating our UG research model - one that is highly transferable to teacher-researchers in other model system communities with genome annotation needs. Our student results database now has a highly adaptable interface for use by any community. Disseminating the model reduces need for specific training workshops for work with Tetrahymena.

Describe your completed dissemination activities and your plans for continuing dissemination: The Ciliate Genomics Consortium opportunities and outcomes were disseminated through multiple presentations at both scientific and education conferences, through workshops during a primary biannual conference for ciliate biologists, and independent consortium workshops. A CGC website provides one avenue for new people to join the consortium (https://tet.jsd.claremont.edu). At least three publications on consortium activities and outcomes are in preparation. Enhanced efforts to disseminate the consortium model to other model system communities are being planned, and a proposal to NSF to support these and future faculty/student training workshops was submitted.

Acknowledgements: This project was supported by an NSF CAREER award to E. Wiley (MCB-0545560) and HHMI funding to Washington University. The project was developed through the combined efforts of the The Ciliate Genomics Consortium Steering Committee members: Douglas Chalker, Washington University; Joshua Smith, Missouri State University; Nicholas Stover, Bradley University; and Emily Wiley, Claremont McKenna, Pitzer, and Scripps Colleges.

DNA Barcoding: Scalable Infrastructure for Student Research

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Title of Abstract: DNA Barcoding: Scalable Infrastructure for Student Research

Name of Author: David Micklos
Author Company or Institution: Cold Spring Harbor Laboratory
Author Title: Executive Director
PULSE Fellow: No
Applicable Courses: Biochemistry and Molecular Biology, Bioinformatics, Biotechnology, Ecology and Environmental Biology, Evolutionary Biology, General Biology, Integrative Biology, Plant Biology & Botany
Course Levels: Across the Curriculum, Faculty Development, Introductory Course(s)
Approaches: Material Development
Keywords: DNA barcoding, genetics, conservation biology, DNA sequencing, bioinformatics

Name, Title, and Institution of Author(s): Bruce Nash, Cold Spring Harbor Laboratory Jermel Watkins, Cold Spring Harbor Laboratory Cornel Ghiban, Cold Spring Harbor Laboratory Mohammed Khalfan, Cold Spring Harbor Laboratory Sheldon McKay, Cold Spring Harbor Laboratory Eunsook Jeong, Cold Spring Harbor Laboratory Susan Lauter, Cold Spring Harbor Laboratory Christine Marizzi, Cold Spring Harbor Laboratory Melissa Lee, Cold Spring Harbor Laboratory Antonia Florio, Cold Spring Harbor Laboratory Oscar Pineda-Catalan, American Museum of Natural History

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: Many science educators search for ways to scale student research from local, individual projects to distributed, class-based experiments that involve many students working simultaneously on aspects of the same problem. DNA barcoding fulfills the promise of modern, Internet-enabled biology – allowing students to work with the same data, with the same tools, at the same time as high-level researchers. DNA barcoding projects can stimulate independent student thinking across different levels of biological organization, linking molecular genetics to ecology and evolution – with the potential to contribute new scientific knowledge about biodiversity, conservation biology, and human effects on the environment. DNA barcoding also integrates different methods of scientific investigation – from in vivo observations to in vitro biochemistry to in silica bioinformatics. DNA barcoding provides a practical way to bring open-ended experimentation into lower-level undergraduate courses. Projects can operate at various scales – from working with other students to investigate a local ecosystem, museum collection, or conservation issue to joining an International Barcode of Life ‘campaign’ to explore an entire taxonomic group or global biome. Projects may also take on a forensic slant, when students attempt to identify product fraud (such as mislabeled food items) or to identify the sources of commercial products (such as plants or animals used in traditional medicines). The core lab and phylogenetic analysis can be mastered in a relatively short time, allowing students to reach a satisfying research endpoint within a single academic term. Using DNA barcoding as the common method across a range of projects decreases the need for intensive, expert preparation and mentoring – thus providing a practical means to engage large numbers of students in meaningful research.

Describe the methods and strategies that you are using: Just as the unique pattern of bars in a universal product code (UPC) identifies each consumer product, a short ‘DNA barcode’ (about 600 nucleotides in length) is a unique pattern of DNA sequence that can potentially identify any living thing. We developed an integrated biochemical and bioinformatics (B&B) workflow for DNA barcode analysis. The biochemistry uses non-caustic reagents to isolate DNA from plant, animal, or fungi. The barcode region is amplified by polymerase chain reaction and visualized by agarose gel electrophoresis. The barcode amplicons are mailed to GENEWIZ, which provides inexpensive sequencing – $3.00 per forward and reverse read. Within 48 hours, the finished barcode sequences are automatically uploaded to DNA Subway, the DNALC’s bioinformatics workflow for education. The Blue Line of DNA Subway includes all tools needed to visualize and edit barcode sequences, search GenBank (www.ncbi.nlm.nih.gov/genbank/) for matches, align sequences, and construct phylogenetic trees. The Blue Line includes web applications that heretofore could only be used as stand-alone applications – including an electropherogram viewer/editor and a ‘zoomable’ sequence aligner/barcode viewer. An export feature simplifies barcode sequence submissions to GenBank, automatically providing sequence files, associated metadata, and sequence annotations in the required NCBI format. The barcode experiment, including extensive teacher prep and planning, is available in three formats: the online lab notebook www.dnabarcoding101.org, the lab-text Genome Science: A Practical and Conceptual Introduction to Molecular Genetic Analysis in Eukaryotes (Cold Spring Harbor Laboratory Press, 2012), and a stand-alone kit marketed by Carolina Biological Supply Company.

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 evaluate the impacts of DNA barcoding research programs on both students and teachers, using mixed methods to provide both breadth and depth of perspectives. In addition to project statistics (participant demographics, completed projects, novel DNA sequences, etc.) we use online surveys and structured interviews. Teachers and students complete pre- and post-experience surveys to gauge changes in knowledge, attitudes and behaviors, and to compare the barcoding research projects with other research experience. Students complete the validated Survey of Undergraduate Research Experience (SURE-III) which allows comparisons with national cohorts. Structures interviews at completion of projects delve further into participant experiences and how programs could be improved.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: In terms of student impact, the largest gains in self-confidence (78% ‘Large’ or ‘Very large gain’), learning laboratory techniques (78%), working independently (78%), analyzing data (78%), and becoming part of a learning community (77%). Surveys and structured interviews overwhelming show that students appreciated ownership of barcoding projects and the sense of ‘doing real science.’ For most, it is their first experience with open-ended research. When compared with other research experiences DNA barcoding provides more ‘real world’ science (81% of students), more chance for hands-on experience (69%) and to learn science (76%), more opportunity to develop critical thinking (83%) and independent inquiry skills (70%), and more understanding of the scientific process (68%). The experience increases students’ interest in studying science or pursuing a career in science (83%), while still being more fun than other research experiences (84%). DNA barcoding research projects have a broader impact, potentially improving the quality of instruction for many students beyond those who actually did barcoding projects. Participating teachers state they had, or plan to, incorporate into their classroom instruction: DNA barcoding concepts (73%), more independent research (68%), bioinformatics exercises (59%), and wet labs (41%). These changes are in a range of classes – including general biology (55%), AP Biology (41%), biology electives (40%), environmental science (18%), and honors biology (18%). In addition, 59% had or planned to share resources or train colleagues in new biochemical (36%) and bioinformatics (32%) techniques. These results demonstrate that the DNA barcoding infrastructure developed at the DNALC can scale to introduce large numbers of students to authentic research.

Describe any unexpected challenges you encountered and your methods for dealing with them: Formative evaluation of DNA barcoding projects revealed some challenges, which we have addressed. We schedule project cycles to allow sufficient time for recruitment and training so that sample collection occurs during warmer weather. Teacher training is critical to the success of student projects, so we provide at a minimum one-day training sessions in biodiversity, DNA barcoding, and bioinformatics. Individual project settings vary greatly (for example, student grade level, background and familiarity with laboratory techniques, access to equipment at their school) so we now provide an array of support options: Open Labs at the Harlem DNA Lab and Genspace; equipment footlockers; and virtual and real staff. We refined the B&B workflows, including a specimen database and DNA Subway function to submit novel sequences to Genbank.

Describe your completed dissemination activities and your plans for continuing dissemination: We have conducted several DNA barcoding programs to date. These include the New York City-based Urban Barcode Project, DNALC summer camps, and teacher training programs. We have developed two websites: www.dnabarcoding101.org and www.urbanbarcodeproject.org. The websites include vodcasts on barcoding and student projects, protocols, guidelines for proposal preparation, and database management tools for tracking student projects and metadata. We also developed a DNA barcoding kit that is disseminated through Carolina Biological Supply Company. To date we have trained over 1000 teachers, and more than 450 students have participated in the UBP and barcoding summer camps. Students’ projects have examined: 1) wildlife in parks and public spaces; 2) traded products and possible commerce of endangered species; 3) food mislabeling; 4) public health and disease vectors; and 5) exotics and invasive species. Each project culminates in a poster presentation, with the UBP also including a symposium of finalist oral presentations at the American Museum of Natural History. For the UBP alone, more than 1,600 samples and 4,000 single sequence reads have been processed, and 65 novel sequences have been submitted to GenBank with student authors

Acknowledgements: Funding from Alfred P. Sloan Foundation, Pinkerton Foundation, NSF Advanced Technology Education, NSF Transforming Undergraduate Education in Science, and NSF Plant Science Cyberinfrastructure Collaborative. Project collaborators include American Museum of Natural History, Genspace, the Gateway Institute for Precollege Education, and NYC Department of Education.

Bio-Link Aligns With Vision and Change Recommendations

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Title of Abstract: Bio-Link Aligns With Vision and Change Recommendations

Name of Author: Elaine Johnson
Author Company or Institution: City College of San Francisco
Author Title: Bio-Link Executive Director
PULSE Fellow: No
Applicable Courses: Agricultural Sciences, Bioinformatics, Biotechnology, Cell Biology, General Biology, Genetics, Microbiology, Virology
Course Levels: Across the Curriculum, Faculty Development, Introductory Course(s)
Approaches: Adding to the literature on how people learn, Assessment, Changes in Classroom Approach (flipped classroom, clickers, POGIL, etc.), Internships, Material Development, Mixed Approach
Keywords: Interdisciplinary Contextual Skills-based Evidence-based Competency

Goals and intended outcomes of the project or effort, in the context of the Vision and Change report and recommendations: The Bio-Link Next Generation National Advanced Technological Education (ATE) Center for Biotechnology and Life Sciences builds on the success of the original Bio-Link National Center for Biotechnology that was first funded by NSF in 1998. Bio-Link’s mission is to 1) increase the number and diversity of well-trained technicians in the workforce; 2) meet the growing needs of industry for appropriately trained technicians; and 3) institutionalize community college educational practices that make high-quality education and training in the concepts, tool, skills, processes, regulatory structure, and ethics of biotechnology available to all students. The means for fulfilling the mission are aligned with today’s new biotechnology environment. The goals of the Next Generation Bio-Link National Center are to: 1) strengthen and expand biotechnology education programs across the nation; 2) enable biotechnology faculty, students, and technicians to work more efficiently; and 3) support a smoother transition of students to the technical workforce in the biosciences and related industries.

Describe the methods and strategies that you are using: In order to achieve its goals, Bio-Link emphasizes three categories of activities and products. Category I. Providing direct services to faculty, teachers, counselors, students, biotechnology programs, and educational institutions. Category II. Stimulating information sharing and collaboration among students, faculty, industry and educational institutions. Category III. Supplying greatly expanded and improved information to students and to life-sciences and related companies. Bio-Link is one of thirteen ATE Centers that is participating in the Synergy Collaboratory for Research, Practice and Transformation that focuses on practices and processes that lead to achieving scale. Bio-Link is also connecting with Vision and Change recommendations suggested by the American Association for the Advancement of Science (AAAS).

Describe the evaluation methods that you used (or intended to use) to determine whether the project or effort achieved the desired goals and outcomes: The annual five day Summer Fellows Forum provides educators from community colleges and high schools across the country with a series of workshops and presentations. Between 1999 and 2012, some 678 instructors and administrators had attended the Forum. Feedback questionnaires and follow-up surveys administered to Forum participants from 1999 through 2012 indicate that the great majority of them had modified their curriculum (92%) and teaching strategies (87%) as a result of what they had learned.

Impacts of project or effort on students, fellow faculty, department or institution. If no time to have an impact, anticipated impacts: Together with other workshops conducted by the Center (over 384 to date), Bio-Link’s professional development has made a substantial impact on biotechnology education across the country. Instructors who have participated in Bio-Link professional development over the years teach approximately 128,800 students (52,800 by Forum participants and 76,000 by other workshop participants).

Describe any unexpected challenges you encountered and your methods for dealing with them: One challenge was the lack of awareness about biotechnology careers. In every one of the past three years, the phrase 'biotech careers' has been one of the top ten search terms that people use to find the Bio-Link web site. The repeated use of this phrase for web searches indicates a strong interest in locating information about biotech careers. Bio-Link officially launched www.biotech-careers.org at the 2012 Bio-Link Summer Fellows Forum. We see the career site functioning in the following ways: Students will come to the site to learn about different biotech careers. They will look at the photo journals, read the interviews, and watch videos to see people who work in biotech jobs and hear what they have to say about the careers. They may also read the articles to learn about job-hunting tips or new job areas.

Describe your completed dissemination activities and your plans for continuing dissemination: The Clearinghouse is as an online collection of 130 instructional and curriculum materials for biotechnology. Clearinghouse website usage metrics indicate that Bio-Link’s strategies for improving and managing the Clearinghouse are proving effective, and there are positive trends in site usage from 2010-2011 to 2011-2012. Total unique visitors continued to grow, (767 to 890), as did total visits (1,086 to 1,324), average visit duration, and the percentage of repeat visitors (34% to 37%). In the National Biotechnology Program Survey, almost three-quarters (73%) of the respondents indicated that they had a high level of interest in the Clearinghouse, the highest of any Bio-Link product or service.

Acknowledgements: NSF funding of Bio-Link through Award No. 0903317 with a total of $5,086,040 from September 1, 2009 through August 31, 2014. Co-PI's: Barton Gledhill, VMD, PhD; Linnea Fletcher, PhD, Austin Community College; Sandra Porter, PhD, Digital World Biology; Lisa Seidman, PhD, Madison College. Evaluators: Dan Weiler and Candiya Mann Industry Partners who have provided support and insight and educators across the nation who have provided guidance and collaboration.