Kari Clase

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

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. 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.

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 Survey of Scholarly Literature Describing the Field of Bioinformatics Education and Bioinformatics Educational Research

This article provides an overview of the state of research in bioinformatics education in the years 1998 through 2013. It identifies current curricular approaches for integrating bioinformatics education, concepts and skills being taught, pedagogical approaches and methods of delivery, and educational research and evaluation results.

FGF5 stimulates expansion of connective tissue fibroblasts and inhibits skeletal muscle development in the limb

FGF5 is expressed in the mesenchyme and skeletal muscle of developing and adult mouse limbs. However, the function of FGF5 during development of the limb and limb musculature is unknown. To elucidate the inherent participation of FGF5 during limb organogenesis, a retroviral delivery system (RCAS) was used to overexpress human FGF5 throughout developing hind limb of chicken embryos. Misexpression of the soluble growth factor severely inhibited the formation of mature myocytes. Limbs infected with RCAS‐FGF5 contained smaller presumptive muscle masses as evidenced by a decrease in MyoD and myosin heavy chain expressing cells. In contrast, ectopic expression of FGF5 significantly stimulated proliferation and expansion of the tenascin‐expressing, connective‐tissue fibroblast lineage throughout the developing limb. Histological analysis demonstrated that the increase in tenascin immunostaining surrounding the femur, ileum, and pubis in the FGF5 infected limbs corresponded to the fibroblasts forming the stacked‐cell perichondrium. Furthermore, pulse labeling experiments with the thymidine analog, BrdU, revealed that the increased size of the perichondrium was attributable to enhanced cell proliferation. These results support a model whereby FGF5 acts as a mitogen to stimulate the proliferation of mesenchymal fibroblasts that contribute to the formation of connective tissues such as the perichondrium, and inhibits the development of differentiated skeletal muscle. These results also contend that FGF5 is a candidate mediator of the exclusive spatial patterning of the hind limb connective tissue and skeletal muscle.

Cluster M mycobacteriophages Bongo, PegLeg, and Rey with unusually large repertoires of tRNA isotypes

ABSTRACT Genomic analysis of a large set of phages infecting the common host Mycobacterium smegmatis mc2155 shows that they span considerable genetic diversity. There are more than 20 distinct types that lack nucleotide similarity with each other, and there is considerable diversity within most of the groups. Three newly isolated temperate mycobacteriophages, Bongo, PegLeg, and Rey, constitute a new group (cluster M), with the closely related phages Bongo and PegLeg forming subcluster M1 and the more distantly related Rey forming subcluster M2. The cluster M mycobacteriophages have siphoviral morphologies with unusually long tails, are homoimmune, and have larger than average genomes (80.2 to 83.7 kbp). They exhibit a variety of features not previously described in other mycobacteriophages, including noncanonical genome architectures and several unusual sets of conserved repeated sequences suggesting novel regulatory systems for both transcription and translation. In addition to containing transfer-messenger RNA and RtcB-like RNA ligase genes, their genomes encode 21 to 24 tRNA genes encompassing complete or nearly complete sets of isotypes. We predict that these tRNAs are used in late lytic growth, likely compensating for the degradation or inadequacy of host tRNAs. They may represent a complete set of tRNAs necessary for late lytic growth, especially when taken together with the apparent lack of codons in the same late genes that correspond to tRNAs that the genomes of the phages do not obviously encode. IMPORTANCE The bacteriophage population is vast, dynamic, and old and plays a central role in bacterial pathogenicity. We know surprisingly little about the genetic diversity of the phage population, although metagenomic and phage genome sequencing indicates that it is great. Probing the depth of genetic diversity of phages of a common host, Mycobacterium smegmatis, provides a higher resolution of the phage population and how it has evolved. Three new phages constituting a new cluster M further expand the diversity of the mycobacteriophages and introduce novel features. As such, they provide insights into phage genome architecture, virion structure, and gene regulation at the transcriptional and translational levels.

Calibrated peer review for computer‐assisted learning of biological research competencies

Recently, both science and technology faculty have been recognizing biological research competencies that are valued but rarely assessed. Some of these valued learning outcomes include scientific methods and thinking, critical assessment of primary papers, quantitative reasoning, communication, and putting biological research into a historical and broader social context. This article presents examples of Calibrated Peer Review (CPR) assignments that illustrate a computer‐assisted method to help students achieve biological research competencies. A new release of CPR is appropriate for engaging students online in reading and writing about investigations. A participant perception inventory was designed for use as a repeated measure to discriminate among beginning, middle, and ending student perceptions. Examples are provided to demonstrate how to assess student perceptions of what they gain from instruction related to science research competencies. Results suggest that students in a large enrollment class consider CPR to be useful for helping them learn about quantitative and categorical research variables; the use of the experimental method to test ideas; the use of controls; analysis, interpretation, and presentation of data; and how to critically read primary papers.

Demand for interdisciplinary laboratories for physiology research by undergraduate students in biosciences and biomedical engineering

Physiology as a discipline is uniquely positioned to engage undergraduate students in interdisciplinary research in response to the 2006-2011 National Science Foundation Strategic Plan call for innovative transformational research, which emphasizes multidisciplinary projects. To prepare undergraduates for careers that cross disciplinary boundaries, students need to practice interdisciplinary communication in academic programs that connect students in diverse disciplines. This report surveys policy documents relevant to this emphasis on interdisciplinary training and suggests a changing role for physiology courses in bioscience and engineering programs. A role for a physiology course is increasingly recommended for engineering programs, but the study of physiology from an engineering perspective might differ from the study of physiology as a basic science. Indeed, physiology laboratory courses provide an arena where biomedical engineering and bioscience students can apply knowledge from both fields while cooperating in multidisciplinary teams under specified technical constraints. Because different problem-solving approaches are used by students of engineering and bioscience, instructional innovations are needed to break down stereotypes between the disciplines and create an educational environment where interdisciplinary teamwork is used to bridge differences.

Work in progress - engagement through a dual credit initiative resulting in collaborative partnerships to create pre-engineering biotechnology curriculum for the high school classroom

A need exists to develop pathways between high schools and universities to facilitate the education of students within Science, Technology, Engineering, and Mathematics (STEM) disciplines. In response to recent legislation, a pilot program has been implemented by Purdue University to develop dual credit courses within local high schools and establish specific criteria to insure that the courses taken in high school are equivalent to the university courses. The pilot program is building upon Project Lead the Way (PLTW), a pre-engineering program for high school students recently cited as a model curriculum within the study, “Rising Above the Gathering Storm: Energizing and Employing America for a Brighter Economic Future,” sponsored by the National Academies to outline strategies to raise American education and remain competitive in the new global marketplace. The PLTW curriculum offers students the opportunity to complete college credit in high school and includes intensive summer training to enhance teachers abilities to teach engineering concepts in the classroom. This project can serve as a model to establish collaborative foundations between high school teachers and university faculty resulting in innovative curriculum development and smooth articulation between high schools and universities.

Improving Students’ Representational Competence through a Course-Based Undergraduate Research Experience

Visual representations are integral for communicating abstract science concepts and promoting insights for new scientific discoveries. Students’ representational competence is positively correlated with problem solving in the sciences and subsequent improvements in academic performance. We explored how students’ participation in the authentic practice of science with the use of visual representations would impact representational competence. We further tested a model of representational competence to understand how the use of student-generated representations in a Course-Based Undergraduate Research Experience (CURE) revealed undergraduate thinking about biological content, scientific literacy and the process of science. In this mixed methods study, we found that the applied theoretical framework could be used to effectively describe students’ representational competence. We observed all seven levels of representational competence with annotated genomes. In this chapter, we present rich descriptions of each level, including connections between content and scientific practice revealed by analysis of 147 student-generated representations. Additionally, we found that students’ competencies significantly improved after participation in the CURE. Our framework to examine representational competence can be used as a novel way to reveal changes in scientific thinking and examine the impact of undergraduate research experiences.

An Education Strategy to Respond to Medicine Inequality in Africa

People living in Africa face a heavy and wide-ranging burden of disease that takes an incalculable toll on social and economic development as well as shortening life expectancy (life expectancy in Tanzania is about 60 vs. about 80 in the United States and Europe. Further, the pharmaceutical market in developing countries is immature and may not support quality medicines. In many cases, a tender system is used, and medicines are bought by the government at the lowest price. In addition to access to medicines, a number of pharmaceutical sciences problems are apparent. The availability of infrastructure and especially standard instruments such as HPLC and X-ray diffraction is minimal. Additionally, there is an important need to increase access to advanced education for men and women in Africa, especially access to state-of-the-art scientific education. Utilizing the mandate of Nelson Mandela, Purdues conceptual approach has been to utilize education to combat these problems.