YIBS 1999-2000 Annual Report

IV.  YIBS RESEARCH CENTERS

A.  The Center for Biological Transformation Report, 1999 - 2000
Center Director, L. Nicholas Ornston

Plasticity In Environmental Microorganisms

The plasticity of microorganisms has long been a source of fascination for biologists. Half a century ago, bacteria offered models for understanding how the expression of genes responds to environmental fluctuations and, after a few good shakes, these models still help to shape thinking in developmental biology.  Such thoughts tend to be focused upon how the genome of a single cell can give rise to the complexity a multicellular organism.  As the world continues to be shaped for us by the biological activity of diverse unicellular organisms, questions shift to how their complexity can be combined to achieve the overall constancy of a single biosphere.  The complexity is staggering, and sophisticated techniques for identifying environmental microorganisms and their activities increase our awareness of our ignorance.  Whatever bliss this ignorance might afford must be overcome by the certainty that microorganisms are the biological reservoir of opportunities for maintaining balance in the environment.

Chemical communication between plants and bacteria is an environmental interaction that has been going on for a very long time.  Survival of plants depends upon their ability to ward off pathogens and to enter into beneficial nutrient exchanges with microbial symbionts.  The relationship extends to animals for whom some of plant products are indigestible, toxic or both.  Removal of plant products from the environment is achieved by microorganisms, and the process requires physiological versatility.  One challenge is how to grow at the expense of a toxic compound.  A second is how to digest a compound designed to endure.  A third is how to achieve the genetic fluidity essential for adaptation to a constantly shifting environment. 

Activities in the Center for Biological Transformation have focused upon a bacterial strain that offers singular advantages for genetic analysis through natural transformation.  The organism, a representative of the genus Acinetobacter, grows at the expense of a wide range of plant products, and many of these are metabolized through a single intermediate, protocatechuate.  Genetic sleight-of-hand makes it possible to select mutants with defects in these metabolic systems.  The mutations have revealed a cluster of about 40 genes that achieve the overall mineralization of complex plant products.  Notable among the newly discovered genes is one that encodes an enzyme that acts upon chlorogenate, a material that presents problems in stockyard feeds because it is remarkably resistant to metabolism by animals.  The bacteria may be able to help out on this one.

Ongoing research continues to elucidate a panoply of transporters, transcriptional regulators and enzymes that contribute to catabolism of protocatechuate, a compound that can be toxic when supplied in high concentrations.  It has been possible to design a system that allows secrets of genes from other organisms to be unraveled by the joy of

Acinetobacter genetics.  Extraordinary genetic fluidity was revealed by investigation of Acinetobacter genes for conversion of vanillate to protocatechuate.  Nevertheless, it was possible to use a novel technique to identify amino acid residues essential for the activity of the proteins that are involved.  Study of spontaneous mutations revealed deletion mutations that are guided by nucleotide sequences.  This finding emphasizes that DNA has a voice in its own destiny, and present studies are designed to explore mechanisms that allow this to take place.  Of particular value for future research will be the recently determined crystal structure of Acinetobacter protocatechuate 3,4-dioxygenase.  This allows interpretation of known mutations and permits design of experiments designed to explore the physical and chemical flexibility of the enzyme.

Publications of the Center for Biological Transformation, 1999-2000:

1.        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.

2.        Segura, A., P. V. Bünz, D. A. D’Argenio, and L. N. Ornston. 1999.  Genetic analysis of a chromosomal region containing vanA and vanB, genes required for conversion of either ferulate or vanillate to protocatechuate in Acinetobacter.  J. Bacteriol. 181:3494-3504.

3.        D’Argenio, D.A.,  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. 181:3505-3515.

4.        D’Argenio, D.A., M. W. Vetting, D. H. Ohlendorf, and L. N. Ornston. 1999.  Substitution, insertion, deletion, suppression, and altered substrate-specificity in functional protocatechuate 3,4-dioxygenases. J. Bacteriol. 181:6478-6487.

5.        Parke, D., D. A. D’Argenio, and L. N. Ornston.  2000. Bacteria are not what they eat: that is why they are so diverse.  J. Bacteriol. 182:257‑263.

6.        Morawski, B., A. Segura, and L. N. Ornston.  2000. Substrate range and genetic analysis of Acinetobacter vanillate demethylase. J. Bacteriol. 182:1383-1389

7.        Morawski, B., A. Segura, and L. N. Ornston.  2000. Repression of Acinetobacter vanillate demethylase synthesis by VanR, a member of the GntR family of transcriptional regulators.  FEMS Microbiol. Lett. 187: 65-68.

8.        Vetting, M.W., D.A. D’Argenio, L.N. Ornston, and D.H. Ohlendorf. 2000. Structure of Acinetobacter strain ADP1 protocatechuate 3,4-dioxygenase at 2.2 Å resolution: implications for the mechanism of an intradiol dioxygenase. Biochemistry 39:7943-7955.

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B.  The Center for Computational Ecology Report, 1999 - 2000
Center Director, Oswald Schmitz

Given that many of our research initiatives, aimed at linking computational modeling with field experimentation, are well underway, the Center for Computational Ecology (CCE) is now shifting more emphasis toward its teaching mission.

In 1998, CCE programmer Ginger Booth developed software (called CourseWare) that would facilitate creating interactive science labs that could be served over the Internet.  A prototype lab course was developed for FES 563b/EEB 340b, Community Ecology, taught by Oswald Schmitz.  The intent was to offer students a way of learning mathematical principles taught in lecture, in a setting in which they could interact with computational-based exercises that could be accessed at their leisure outside of normal lab meeting times.  There were five electronic labs designed to complement various themes presented in lectures.  The electronic labs appeared to serve a valuable role - student grades improved by 10-15% on the first mid-term exam relative to years when such teaching software was unavailable.

Building on the success of this pilot project, CCE applied for and received funding from Yale ITS and from Howard Hughes to develop course modules for other undergraduate courses.  CCE is now actively developing computer-based learning modules for EEB 110, Introduction to Environmental Science (R. Dorit, enrollment 300 students).  These modules will again complement lecture material and allow students the freedom to explore different lecture concepts (e.g., human population growth, risk and spread of infectious diseases, biodiversity and the stability of ecosystems) within and outside of normal weekly discussion sections.  These modules will be designed to be completely interactive such that students can explore concepts in far greater depth than can be covered during lecture.  We have also developed several modules for EEB Conservation Biology (J. Powell, O. Schmitz and A. Caccone, enrollment 50 students), which aids students in understanding the concepts and measures of biodiversity.

The effort to engage CCE in a more active teaching role is a major Center priority for the next one and a half years.

For more detailed information on the Center for Computational Ecology, visit our web site at http://peaplant.biology.yale.edu:8001/

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C.  The Center for Earth Observation Report, 1999 - 2000
Center Director, Ronald Smith

The goals and organization of the Center for Earth Observation (CEO) are unchanged from previous years.  In this annual report, we focus on events of the recent year and plans for the future.

Infrastructure:
In 1999 the Center moved to temporary quarters in the Kline Geology Laboratory.  The space provided by the Department of Geology &Geophysics (G&G) in KGL is excellent and this has allowed us to continue our work unabated.  Current plans are to move to the Environmental Science Facility (ESF) in the summer or fall of 2001.

The Silicon Graphics (SGI) computer systems purchased in 1997 with NASA "Center of Excellence" funds are continuing to provide excellent performance.  We have added considerable disk space, using base CEO funds, to keep up with our growing archive and the increasing demands of users for disk storage.

The SGI systems are starting to approach their expected lifetime as a leading edge scientific computer system (about 4 years).  Discussions at CEO have begun about replacing the entire system in the year 2001 or 2002.  Ideally, the changeover would occur at the same time as the move to ESF, so that we do not have to move and reinstall an outdated computer system.  The funds for this purchase have been requested from General ReInsurance through YIBS, but the outcome of this request is not yet known.

Governance:
The CEO steering committee includes representatives from G&G, Ron Smith; Anthropology, Frank Hole; School of Forestry and Environmental Studies (F&ES), Xuhui Lee; and Epidemiology and Public Health, Durland Fish.  The idea of adding a member from the Department of Ecology and Evolutionary Biology is under consideration, in connection with new initiatives in biodiversity.

Staff:
The CEO has two full time Masters-level staff members.  Laurent Bonneau provides day-to-day management of the Center, assists users and instructors, and works with others around campus on issues of spatial analysis and geographical information systems.  Jie Zhang assists users and instructors, organizes the CEO data archives and works on high-level research projects.  This staff has brought a high standard of professionalism to their positions.  They have established a reputation on campus for knowledge, enthusiasm and efficiency.

Archive:
In 1999, CEO began an effort to expand its archive of Landsat images.  With the help of falling prices and ample research funding, the archive has quickly grown to exceed 500 images.  These images are maintained in a CD cabinet and can be browsed on the revamped CEO web page.  We have concentrated our growth in areas with active projects at Yale: the Middle East, west Africa, southeast Asia, Amazon basin, and New England.

With the launch of NASA's Terra and other satellites last year, the flow of image data has accelerated rapidly.  The Center is gaining experience using some of these new products, especially MODIS, ASTER and IKONOS.  Because of our small size however, we cannot keep fully abreast of all the new products.

The larger archive has been especially helpful for students seeking projects.  Although our coverage is not global, students can often find images of relevance to their interests.  On other occasions, we can assist in purchasing needed images.

Courses:
As in past years, the course "Observing the Earth from Space" was taught in the spring term 2000.  Approximately 31 students enrolled in the course, mostly from F&ES, but with significant numbers from G&G, Studies in the Environment, Anthropology,Epidemiology.  The student projects in the course were impressive in their diversity and quality (see Appendix A).  This course will be offered again in the spring of 2001.

Discussion continues concerning expanding the course size limit or offering a follow-on course at a more advanced level.  While desirable, these options are not feasible because of limited faculty at Yale in the area of remote sensing.  Appointments in the departments or professional schools would be necessary to expand this teaching program.  The recent growth in the teaching of GIS at Yale is a step forward however.  Students who have taken GIS can take fuller advantage of the remote sensing data sets.

The Center has provided some support for other courses at Yale (Appendix B).  Additionally we have been asked to assist in undergraduate recruiting activities.

Supporting users:
The Center assists students, staff, and faculty to carry out remote sensing projects.  This is a continuing activity throughout the year.  We receive no reimbursement for most of these small projects, especially for student thesis projects.  A common request is to provide image analysis support in the grant-writing stage.  A list of current projects is given in Appendix C.

Outreach:
The CEO participates is several activities which might be termed "outreach".  We have assisted the Peabody Museum in a remote sensing demonstration for Martin Luther King Day.  The Tweed Airport Commission has used our images of the New Haven region in their presentations.  We made a remote sensing presentation to the F&ES Pingree workshop concerning monitoring of forest easement land in Maine.  We have worked with the University of Connecticut on a joint EPSCoR proposal to NASA.

Support from YIBS:
The stable support from YIBS since the founding of the Center has allowed CEO to develop a high-quality basic infrastructure and an experienced staff.  With fluctuating research funding, and considerable teaching and student project responsibilities, YIBS support has been a key to CEO's success.

Funded research:
The Center has experienced an unprecedented growth in its funded research this year.  Two major NASA awards were announced in December 1999 and the research began in March 2000.  These grants total about 1.6 million dollars over three years.  They are specifically oriented towards remote sensing and could not have been won without the existence of the CEO.  The Southwest Asia Project (SWAP) examines the changing landscape, hydrology and agriculture in the Middle East.  The P.I.s are Frank Hole from Anthropology, and Ron Smith from G&G.  The Characterization of Eco Regions in Africa (CERA) project examines the changes in forest and agriculture in west central Africa.  The P.I.s are Mark Ashton from F&ES and Dr. Prasad Thenkabail from CEO.  These grants support an expanded research staff during the duration of the funded projects.  The overhead funds from these grants go to Yale and F&ES respectively, and not to CEO.

The future of CEO
The rapid growth in satellite technology and the increased understanding that land use, landscape change, and habitat destruction are fundamental issues in environmental research suggest that the Center's resources will be increasingly in demand.  The growth of Yale's effort in this area is mostly in the hands of the Departments and Schools.  Strong faculty appointments in the areas of remote sensing, spatial analysis, and large scale environmental monitoring are needed to bring Yale to the first rank.

The CEO is in contact with other groups at Yale concerning a coordinated effort to strengthen Yale's geographical resources.  Other players include the Map Library, the Science Library, the GIS lab at F&ES, and the Statistics Laboratory.  For the future, we envision a "Geography Center" that encompasses all of these activities.

APPENDIX A – Observing Earth From Space Class Projects

Section 1:  Oceans
Deborah Liptzin - Primary productivity cycles Amazon and Orinoco River regions
Erika Schaub - Ocean productivity changes in the Gulf of Maine
Neel Kamath - Remote sensing and applicability to coral reef ecosystem mapping

Section 2:  Forests
Sue Barnes - Forest changes in southern Maine
Michael Beman - Correlating landcover change to carbon sequestration of forests
Silvia Benitez - Carbon cycle analysis in the Great Mountain Forest
Valerie Bodet - Temporal changes in an industrial forest in Georgia  
Adriana Casas - Landcover changes in the Brazilian Amazon 1986 to 1996
Sarah Chamberlin - Deforestation in the southern Congo between 1984 and 1994  
Victoria Chow - Examining easement monitoring techniques in Maine forests
Tiffany Lin - Agro-forest changes over time in northern Congo
Juan Zou - Quantify and qualify tropical deforestation in the Amazon
John McKenna - Changes in the Dzanga-Sangha Reserve in the Central African Republic

Section 3:  Arid Lands
Wenbo Cao - Estimating desert water use from evaporative cooling
Sara Chen - Fallow cycle changes over time in Syria
Eden Enclona - Examine changes in irrigated agriculture in Syria
Melissa Droller - Land cover changes in Israel west of the Sea of Galilee

Section 4:  Ecosystems/Geology/Other
Sean Gray - The physics of reflectance in glaciated alpine terrain
Lisa Max - Using the thermal band to improve classification of Cape Cod
Ben Piper - Habitat destruction over time near national parks in southern Brazil
Robert Rosenswig - Landcover issues in Belize
Mark Wishnie - Vegetation classification of sub-basins of the Panama Canal watershed
Heather McGray - Landuse patterns in the buffer zones around the La Amistad Biosphere Reserve in Costa Rica

Section 5: Epidemiology
John Brownstein - Tick borne encephalitis risk map of Europe
Hilary Rosen - West Nile Virus mosquito breeding sites in New York City

Section 6: New Haven and Connecticut Land Classification
William Caldicott - Measuring the ex-urban sprawl in the Greater Hartford area
Stacey Kingsbury - Rattlesnake habitat in Marlborough, CT
Greg Serenbetz - Landcover classification and change in the Mill River watershed
Matthew Morrison - Comparison of land cover classifications of the Naugatuck River watershed
Greg Socha - Multi-temporal landcover classification of northwestern Connecticut
Navis Bermudez -  Quantify the amount of impervious surfaces in the Greater New Haven

APPENDIX B – Lectures presented by the CEO staff to support the following courses

Environmental Studies course taught by Mary Helen Goldsmith – lecture on an introduction to remote sensing with a focus on natural resource applications.

Introduction to Archeology course taught by Lucinda McWeeney – lecture on an introduction to remote sensing with a focus on archeological applications.

G&G Surveying course taught by Robert Gordon – lecture on GPS & GIS (with lab exercise)

Geology course taught by Jonathan Lees – lecture on an introduction to remote sensing.

APPENDIX C – Individual Student and Faculty Projects

Hydrological Modeling of the Levantine
Jeff Albert, F&ES

RS and GIS used to Identify, Map, and Predict Regions of Risk for Lyme Disease
John Brownstein, EPH

Field and numerical studies of glacier Engabreen in Northern Norway
Denis Cohen, G&G

Temperature, Rainfall and Settlement in the Near East
Ben Diebold, Anthropology

Cambodia Genocide Project
Matthew Fladelan, F&ES

Identification of Livingstone's Fruit Bat Roosting Sites in the Comoros Islands
Elise Granek, F&ES

Yale Meyers Forest Model
Anders Halverson, F&ES

Forest Stand Dynamics and Carbon Cycle
Huei-An Chu, F&ES

Mountain Induced Rainfall in the Southern Alps of New Zealand
Juan Zou, G&G

Bamboo-Dominated Forests of the Amazon
Bronson Griscom, F&ES

Investigation Of Paleoanthropological Sites Associated With The East African Rift Valley
John Kingston, G&G

Statistical Analysis of Image Classification Techniques
Olaf Kuegler, FES

Yale Glacier Analysis
Deb Liptzin, G&G

Land Use in Buffer Zones of La Amistad International Biosphere Reserve, Costa Rica
Heather McGray, F&ES

Landcover Classification of the Naugatuck River
Matthew Morrison, F&ES

Temporal Investigation of Cultivation Within and Bordering Araguaia National Park, Brazil
Ben Piper, F&ES/EPH

Northern Belize Landuse Project
Robert Rosenswig, Archeology

Land Cover Type Characterization and Change from AVIRIS Data
Georgia Silvera, F&ES

The Mastadon Project
Jim Wallis, Civil Engineering/F&ES

Mathematical Analysis of Hyperspectral Data
Fred Warner, Math

Analysis of Evaporative Cooling from Vegetation
Wenbo Cao, G&G

Characterization of Riparian Vegetation in Sub-Basins of the Panama Canal Watershed
Mark Wishnie, F&ES

Forest Stand Dynamics and Carbon Cycle
Xuhui Lee, F&ES

Forest Stand Dynamics and Carbon Cycle
Huaiyu Yuan, G&G

Regional Climate Model Simulations of the Middle East
Zav Kothavala, G&G

Major research projects at CEO:

SWAP – SouthWest Asia Project
http://www.yale.edu/ceo/Projects/swap.html

Ron Smith, G&G
Frank Hole,  Anthropology
Roland Geerken,  CEO
Jennifer Arz,  Anthropology
Andrea Mautner,  CEO
Eric Hole,  CEO
Nicholas Kouchoukos,  U of Chicago
Jane Foster,  U of W. Virginia
Kirk Maaech,  U of Maine
Robert Oglesby,  Purdue/NASA
Jason Evans,  ANU/G&G

MAP – Mesoscale Alpine Programme
http://www.geology.yale.edu/~smith/yale_map.html

Ron Smith,  G&G
Qingfang Jiang,  G&G
Sean Gray,  G&G
Steve Skubis,  SUNY
Matthew Fearon,  G&G

CERA – Characterization of Eco Regions in Africa
http://www.geology.yale.edu/~smith/africa_project.html

Prasad Thenkabail,  CEO
Tiffany Lin,  F&ES
Eden Enclona,  F&ES
Mark Ashton,  F&ES

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