Genome Consortium for Active Teaching (GCAT)

by A. Malcolm Campbell

Davidson College Biology Department

Genomics is a new frontier in biology that is leading to basic and biomedical discoveries never imagined five years ago. These dramatic discoveries have made it clear that undergraduates need to understand genomics and bioinformatics and liberal arts institutions are poised to develop these curricular innovations. I applying for an ACS Technology Fellowship for summer salary to help me launch a new non-profit educational consortium that would be the first of its kind. The Genome Consortium for Active Teaching (GCAT; www.bio.davidson.edu/biology/gcat/gcat.html) is designed to promote the use of genome technology in undergraduate teaching and research. Creating and successfully running GCAT will require a lot of time and resources. I have been granted a year-long sabbatical that will begin in the fall of 2000 and I am submitting several grant applications to support different aspects of this project. During the summer of 2000, I propose to develop the necessary web pages that will be the gateway for Members of GCAT. For the development of the web pages, I am seeking summer salary from ACS since I am on a 10 month contract and my sabbatical pay does not begin until August 1.

What is GCAT? GCAT would be the first organization to encourage the introduction of genomic methods into the undergraduate curriculum. As the potential of GCAT is realized, collaboration among ACS biology faculty could further enhance the effectiveness of GCAT and ACS. GCAT would permit undergraduate faculty to use DNA microarrays (or DNA chips) for their teaching and student-based research. Dr. Patrick Brown can produce DNA chips for the genome of the yeast S. cerevisiae where all 6500 genes are spotted on microscope slides in an area that fits under a cover slip (Chu et al., Science 282: 699-705, 1998). These chips are used in combination with fluorescently labeled cDNA from cells grown under two different conditions to examine how gene regulation differs under these two conditions. For example, one might want to know what happens when yeast cells are grown anaerobically vs. aerobically (beer vs. bread). RNA is isolated from cells in each growth condition and cDNA is tagged with green or red fluorophores, respectively. The tagged cDNAs are mixed and hybridized with the DNA chip. A series of green, red and yellow spots result that reveal which genes are transcribed in each condition or both conditions. Data are collected quantitatively with a chip reader. Dr. Brown has agreed to produce 144 slides for GCAT at cost (about $5.00 each). I have secured support from several companies which have agreed to read chips for GCAT members for free. The success of GCAT will depend upon effective utilization of technology, including the internet.

The Project

Development of Curricular Material with Technology Focus The project for which I am requesting support is to develop the web gateway to GCAT. In addition to the key role played by DNA chips and the chip reader, GCAT will depend upon two other technology-based tools; the web and email. The web will be the principle means for providing information about GCAT and functional genomics. From the GCAT Home Page will be links to:

1) Flash-animated tutorials to illustrate the methods used to determine which genes are active within an organism.

2) A form where interested undergraduate faculty can register. On this form, faculty would provide their contact information, list the course(s) which would use the DNA chips, prerequisites for the course, and enrollment numbers. GCAT members will provide the URL where their experimental design and protocols, raw data, and student analysis of these data will be posted for others to read. Faculty will have the option of submitting their email addresses for use in a general GCAT listserv and/or participating as a person novices can email for technical support. Finally, there will be a way to delete one's own name from these lists.

3) A list of URLs with genomics and bioinformatics related research information. This list would be accompanied by brief descriptions of each site and be updated regularly.

4) A list of URLs with course materials that are related to genomics and bioinformatics. This list would be accompanied by brief descriptions of each site and would be added to the ACS online Biology laboratory index currently under development.

Potential Application at Other ACS Schools GCAT, and its web gateway, is designed specifically for use at many different biology departments. The very nature of GCAT is one of a cooperative where members help each other learn this new technology and how to apply it to teaching. Although DNA chips are a powerful new tool that is drastically reshaping biology, a DNA chip reader is too expensive for each ACS biology department to buy its own, especially since it would be used only a few times each year. Therefore, GCAT will become a core facility at Davidson College, that promotes technological improvements for other ACS biology faculty members.

Once GCAT is operational, I would like to offer a course for ACS faculty (proposal to be submitted in two to three years). This course would be conducted at Davidson College and would provide faculty with hands-on experience with DNA chips and how they can be used in courses. I think this ACS course would be extremely helpful in the development of genomics in ACS biology departments.

Technical Requirements of Project I am very well equipped to design the web pages and the Flash animations. I have attended two ACS web workshops and am the webmaster for my department's web server. My only technical limitation is finding and modifying the appropriate cgi and Perl scripts. I have some experience with these applications from my attendance of an ACS workshop at Furman University in 1998. Examples of my web development skills can be viewed at these URLs:

Institutional Support The Davidson College Biology Department has supported the development of GCAT in several ways. First, Drs. David Wessner and Karen Bernd have agreed to assist me in running GCAT. Second, in October, the Department will submit a grant proposal to HHMI which includes requests for several genomics-related devices, including a DNA chip reader. Finally, the Department and the Educational Policy Committee have endorsed my proposal to develop a new course called "Genomics and Bioinformatics". This course will be voted upon by the entire Davidson College faculty on October 5. Therefore, GCAT is an integral part of a departmental curriculum improvement to provide students with training in genomics and bioinformatics.

The College has granted me a sabbatical year to develop the proposed course Genomics and Bioinformatics. During this time, I will spend a year in the laboratory of Dr. Leroy Hood at the University of Washington in Seattle. In short, I have obtained enthusiastic support at all levels of the College for the development of the new course and GCAT.

How and When Will the Project be Integrated into the Curriculum? The web gateway to GCAT will be integrated into the curriculum in several ways. First, Dr. Wessner will use DNA chip technology in his microbiology course which is taught every other year. Second, Dr. Karen Bernd will use DNA chip technology in her Cell Biology course which is taught every year. I will use DNA chip technology in the proposed course Genomics and Bioinformatics. All three of us might use DNA chips in our personal research as well. Finally, Davidson College will hire two new tenure-track biologists who will begin in the fall of 2000. One will be a geneticist and the other will be a developmental biologist. Both Genetics and Development could benefit from the use of DNA chips for student labs and faculty research.

It is difficult to know exactly when DNA chip technology will be worked into each of these courses. The only course I can be certain of is my Genomics and Bioinformatics course which will be offered for the first time in the fall semester of 2001. The Cell Biology laboratory curriculum focuses on signaling during the yeast mating reaction. Dr. Karen Bernd is enthusiastic about including cutting-edge DNA chip technology to investigate this process which is controlled by gene activation and inhibition.

How will the project enhance teaching and/or student learning? GCAT will dramatically enhance both teaching and student learning. As all science faculty know, the best way to teach science is to have students do science. Students cannot do genomics without the use of DNA chips. The web gateway will enable faculty from ACS institutions to incorporate genomic technology into their courses more rapidly. The gateway will also facilitate the use of bioinformatics in classes as well. I am unaware of any undergraduate institution that has a DNA chip reader so providing one as a part of a core facility will permit ACS faculty to develop teaching labs that utilize the latest and most powerful methods developed for the human genome project. ACS biology faculty will be able to collaborate on genomics curriculum development when most colleges still have not incorporated into their curriculum any aspect of this new revolution in biology.

Mechanism for Assessment I have begun to utilize assessment in my courses. For example, I use a program called WebAssign to generate quizzes and problem sets that are automatically graded. I use this to conduct pre- and post-laboratory surveys to determine if students are learning the key concepts during labs. However, the purpose of GCAT is different since it is designed to be shared with faculty at other institutions. Therefore, assessment will also be conducted by surveying GCAT membership and monitoring the number of hits on GCAT web pages.

How will results of the project be shared with colleagues at other ACS institutions? As explained above, I will contact ACS biology departments a second time to invite them to participate in the first year of GCAT. As GCAT matures and becomes more productive for teachers, I will update ACS biology departments on GCAT’s utility and encourage them to participate if they have not already done so. To contact the schools, I will utilize the ACS Biology Home Page developed during the summer of 1999 and post GCAT information in the ACS Online Biology Laboratory Index.

What technical expertise will be sought from ACS institutions (including Davidson)? I will need assistance from webmasters and faculty who are familiar with Macintoshes. I need to learn how to enable our Macintosh/WebStar server to serve cgi and Perl scripts. I would also like to solicit help from Suzanne Bonefas who has experience with creating web databases that can be updated by different users. Finally, I will solicit help from the Physics and Math Departments at Davidson College where there are many faculty who can help me with modifying public domain cgi and Perl scripts.