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      A Broadly Implementable Research Course in Phage Discovery and Genomics for First-Year Undergraduate Students

      a , b , c ,   d , e , f , g , h , i , j , k , l , m , n , o , p , p , q , r , s , t , u , v , w , x , d , j , h , y , w , z , aa , aa , bb , bb , bb , cc , dd , aa , bb

      mBio

      American Society of Microbiology

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          There is no author summary for this article yet. Authors can add summaries to their articles on ScienceOpen to make them more accessible to a non-specialist audience.

          ABSTRACT

          Engaging large numbers of undergraduates in authentic scientific discovery is desirable but difficult to achieve. We have developed a general model in which faculty and teaching assistants from diverse academic institutions are trained to teach a research course for first-year undergraduate students focused on bacteriophage discovery and genomics. The course is situated within a broader scientific context aimed at understanding viral diversity, such that faculty and students are collaborators with established researchers in the field. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunters Advancing Genomics and Evolutionary Science (SEA-PHAGES) course has been widely implemented and has been taken by over 4,800 students at 73 institutions. We show here that this alliance-sourced model not only substantially advances the field of phage genomics but also stimulates students’ interest in science, positively influences academic achievement, and enhances persistence in science, technology, engineering, and mathematics (STEM) disciplines. Broad application of this model by integrating other research areas with large numbers of early-career undergraduate students has the potential to be transformative in science education and research training.

          IMPORTANCE

          Engagement of undergraduate students in scientific research at early stages in their careers presents an opportunity to excite students about science, technology, engineering, and mathematics (STEM) disciplines and promote continued interests in these areas. Many excellent course-based undergraduate research experiences have been developed, but scaling these to a broader impact with larger numbers of students is challenging. The Howard Hughes Medical Institute (HHMI) Science Education Alliance Phage Hunting Advancing Genomics and Evolutionary Science (SEA-PHAGES) program takes advantage of the huge size and diversity of the bacteriophage population to engage students in discovery of new viruses, genome annotation, and comparative genomics, with strong impacts on bacteriophage research, increased persistence in STEM fields, and student self-identification with learning gains, motivation, attitude, and career aspirations.

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          Most cited references 54

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          Improved microbial gene identification with GLIMMER.

          The GLIMMER system for microbial gene identification finds approximately 97-98% of all genes in a genome when compared with published annotation. This paper reports on two new results: (i) significant technical improvements to GLIMMER that improve its accuracy still further, and (ii) a comprehensive evaluation that demonstrates that the accuracy of the system is likely to be higher than previously recognized. A significant proportion of the genes missed by the system appear to be hypothetical proteins whose existence is only supported by the predictions of other programs. When the analysis is restricted to genes that have significant homology to genes in other organisms, GLIMMER misses <1% of known genes.
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            The generic genome browser: a building block for a model organism system database.

            The Generic Model Organism System Database Project (GMOD) seeks to develop reusable software components for model organism system databases. In this paper we describe the Generic Genome Browser (GBrowse), a Web-based application for displaying genomic annotations and other features. For the end user, features of the browser include the ability to scroll and zoom through arbitrary regions of a genome, to enter a region of the genome by searching for a landmark or performing a full text search of all features, and the ability to enable and disable tracks and change their relative order and appearance. The user can upload private annotations to view them in the context of the public ones, and publish those annotations to the community. For the data provider, features of the browser software include reliance on readily available open source components, simple installation, flexible configuration, and easy integration with other components of a model organism system Web site. GBrowse is freely available under an open source license. The software, its documentation, and support are available at http://www.gmod.org.
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              Gepard: a rapid and sensitive tool for creating dotplots on genome scale.

              Gepard provides a user-friendly, interactive application for the quick creation of dotplots. It utilizes suffix arrays to reduce the time complexity of dotplot calculation to Theta(m*log n). A client-server mode, which is a novel feature for dotplot creation software, allows the user to calculate dotplots and color them by functional annotation without any prior downloading of sequence or annotation data. Both source codes and executable binaries are available at http://mips.gsf.de/services/analysis/gepard
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                Author and article information

                Journal
                mBio
                MBio
                mbio
                mbio
                mBio
                mBio
                American Society of Microbiology (1752 N St., N.W., Washington, DC )
                2150-7511
                4 February 2014
                Jan-Feb 2014
                : 5
                : 1
                Affiliations
                [ a ]College of Arts and Sciences, Lewis and Clark College, Portland, Oregon, USA
                [ b ]Department of Microbiology and Molecular Biology, Brigham Young University, Provo, Utah, USA
                [ c ]Biotechnology Program and Department of Plant and Microbial Biology, North Carolina State University, Raleigh, North Carolina, USA
                [ d ]Department of Biological Sciences, University of Maryland, Baltimore County, Baltimore, Maryland, USA
                [ e ]Technology Leadership and Innovation, Agricultural and Biological Engineering, Purdue University, West Lafayette, Indiana, USA
                [ f ]Department of Biology, Calvin College, Grand Rapids, Michigan, USA
                [ g ]Department of Biology, Queens College and the Graduate Center of the City University of New York, Flushing, New York, USA
                [ h ]Department of Zoology, Oregon State University, Corvallis, Oregon, USA
                [ i ]Department of Biology, Cabrini College, Radnor, Pennsylvania, USA
                [ j ]Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
                [ k ]Department of Biology, University of Louisiana at Monroe, Monroe, Louisiana, USA
                [ l ]Department of Basic Pharmaceutical Sciences, University of Louisiana at Monroe, Monroe, Louisiana, USA
                [ m ]Department of Biology Sciences and Geology, Queensborough Community College, City University of New York, New York, New York, USA
                [ n ]Department of Molecular, Cellular and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado, USA
                [ o ]Department of Molecular, Cell and Developmental Biology, University of California, Santa Cruz, California, USA
                [ p ]Department of Biology, North Carolina Central University, Durham, North Carolina, USA
                [ q ]Department of Biological Sciences, University of North Texas, Denton, Texas, USA
                [ r ]Center for the Study of Biological Complexity, Virginia Commonwealth University, Richmond, Virginia, USA
                [ s ]Department of Biology, Western Kentucky University, Bowling Green, Kentucky, USA
                [ t ]Department of Biological Sciences, University of Mary Washington, Fredericksburg, Virginia, USA
                [ u ]Master of Physician Assistant Studies Program, Indiana University, Indianapolis, Indiana, USA
                [ v ]Department of Biological Sciences, University of Montana, Missoula, Montana, USA
                [ w ]Department of Biology, University of Puerto Rico at Cayey, Cayey, Puerto Rico
                [ x ]Department of Biology, College of William and Mary, Williamsburg, Virginia, USA
                [ y ]Department of Integrated Science and Technology, James Madison University, Harrisonburg, Virginia, USA
                [ z ]Department of Biological Sciences, Lehigh University, Bethlehem, Pennsylvania, USA
                [ aa ]Undergraduate and Graduate Science Education, Howard Hughes Medical Institute, Chevy Chase, Maryland, USA
                [ bb ]Department of Biological Sciences, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
                [ cc ]Department of Biology, James Madison University, Harrisonburg, Virginia, USA
                [ dd ]Department of Psychology, Grinnell College, Grinnell, Iowa, USA
                Author notes
                Address correspondence to Cheryl P. Bailey, baileyc@ 123456hhmi.org , or Graham F. Hatfull, gfh@ 123456pitt.edu .

                Editor Richard Losick, Harvard University

                Article
                mBio01051-13
                10.1128/mBio.01051-13
                3950523
                24496795
                Copyright © 2014 Jordan et al.

                This is an open-access article distributed under the terms of the Creative Commons Attribution-Noncommercial-ShareAlike 3.0 Unported license, which permits unrestricted noncommercial use, distribution, and reproduction in any medium, provided the original author and source are credited.

                Page count
                Pages: 8
                Categories
                Research Article
                Custom metadata
                January/February 2014

                Life sciences

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