Cheryl Bailey

The Genomics Education Partnership: Successful Integration of Research into Laboratory Classes at a Diverse Group of Undergraduate Institutions

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 million bases of draft genomic sequence from several species of Drosophila and have produced hundreds of gene models using evidence-based manual annotation. Students appreciate their ability to make a contribution to ongoing research, and report increased independence and a more active learning approach after participation in GEP projects. They show knowledge gains on pre- and postcourse quizzes about genes and genomes and in bioinformatic analysis. Participating faculty also report professional gains, increased access to genomics-related technology, and an overall positive experience. We have found that using a genomics research project as the core of a laboratory course is rewarding for both faculty and students.

A Course-Based Research Experience: How Benefits Change with Increased Investment in Instructional Time

While course-based research in genomics can generate both knowledge gains and a greater appreciation for how science is done, a significant investment of course time is required to enable students to show gains commensurate to a summer research experience. Nonetheless, this is a very cost-effective way to reach larger numbers of students.

Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum

Community Page Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum Jayna L. Ditty 1 , Christopher A. Kvaal 2 , Brad Goodner 3 , Sharyn K. Freyermuth 4 , Cheryl Bailey 5 , Robert A. Britton 6 , Stuart G. Gordon 7 , Sabine Heinhorst 8 , Kelynne Reed 9 , Zhaohui Xu 10 , Erin R. Sanders-Lorenz 11 , Seth Axen 12 , Edwin Kim 12 , Mitrick Johns 13 , Kathleen Scott 14 , Cheryl A. Kerfeld 12,15 * 1 Department of Biology, University of St. Thomas, St. Paul, Minnesota, United States of America, 2 Department of Biological Sciences, St. Cloud State University, St. Cloud, Minnesota, United States of America, 3 Department of Biology, Hiram College, Hiram, Ohio, United States of America, 4 Biochemistry Department, University of Missouri- Columbia, Columbia, Missouri, United States of America, 5 Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, United States of America, 6 Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan, United States of America, 7 Department of Biology, Presbyterian College, Clinton, South Carolina, United States of America, 8 Department of Chemistry and Biochemistry, The University of Southern Mississippi, Hattiesburg, Mississippi, United States of America, 9 Biology Department, Austin College, Sherman, Texas, United States of America, 10 Department of Biological Sciences, Bowling Green State University, Bowling Green, Ohio, United States of America, 11 Department of Microbiology, Immunology and Molecular Genetics, University of California – Los Angeles, Los Angeles, California, United States of America, 12 Department of Energy-Joint Genome Institute, Walnut Creek, California, United States of America, 13 Department of Biological Sciences, Northern Illinois University, DeKalb, Illinois, United States of America, 14 Department of Integrative Biology, University of South Florida, Tampa, Florida, United States of America, 15 Department of Plant and Microbial Biology, University of California Berkley, Berkeley, California, United States of America Introduction Undergraduate life sciences education needs an overhaul, as clearly described in the National Research Council of the National Academies’ publication BIO 2010: Transforming Undergraduate Education for Future Research Biologists. Among BIO 2010’s top recommendations is the need to involve students in working with real data and tools that reflect the nature of life sciences research in the 21st century [1]. Education research studies support the importance of utilizing primary literature, designing and implementing experiments, and analyzing results in the context of a bona fide scientific question [1–12] in cultivating the analytical skills necessary to become a scientist. Incorporating these basic scientific methodologies in under- graduate education leads to increased undergraduate and post-graduate reten- tion in the sciences [13–16]. Toward this end, many undergraduate teaching orga- nizations offer training and suggestions for faculty to update and improve their teaching approaches to help students learn as scientists, through design and discovery (e.g., Council of Undergraduate Research [www.cur.org] and Project Kaleidoscope [ www.pkal.org]). With the advent of genome sequencing and bioinformatics, many scientists now formulate biological questions and inter- pret research results in the context of genomic information. Just as the use of bioinformatic tools and databases changed the way scientists investigate problems, it must change how scientists teach to create new opportunities for students to gain experiences reflecting the influence of genomics, proteomics, and bioinformatics on modern life sciences research [17–41]. Educators have responded by incorpo- rating bioinformatics into diverse life science curricula [42–44]. While these published exercises in, and guidelines for, bioinformatics curricula are helpful and inspirational, faculty new to the area of bioinformatics inevitably need training in the theoretical underpinnings of the algo- rithms [45]. Moreover, effectively inte- grating bioinformatics into courses or independent research projects requires infrastructure for organizing and assessing student work. Here, we present a new platform for faculty to keep current with the rapidly changing field of bioinfor- matics, the Integrated Microbial Genomes Annotation Collaboration Toolkit (IMG- ACT) (Figure 1). It was developed by instructors from both research-intensive and predominately undergraduate institu- tions in collaboration with the Department of Energy-Joint Genome Institute (DOE- JGI) as a means to innovate and update undergraduate education and faculty de- velopment. The IMG-ACT program pro- vides a cadre of tools, including access to a clearinghouse of genome sequences, bioin- formatics databases, data storage, instruc- tor course management, and student notebooks for organizing the results of their bioinformatic investigations. In the process, IMG-ACT makes it feasible to provide undergraduate research opportu- nities to a greater number and diversity of students, in contrast to the traditional mentor-to-student apprenticeship model for undergraduate research, which can be too expensive and time-consuming to provide for every undergraduate. The IMG-ACT serves as the hub for the network of faculty and students that use the system for microbial genome analysis. Open access of the IMG-ACT infrastructure to participating schools en- sures that all types of higher education institutions can utilize it. With the infra- structure in place, faculty can focus their efforts on the pedagogy of bioinformatics, involvement of students in research, and use of this tool for their own research agenda. What the original faculty mem- bers of the IMG-ACT development team present here is an overview of how the IMG-ACT program has affected our Citation: Ditty JL, Kvaal CA, Goodner B, Freyermuth SK, Bailey C, et al. (2010) Incorporating Genomics and Bioinformatics across the Life Sciences Curriculum. PLoS Biol 8(8): e1000448. doi:10.1371/journal.pbio.1000448 Published August 10, 2010 Copyright: s 2010 Ditty et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Funding: No specific funding was received for this work. The Community Page is a forum for organizations and societies to highlight their efforts to enhance the dissemination and value of scientific knowledge. Competing Interests: The authors have declared that no competing interests exist. Abbreviations: IMG-ACT; Integrated Microbial Genomes Annotation Collaboration Toolkit * E-mail: ckerfeld@lbl.gov PLoS Biology | www.plosbiology.org August 2010 | Volume 8 | Issue 8 | e1000448

Learning transferable skills in large lecture halls: Implementing a POGIL approach in biochemistry

As research‐based, active learning approaches become more common in biochemistry classrooms, the large lecture course remains the most challenging to transform. Here, we provide a case study demonstrating how process oriented guided inquiry learning (POGIL) can be implemented in a large class taught in a traditional lecture hall. Course structure and multiple strategies to support student learning and encourage engagement are described in detail. Therefore, this case study could act as a model for others wishing to transform their own courses from lecture to a more student‐centered format. Student feedback about the course format was overwhelmingly positive and preliminary assessment data demonstrated student learning gains in several important areas. BIOCHEMISTRY AND MOLECULAR BIOLOGY EDUCATION, 2012

The Small Ubiquitin-Like Modifier (SUMO) and SUMO-Conjugating System of Chlamydomonas reinhardtii

The availability of the complete DNA sequence of the Chlamydomonas reinhardtii genome and advanced computational biology tools has allowed elucidation and study of the small ubiquitin-like modifier (SUMO) system in this unicellular photosynthetic alga and model eukaryotic cell system. SUMO is a member of a ubiquitin-like protein superfamily that is covalently attached to target proteins as a post-translational modification to alter the localization, stability, and/or function of the target protein in response to changes in the cellular environment. Three SUMO homologs (CrSUMO96, CrSUMO97, and CrSUMO148) and three novel SUMO-related proteins (CrSUMO-like89A, CrSUMO-like89B, and CrSUMO-like90) were found by diverse gene predictions, hidden Markov models, and database search tools inferring from Homo sapiens, Saccharomyces cerevisiae, and Arabidopsis thaliana SUMOs. Among them, CrSUMO96, which can be recognized by the A. thaliana anti-SUMO1 antibody, was studied in detail. Free CrSUMO96 was purified by immunoprecipitation and identified by mass spectrometry analysis. A SUMO-conjugating enzyme (SCE) (E2, Ubc9) in C. reinhardtii was shown to be functional in an Escherichia coli-based in vivo chimeric SUMOylation system. Antibodies to CrSUMO96 recognized free and conjugated forms of CrSUMO96 in Western blot analysis of whole-cell extracts and nuclear localized SUMOylated proteins with in situ immunofluorescence. Western blot analysis showed a marked increase in SUMO conjugated proteins when the cells were subjected to environmental stresses, such as heat shock and osmotic stress. Related analyses revealed multiple potential ubiquitin genes along with two Rub1 genes and one Ufm1 gene in the C. reinhardtii genome.

RNase One Gene Isolation, Expression, and Affinity Purification Models Research Experimental Progression and Culminates with Guided Inquiry-Based Experiments.

This new biochemistry laboratory course moves through a progression of experiments that generates a platform for guided inquiry‐based experiments. RNase One gene is isolated from prokaryotic genomic DNA, expressed as a tagged protein, affinity purified, and tested for activity and substrate specificity. Student pairs present detailed explanations of materials and methods and the semester culminates in a poster session. Experimental plans take into account the expense and time required to move from gene isolation to enzyme assays. This combination of instructor‐guided and student‐designed experiments is a manageable foray into guided inquiry‐based learning in a biochemistry laboratory course, while providing a cohesive story and context for individual experiments.

Probabilistic peak calling and controlling false discovery rate estimations in transcription factor binding site mapping from ChIP-seq.

Localizing the binding sites of regulatory proteins is becoming increasingly feasible and accurate. This is due to dramatic progress not only in chromatin immunoprecipitation combined by next-generation sequencing (ChIP-seq) but also in advanced statistical analyses. A fundamental issue, however, is the alarming number of false positive predictions. This problem can be remedied by improved peak calling methods of twin peaks, one at each strand of the DNA, kernel density estimators, and false discovery rate estimations based on control libraries. Predictions are filtered by de novo motif discovery in the peak environments. These methods have been implemented in, among others, Valouev et al.s Quantitative Enrichment of Sequence Tags (QuEST) software tool. We demonstrate the prediction of the human growth-associated binding protein (GABPalpha) based on ChIP-seq observations.

Use of a laboratory exercise on molar absorptivity to help students understand the authority of the primary literature

To promote understanding of the authority of the primary literature in students taking our biochemistry laboratory courses, a biochemistry laboratory exercise on the determination of an acceptable molar absorptivity value of 2‐nitrophenol (2‐NP) was developed. This made the laboratory course much more relevant by linking to a thematic thread, β‐galactosidase, that scaffolds concepts in one exercise with those in later exercises. The substrate for the continuous assay of β‐galactosidase is the chromogenic 2‐nitrophenyl‐β‐D‐galactopyranoside that produces 2‐NP. In an early laboratory exercise, students determine the wavelength of maximum absorption for the protonated and deprotonated form of 2‐NP at various pH values and then determine the molar absorptivity of 2‐NP. Students were encouraged to discuss apparent discrepancies not only in their own determinations of molar absorptivity values for 2‐NP, but also in the published molar absorptivity values for 2‐NP (2,150–21,300 M−1 cm−1) at almost the same pH and at 420 nm. Finally, the students were led to a publication that serves as an authentic source for molar absorptivity of 2‐NP.

Commentary: Biochemistry and Molecular Biology Educators Launch National Network.

From the †Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska, ‡Department of Biochemistry and Molecular Biology, University of Richmond, Richmond, Virginia, §Department of Biological Sciences, University of Alabama, Tuscaloosa, Alabama, |Biochemistry Department, North Carolina State University, Raleigh, North Carolina, ||Department of Molecular, Cellular and Developmental Biology, University of California Santa Barbara, California, and ¶Department of Chemistry and Biochemistry, University of Delware, Newark, Delware

Overcome inertia and publish your science education scholarship

For those of us who have been publishing research manuscripts for decades, it is relatively easy to make the transition to publishing a study or innovation in a science education journal. However, for junior science faculty, a foray into science education can be intimidating. There are few resources available to help junior faculty with the preparation of manuscripts [1, 2], and some are specific to other disciplines [3, 4]. Traditionally, the art of writing a manuscript for publication has been learned through an apprenticeship in research, but junior faculty may lack the confidence to initiate scholarship and submit a manuscript in the area of science education. The following is a dialog developed by a junior and senior instructor to explore the causes for inertia in developing and publishing science education scholarship. The intent is to stimulate more instructors to share the results of their innovations in journals such as BAMBED. How do I write a single author publication as a newcomer in the field? My past experience has been with multiple authors that contribute different expertise to the paper and who also participate in the many rounds of editing the paper. Usually only well established investigators write single author publications. For many junior faculty, this is a valid cause of inertia. They have worked as a graduate student or post doc with a senior professor who did not let them go very far in the wrong direction. You may have had writing a good manuscript and a submission letter modeled for you, but you did not have a chance to do it wrong and learn from the experience. This would be like learning to ride a bicycle and never suffering a fall. The key to overcoming a fear of doing it alone is to find a mentor, which every junior faculty member should have anyway. Find someone who knows the culture of your institution, with whom you feel comfortable, and who is willing to invest their time in you. When you have an idea for a project that could lead to a publication, share an outline with your mentor and talk over the project. Let them know what has already been published in this area and what journal you are thinking might be appropriate. Get their advice at the outset and communicate with them regularly. An additional tactic might be to find someone at your institution already active in science education scholarship and start to work with them. If you are at a small institution, you might look for someone at a neighboring university, or start attending the annual ASBMB meeting and networking with other faculty attending the education sessions. How much time should I anticipate for writing a single author paper? As for research, the writing time is very small relative to planning and conducting the study. Because most education is on an annual cycle, it is a bit like agricultural research. Agronomists plan for the next season, plant, cultivate, maintain proper fertilizer and water, harvest, determine yield, and analyze the data. If you intend research on student learning in classes, this will follow a similar cycle. Are education papers segmented into the usual introduction, material and methods, results and conclusion sections? What types of data are included in the material and methods sections? Are education papers usually similar in length to research publications? In some ways, there is no difference. Manuscripts in both arenas need to be original and significant. Without these two requisites, there is no justification for an editor to agree to publish your manuscript. Both types of manuscripts include a literature review to place the work in context and make it clear that the work is original and cites previous work upon which it builds. However, with a scientific research publication, there is as much emphasis on the details of your methods and their citation as on the results of the work. Also, many biochemists and molecular biologists are accustomed to quantitative data, whereas data used to document educational improvement is often affective data (measurement of feelings and emotions) on student response to the change in what was done. Positive increases in student affective response can be directly linked to increased student motivation and learning, but it is a type of data most of us have not previously used. A second difference from research publications, which focus on new understanding, is that education publications focus on learning. Do not confuse learning with teaching; our efforts should be focused on facilitating learning and not facilitating teaching. Also be aware that some learning situa‡ To whom correspondence should be addressed. Tel.: 4024722924; Fax: 4024727842. E-mail: jmarkwell2@unl.edu.