Gary R. Skuse

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.

Genomics Education Partnership

The Genomics Education Partnership offers an inclusive model for undergraduate research experiences, with students pooling their work to contribute to international databases.

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.

A Central Support System Can Facilitate Implementation and Sustainability of a Classroom-Based Undergraduate Research Experience (CURE) in Genomics

There have been numerous calls to engage students in science as science is done. A survey of 90-plus faculty members explores barriers and incentives when developing a research-based genomics course. The results indicate that a central core supporting a national experiment can help overcome local obstacles.

The role of computer science in undergraduate bioinformatics education

The successful implementation of educational programs in bioinformatics presents many challenges. The interdisciplinary nature of bioinformatics requires close cooperation between computer scientists and biologists despite inescapable differences in the ways in which members of these professions think. It is clear that the development of quality curricula for bioinformatics must draw upon the expertise of both disciplines. In addition, biologists and computer scientists can benefit from opportunities to carry out interdisciplinary research with one another. This paper examines the role of computer science in undergraduate bioinformatics education from the perspectives of two bioinformatics program directors. Their respective programs exemplify two substantively different approaches to undergraduate education in bioinformatics due to the fact that they are at markedly different institutions. One institution is a large, technical university, offering both undergraduate and graduate degrees in bioinformatics while the other is a small, Jesuit liberal arts college with an undergraduate program in bioinformatics. Despite these differences there is considerable overlap with respect to the role of computer science. This paper discusses the ways in which computer science has been integrated into these two undergraduate bioinformatics programs, compares alternative approaches, and presents some of the inherent challenges.

Developmentally regulated alternate modes of expression of the Gpdh locus of Drosophila.

Immunoblot analyses have been performed on extracts prepared from Drosophila melanogaster. Those analyses have revealed two subunit forms of enzyme glycerol 3‐phosphate dehydrogenase (GPDH) in larval tissues and in adult abdominal tissues. Thoracic tissue, which accounts for the bulk of the adult GPDH, has only one subunit form, the smaller. The two subunit forms differ by approximately 2400 daltons. In agreement with previous genetic and biochemical data indicating that this enzyme is encoded by a single structural gene, analyses of extracts prepared from a strain carrying a GPDH null mutation detect no GPDH polypeptides in larvae or adults. Similarly, analyses of extracts prepared from a strain carrying a mutation which produces a GPDH polypeptide that differs in size from wild‐type reveal a change in the adult thoracic GPDH polypeptide as well as a change in both GPDH polypeptides found in larvae. Total Drosophila RNA prepared from larvae or newly eclosed adults has been translated in a mRNA‐dependent cell‐free system. GDPH was immunoprecipitated from the translation products and analyzed. Two subunit forms of GPDH were immunoprecipitated from translation products whose synthesis was directed by larval RNA and only one was detected in the polypeptides synthesized from adult RNA. The GPDH polypeptides synthesized in vitro are approximately the same size as the corresponding polypeptides found in vivo. The relative proportion of total GPDH represented by each subunit form synthesized in vitro is similar to those found in vivo.(ABSTRACT TRUNCATED AT 250 WORDS)

Multidisciplinary Undergraduate Nano-Science, Engineering and Technology Course

Using basic fundamentals, engineering and science encompass continuously evolving technologies. In response to these changes and emerging opportunities, engineering and science curricula evolve revisiting program objectives, goals and outcomes. By integrating various disciplines and tools, nanotechnology-centered engineering and science provides a multidisciplinary approach to these needed curricula changes needed to meet societal challenges and industry needs. Extensive advances in biotechnology, electronics, energy sources, information technology and nanosystems, have brought new challenges to academia. As a result, many engineering and science schools have revised their curricula to offer relevant courses. At the RIT, a cross-listed (Electrical Engineering and Physics) multidisciplinary sophomore-level Nano-Science, Engineering and Technology (NanoSET) course has been developed and offered with support from the National Science Foundation. This course is offered as a restricted science elective within the Electrical Engineering curriculum, while students from various science and engineering departments can take the course as a science or free elective. This paper reports the course goals, objectives, emphasis, coverage, accomplishments, dissemination and assessment. Strategies for interactive team-teaching, material delivery and coverage are reported. We articulate our innovative practice and strategies for teaching nanotechnology inside and outside of the classroom through lectures, workshops and laboratories. We emphasize the need for large-scale coherent efforts in defining and developing nanotechnology at the college, institutional and multi-institutional levels. To pursue the nanotechnology-centered developments and educational innovations, a number of obstacles and impediments should need to be overcome, and serious long-term commitments are needed.

Bioinformatics Tools for Plant Genomics

The articles in this special issue reflect a convergence of developments in the fields of bioinformatics and plant genomics. Bioinformatics has its roots vaguely seated in the early 1980s, a time when personal computers began appearing in research laboratories and researchers began recognizing that those computers could be used as tools to organize, analyze and visualize their data. In the ensuing years bioinformatics tools began appearing at various sites including the European Molecular Biology Laboratory, the Molecular Biology Research Resource at the Dana-Farber Cancer Institute in the mid 1980s, the National Center for Biotechnology Information (NCBI) in 1988, the Genome Database Project at Johns Hopkins University in early 1989, and in countless laboratories throughout the world. These last efforts resulted in the development of many of the tools described in this special issue. Progress and interest in plant genomics have been accelerating since the time in late 2000 when the genome of Arabidopsis thaliana was published. Since then many genome sequencing projects have been undertaken that include poplar (Populus), grape (Vitis), the moss Physcomitrella, the biflagellate algae Chlamydomonas and several globally crucial crop plants such as corn (Maize) and rice (Oryza). However, as we have witnessed on numerous occasions, determining the sequence of a genome is only the first step toward understanding genome organization, gene structure, gene expression patterns, disease pathogenesis and a host of other features of both scientific and commercial interests. Computational tools of genomic annotation and comparative genomics must be applied to gain a useful understanding of any genome. In this special issue we present a collection of papers that together describe a powerful and impactful toolbox of applications and resources for plant genomic analysis. Among those articles you will find a description of research performed by the Mexican headquartered Generation Challenge Programme (GCP) which led to the GCP Platform (Bruskiewich et al.). This research support tool supports a number of data formats and web services and provides access to high performance computing facilities and platform-specific middleware collectively designed to support crop science research. Probably one of the most promising empirical tools for investigating gene expression developed in the last 15 or so years is that of microarray technology. While the technology has become commonplace, with tools for generating and hybridizing arrays available to all, the analysis of microarray-derived data has been challenging. Many laboratories have struggled not only with this challenge but also with the task of sorting through the plethora of analytical tools available in an effort to find the ones that may be best suited to their own work. In this issue there are two reviews by Page and Coulibaly which examine and describe bioinformatics tools for inferring functional information from plant microarray data. Together these papers step the reader through a collection of tools, and their applications, for analyzing the expression of single and multiple gene expression profiles. This theme of microarray analysis is continued in the description of the cross chip probe matching tool (CCPMT) by Page et al. Indeed it expands the readers horizons beyond the analysis of individual microarrays with the ability to associate probes across species. And of course, microarray analysis is facilitated by careful experimental design from the start so Robert Tempelman provides a review of statistical methods used to design efficient two-color microarray experiments. Taken together, these microarray papers provide an overview of the design of microarray experiments and the interpretation of the complex results of those experiments that will be informative for new and experienced laboratorians alike. Several other novel tools are described herein. One, Blast2GO is a suite of tools for the analysis and functional annotation of plant genomes (Conesa and Goetz). It provides an intuitive interface for identifying functional regions within DNA sequences. Another sequence analysis tool described by da Maia et al. is the SSR locator. That tool enables researchers to identify suitable targets for binding PCR primers in order to ensure that those targets are unique within the genome. It also assists with primer design and has a PCR simulator which facilitates comparisons of hypothetical amplification products among different species. Another challenge facing scientists today is the need to stay abreast of advances in a field that is progressing rapidly as a consequence of newly available technologies. In order to address this challenge there are two review articles that together provide insights into the discovery of relationships among a varied array of plant species. The first article, by Abdurakhmonov and Abdukarimov, describes the application of association mapping to understanding traits in crop species. Their work is directed toward novices within the crop breeding community in order to expose them to potential problems that they may face and solutions they may employ to overcome those problems. The second article describes the tools available for phylogenetic analyses and the increased use of Bayesian methods in those tools (Aris-Brosou and Xia). Constructing phylogenies has traditionally been a challenge to even the most experienced researcher but modern bioinformatics tools are lowering the bar for those interested in detecting adaptive evolution and estimating divergence among species. The wealth of information available to researchers today can be overwhelming. In order to address this potential, two papers describe information resources which consolidate and organize related information. PPNEMA is a database resource for those interested in plant-parasitic nematode ribosomal genes (Rubino et al.). That resource allows the user to browse, search and generally explore phytoparasite ribosomal DNA. A second database described in these pages is the MaizeGDB (Lawrence et al.). This resource contains information about Zea mays which includes genomic sequences as well as functional information and the tools to explore both. The body of the papers in this special issue represents the leading edge of plant genomics research. Together they provide the reader with descriptions of the tools and resources necessary to understand and promote advances in this important field. Gary R. Skuse Chunguang Du

Exploring the Role of Computer Science in the Liberal Arts (Abstract Only)

There is a growing body of evidence that indicates that many students would benefit from coursework in computer science regardless of their academic majors. While there are obvious advantages to learning computer science for students in the quantitative and analytical fields that comprise the STEM disciplines, the advantages to other students are less obvious. In order to investigate the impact of computer science principles and methods on students in the liberal arts we convened a workshop of faculty comprised of an equal number of participants from each discipline, i.e. computer science and the various liberal arts. We identified a clear need to better understand the computational needs of liberal arts students and faculty and we identified opportunities for computer scientists and liberal arts students and faculty to work together to better prepare students in both disciplines and better support faculty research in the liberal arts.

Recombinant Virus Vaccines

Vaccination is considered to be the most effective method of preventing infectious or other diseases. Adenovirus (Ad) is one the most promising vectors in vaccine research and development. It can induce not only potent humoral but also cellular immune responses, and has therefore been widely applied in basic and translational studies. Chimpanzee Ad is a rare serotype circulating in humans. This circumvents the problem of preexisting immunity to human Ad serotypes, enhancing Chimpanzee Ad prospects in vaccine development. Here we describe experimental procedures used to generate a new generation of rabies vaccine based on a chimpanzee Ad vector, which can be extended in the development of novel vaccines against other infectious diseases.