Highlights

ASM/JGI Functional Genomics Institute: Connecting Bioinformatics-Driven Hypotheses to Wet-Lab Projects

Overview

The ASM/JGI Functional Genomics Institute aims to meet the need for more undergraduate faculty in science, technology, engineering, and math (STEM) disciplines to involve their students in hands-on experiences in molecular genetics and to relate that work to ongoing functional genomics research. The Institute features the functional analysis of microbial genomes through forward genetics, reverse genetics and protein expression approaches, connecting functional information to genome annotations, and providing a framework for developing classroom activities and research projects for undergraduate students.

At the completion of the Institute, participants will take home a working knowledge of several experimental strategies and a strengthened ability to connect scientific questions to learning goals and pertinent functional genomics projects. As participants begin to use the skills and ideas they gain at the Institute back at their home institutions, several measurable outcomes should be generated or enhanced. In terms of students, more of them will:

• Understand the role of scientific research and the process through which it occurs

• Use one or more functional genomics approaches to connect genes to cellular functions

• Seek out independent research opportunities

Faculty should see increased student engagement in course material and find it easier to incorporate (i) discussions of research into courses and (ii) their own research ideas into courses. All of this increased engagement by students and faculty will allow them to see that educational goals can be met while still generating meaningful scientific results, such as testing bioinformatics-driven predictions of gene functions, discovering new cellular functions and the corresponding genes, discriminating the functional importance of multiple potentially redundant genes, and adding a much deeper understanding to the annotation of microbial genomes.

Audience

The Institute is directed to STEM faculty who teach undergraduate courses at community colleges, 4-year colleges, and research universities and who are ready to connect bioinformatics-driven hypotheses to wet-lab projects within one or more of their courses.  Some previous training or background knowledge in bioinformatics and the genomic sciences is preferred, but by no means do you have to be a genomics expert to attend.  Interest and enthusiasm in the goals of the institute are much more important. Faculty participants will have opportunities to address the following questions:

• You find two genes in a given microbial genome annotated to do the same job. How can you test such a hypothesis?

• A given cellular function appears to be missing in a given genome while all the other steps of the pathway are present – how might you go about finding the missing gene through wet lab experiments?

• Do you know how to construct a targeted gene disruption or knockout in a microbial genome?

• How do you go about overexpressing a protein for enzymatic or crystallographic analysis?

Participation in the Institute is by application. Applicants must be currently teaching full time at U.S.-accredited institutions of higher education.

Goals

The goals of the program are to:

• Introduce participants to questions related to functional genomics as they apply to specific teaching situations and to the experimental strategies and lab tools available to address those questions

• Introduce participants to the theoretical basis for and experimental strategies involved in reverse genetics (gene disruptions), forward genetics (transposon mutagenesis), functional complementation, and protein overexpression                                                                    
• Introduce participants to several model microbial systems for functional genomics analysis

• Immerse participants in the details of running functional genomics experiments within  a laboratory course format in terms of timing, outcomes, and assessment

• Help participants form a learning network that will continue to foster their future experiences with and uses of functional genomics in their courses

Outcomes

Participants will leave with:

• Working knowledge of experimental strategies and techniques for gene disruption/knockout, transposon mutagenesis, functional complementation, and protein overexpression                                                                                                                                    
• Working knowledge of how to connect bioinformatics-driven gene predictions to lab-derived experimental results

• Experience with connecting biological questions of interest to learning concepts, skills training, and experimental tools to address pertinent questions

• Curriculum activities, problem sets, course exercises, and/or research projects that can (i) be incorporated into courses immediately and (ii) engage students

• A network of colleagues to help with brainstorming, troubleshooting, and refining new uses of bioinformatics in undergraduate education

Institute Faculty

Brad Goodner, Hiram College, Hiram, OH

Chris Kvaal, Saint Cloud State University, Saint Cloud, MN

Steve Slater, University of Wisconsin, Madison, WI

Kathleen (KT) Scott, University of South Florida, Tampa, FL

Format

Through the combination of plenary sessions, small-group lab projects, and discussions, the Institute will provide hands-on lab experiences in functional genomics, and the strategies, tools, model organisms, and bioinformatics resources for developing classroom activities and research projects. Discussion, skills training and practice, and pedagogical advice will be provided. All participants will become part of a larger community of practice to advance interdisciplinary training through bioinformatics and genomic sciences.

Requirements for Participation

Upon acceptance to the Institute, participants will be required to

• Complete three to five pre-Institute readings and assignments

• Participate in a follow-up session within 10 to 18 months after the Institute at the ASM Conference for Undergraduate Educators (ASMCUE)

• Present a poster at ASMCUE about a new bioinformatics curriculum activity within 2 years of completing the Institute

• Submit for publication a curriculum activity enhancing students’ learning about bioinformatics either to the ASM MicrobeLibrary curriculum collection or to another national digital library of peer-reviewed resources

• Participate in longitudinal studies to ascertain the effectiveness of such training

The preparatory work is required, as it provides a solid foundation for enhancing a participant's training and for benefiting from the Institute. Participants are asked to bring their own laptop computers to the Institute for preparing and sharing their work.

The follow-up work is also required, as it ensures that such professional development results in the advancement of bioinformatics training across the undergraduate curriculum through presentations and publications.

Sponsorship and Credentials

The ASM/DOE-JGI Bioinformatics Institute is managed by the American Society for Microbiology and sponsored by the U.S. Department of Energy Joint Genome Institute and Hiram College.

The American Society for Microbiology is a recipient of the 2000 Carnegie Foundation for the Advancement of Teaching Award and was recognized by President Clinton with the 2000 Presidential Award for Excellence in Mentoring in Science, Mathematics, and Engineering Education for its contribution to education in the sciences and engineering.

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