A. Center for Biological Transformation
May 1999
L. Nicholas Ornston, Director
The challenge for environmental bacteria is to minimize the toxicity of undesirable chemicals while maximizing opportunities for growth with desirable compounds. Toxic in high concentration, some chemicals may serve as growth substrates in diluted form. Such chemicals present bacteria with adversity that may be turned to advantage. The objective for the bacterium is to present barriers to adversity while fostering potential advantage. Much of this can be achieved at the outer membrane by selective filtration and at the inner membrane by pumping in what is beneficial and pumping out what is detrimental.
Viewed from this perspective, the core of nutritional versatility in bacteria becomes much more than a complex set of metabolic reactions. Physical as well as chemical responses are required to shifting conditions, and bacteria must anticipate both opportunity and hazard in their changing chemical environment. Evolution builds upon precedent, and the small genome size of bacteria makes it inevitable that different sets of responses have evolved in response to similar challenges. So analysis of the nutritional versatility of bacteria leads directly to a study of the origins of evolutionary diversity.
If a single theme emerges from this recent research, it is the fluidity of biological systems. DNA, often heralded as the secure store of genetic information, can undergo programmed loss or change. Enzymes can function despite seemingly major changes in their structure. One transport system can compensate for loss of function in another. Complex metabolic transformations that might be harmful inside the cell can be achieved outside the cell membrane. Emerging from these investigations are strategies that have been successfully applied by bacteria over the ages and that form a repository of knowledge for design of bacteria to meet novel challenges.
Publications:
1. Gerischer, U., A. Segura, and L. N. Ornston. 1998. PcaU, transcriptional activator of genes for protocatechuate utilization in Acinetobacter. J. Bacteriol. 180:1512-1524.
2. Kok, R. G., D. A. D’Argenio, and L. N. Ornston. 1998. Mutation analysis of PobR and PcaU, closely related transcriptional activators in Acinetobacter. J. Bacteriol. 180: 5058-5079.
3. Kok, R. G., D. M. Young, and L. N. Ornston. 1999. Phenotypic expression of PCR-generated random mutations in a Pseudomonas putida gene after its introduction into an Acinetobacter chromosome by natural transformation. Appl. Env. Microbiol. 65: 1675-1680.
4. A. Segura, P. V. Bünz, D. A. D’Argenio, and L. N. Ornston. 1999. Genetic analysis of a chromosomal region containing vanA and -B, genes required for conversion of either ferulate or vanillate to protocatechuate in Acinetobacter. J. Bacteriol. In Press
5. D. A. D’Argenio, A. Segura, W. M. Coco, P. V. Bünz, and L. N. Ornston. 1999. The physiological contribution of Acinetobacter PcaK, a transport system that acts upon protocatechuate, can be masked by the overlapping specificity of VanK. J. Bacteriol. In Press
B. Center for Computational Ecology (CCE)
May 1999
Oswald J. Schmitz, Acting Director
During the past year, The Center for Computational Ecology (CCE) maintained its high level of research productivity, producing ten research papers published in, or submitted to top peer-review journals.
Some of the products of the research (e.g., Gecko simulator for complex ecological systems) are available to researchers outside of Yale University to assist in their endeavors to model dynamics in their own specific systems. For example, researchers in the United Kingdom, in conjunction with CCE computer programmer Ginger Booth, have developed Bacsim, a second-generation version of Gecko which they used to do individual-based modeling of bacterial colony growth. More importantly, this research collaboration was done entirely electronically via the World Wide Web.
CCE has also moved vigorously forward to satisfy its teaching mission. It was awarded three separate grants (Howard Hughes, NECUSE and Yale ITS) to develop and implement teaching software to support existing science courses at Yale. The first phase of this initiative required the development of generic software that could be implemented in courses served over the Web. CCE programmer Ginger Booth designed and programmed CourseWare, a generic software platform that facilitates the implementation of simulation programs for specific class assignments. CourseWare not only runs specific simulations, it also produces graphical output to display data from the simulations and can be viewed at http://frog.biology.yale.edu/ginger/java/index.html. The intent of this software is to allow different science courses to develop assignments that complement material covered in a lecture, and implement those assignments with minimal up-front software development each time a new course is developed. The idea to serve the assignments over the Web is based on the idea that students should have freedom to access the assignments at any time and place. Also, they should have complete freedom to explore and play with assignments outside the strict confines of a protracted weekly lab meeting. This represents a fundamental move toward greater self-directed learning. Funding was also used to implement Community Ecology Lab Assignments in CourseWare. This was completed at the end of December. The web-served lab assignments were implemented this past winter in the School of Forestry and Environmental Studies (F&ES) course number 563/Department of Ecology and Evolutionary Biology (EEB) course number 340, Community Ecology. F&ES/EEB Professor Oswald Schmitz taught Community Ecology with very promising success.
The goals of CCE for the upcoming year are: to continue with research progress on modeling problems of scaling in complex systems; to develop additional laboratory assignments in CourseWare to support Landscape Ecology taught by F&ES/EEB Professor D.K. Skelly; and to begin to offer small grants and fellowships to support graduate student research in CCE.
C. Center for Earth Observation (CEO)
May 1999
Ron Smith, Director
The Yale Center for Earth Observation (CEO) was formed in 1992 as one of the original Yale Institute for Biospheric Studies’ (YIBS) Centers. With two full time staff members, CEO supports remote sensing research and mapping activities of Yale students, faculty and staff, as well as assisting regional organizations. The current CEO steering committee members are Ronald Smith, Department of Geology and Geophysics (G&G), Frank Hole, Department of Anthropology, Xuhui Lee, Yale School of Forestry and Environmental Studies (F&ES), and Durland Fish, Department of Epidemiology and Public Health (EPH).
Activities:
1) The summer and fall of 1998 was the transitional period for the new CEO computer system. This system, two SGI servers and eight SGI workstations, were purchased with funds from a NASA Centers of Excellence Grant awarded in the previous year. With new documentation and software added during the fall semester, the capability of CEO's remote sensing analysis system ranks as one of the best in the country.
2) The largest research project at CEO, the South West Asia Project (SWAP), entered its third year in 1999. This NASA-funded project examines the changing landscape and related water resources of the Middle East using a variety of remote sensing methods. Center staff sponsored a Workshop on Remote Sensing in the Middle East in Aleppo, Syria in November 1998, in cooperation with the International Center for Agricultural Research in Dry Areas. Other active CEO projects include risk factors for Lyme disease, agroforestry in Africa, and coastal wind dynamics.
3) After a year's break, the course Observing the Earth from Space was offered in the spring term (1999). The student enrollment of 35 included about 18 from the F&ES Master's program as well as graduate and undergraduate students from G&G, Anthropology, Economics, Astronomy and Studies in the Environment. Student project topics included ocean productivity, Quinnipiac River watershed, deforestation in Africa, erosion in the Alps, carbon cycle dynamics, Cambodia burial sites, fruit bat ecosystems, Gulf Stream eddies, Malaria in Australia, Suburban sprawl, dust storms, and mangrove changes in Indonesia. Oral reports of the projects were given on April 29, 1999.
CEO faces several challenges in the coming year. It must meet the growing student demand for remote sensing courses and project assistance and prepare for the onslaught of new remote sensing data sets in 1999 and beyond, from the suite of EOS satellites. It must broaden the remote sensing expertise of the Yale faculty so that the innovative teaching and research programs made possible by CEO are more fully explored.
In May of 1999, CEO will move from Bingham Laboratory to Kline Geology Laboratory in rooms 103 and 116. CEO will occupy these quarters until new space in the Environmental Sciences Facility is completed in mid 2001.
Further information about CEO is available from Mr. L. Bonneau at (203) 432-3142, or from its website at http://www.stormy.geology.yale.edu/ceo.html.
