Fiscal Year 1999 Awards

Division of Biological Infrastructure

Postdoctoral Research Fellowships in Biological Informatics



Fellow's Name Host Institution Research Area/Training Plan NSF Award #
Title of Research and Training Plan
Abstract


Dean Adams Iowa State University Biophysics 9974207
"Comparison of Three-Dimensional Protein Structures Using Geometric Morphometric Methods: An Assessment of Structural Similarity"
Geometric morphometric algorithms are being used to identify proteins with similar three-dimensional structures. These methods compare proteins using the x,y,z coordinates of homologous points and are robust to heterogeneous variation among landmarks. They compare multiple protein structures simultaneously and can thus be used to construct a protein structure space for identifying functionally similar proteins.


Suzanne Alonzo University of California - Santa Cruz Animal Behavior 9974233
"Multi-Player Dynamic Programming Game Methods, With Applicatin to Evolutionary Biology"
Dynamic game models have an extensive history in many fields. In this research, algorithms are being developed to explore dynamic programming games between multiple players and make these methods and computer algorithms available to biologists. To demonstrate the method, two popular areas of evolutionary biology, mating systems and predator-prey interactions, are being used for the study.


David Ardell Princeton University Eukaryotic Genetics 9974248
"Gene Splicing and Altered Genetic Codes in Hypotrichous Ciliates"
This is a study of codon usage and base composition in hypotrichous ciliates --unicellular eukaryotes with altered nuclear genetic codes. The hypothesis being tested is that certain hypotrichs evolved to translate the "nonsense" that occurs where their genes are spliced together during development. Software is being modified and developed for gene annotation in ciliate genome projects.


Reed Beaman Royal Botanic Gardens, Sydney Systematic Biology 9974217
"Automated Mapping of Plant Distributions and Mining of Biological, Geological, and Geographical Data by Parsing Locality Descriptions on Specimen Labels"
Museum and herbarium specimen labels rarely contain specific geographical coordinates, but often provide physical and biological descriptions of where a specimen was collected. These descriptions are being automatically parsed and compared to physical and biological data stored in a geographical information system (GIS) to generate probabilistic models of taxon distributions.


Frank Brown University of California
San Diego
Cell Biology 9974250
"Theoretical Studies of the Interface Between Cells and Their Environment: Simulating Protein Motion on the Cell Membrane"
In this study, the diffusive-like lateral motion of membrane proteins will be theoretically modeled and simulated. Emphasis will be placed on understanding how internal cellular structure acts to regulate protein diffusion, and to what extent this regulation is a dynamic process. How this diffusion is coupled to cellular functioning will be studied by working closely with experimentalists.


Rob Brumfield International Center for Tropical Agriculture, Cali Population Biology 9974235
"Integration of Genetic and Environmental Data Into a Comparative Database: Elucidating the Role of Across-Andes Dispersal in the Diversification of Lowland Organisms"
This research bridges genetic and geographic (GIS) technologies to examine the role of the Andes in biological diversification. Relevant environmental parameters are characterized across a known across-Andes dispersal corridor. These data, coupled with natural history information of the dispersing organisms, are being used to construct models of genetic structure. The model's predictions are then tested using empirical genetic data.


David B. Finkelstein Carnegie Institute of Washington Integrated Plant Biology 99742535
"Using DNA Micro-Arrays to Search for Patterns of Gene Expression in Plants Subject to Environmental Stress"
DNA micro-arrays allow the observation of gene expression patterns on a whole genome scale. Micro-arrays are being used to collect expression data from Arabidopsis grown in elevated levels of carbon dioxide. These data are being statistically sorted and expression patterns identified using software developed for the project. This software can then be applied to search for patterns caused by other environmental stresses.


Boris Gutkin Institute Alfred Fessard, Gif-sur-Yvette Computational Neuroscience 9974208
"Developing Hybrids of Real-Time Computer Neuroal Models and in vivo Cells to Explore Activity Dependent Plasticity of Cortical Visual Receptive Fields"
Experience dependent learning in local cortical circuits of the primary visual cortex are being studied in vivo. A new computer-based technique called in vivo dynamic clamp is being used to construct hybrid networks, where a cortical neuron is reciprocally interconnected with real time computer simulated neural models through a whole-cell clamp intracellular electrode. Novel real time data analysis methods, such as real time reverse correlation analysis, are being developed. Using these techniques, changes will be induced in the classical receptive fields by supervised Hebbian learning, with the computer-generated model neuron acting as the teacher. The use of the hybrid networks will permit the clear demonstration that activity dependent learning does take place in the visual cortex at the level of a single cell.


Charles Hershberger University of Minnesota Metabolic Biochemistry 9974209
"A Computer Program to Predict the Biodegradation of Environmental Pollutants"
This project concerns the environmental breakdown of pollutants by microbial action, biodegradation. An artificially intelligent system capable of predicting the biodegradation pathways of novel compounds will be developed by combining two existing databases. Automated learning techniques to populate a knowledge base with biodegradation knowledge will be devised. This will be used in an expert system to predict multiple potential biodegradation pathways.


Hunter Moseley Rutgers University Biophysics 9974200
"Automatic Analysis of Protein NMR Spectra for High-Throughput NMR Structure Determination: A New Technique for the Human Proteome Project"
High-throughput protein structure determination (HTPSD) will be a key technique in the Human Proteome Project. For NMR HTPSD, automation of spectral resonance assignment is essential. AutoAssign is a constraint-based expert system that automatically determines backbone resonance assignments using nine specific NMR experiments. This project supports further development of AutoAssign to robustly determine "complete" resonance assignments using many kinds of NMR data.


Andrew Peek University of California
Irvine
Prokaryotic Genetics 9974237
"Molecular Evolution and Population Genetic Variation of Neutral and Non-Neutral Loci in the E. coli Genome"
The amount of genetic variation within the model organism Escherichia coli's genome is controlled by the forces of population size, recombination, mutation, selection, recombination and gene duplication or loss. Many loci are suspected to be subject to different combinations of these forces. The level of naturally occurring genetic variation is being surveyed for nucleotide sequence level variation at several gene loci of known function. Genetic estimates and statistical tests for the amount, nature, and distribution of genetic variation under various models of molecular evolution are being performed.


Steven Plotkin University of California
San Diego
Biophysics 9974199
"Computational and Theoretical Investigation of the Protein Folding Mechanisms and Protein Design: Topological and Energetic Effects"
The goal of this research is to explore how topological structural information governs the sequence designability of the native conformation, and how native topology along with energetic sequence information controls the protein folding mechanism. It uses an analytical framework and detailed numerical simulations to give a full understanding of the molecular mechanisms. This new approach will be helpful for further developments in structural prediction methods and design of novel proteins.


Maria Sanchez University of California
Davis
Population Biology 9974202
"Bioinformatic Analysis of the Effects of Genetic and Spatial Diversity on the Survival and Variability of Host-Symbiont Systems"
Different degrees of genetic and spatial heterogeneity, in relation to interspecific selection and comigration, will affect the spatial and temporal distribution of host species and their symbionts. This bioinformatic study analyzes how these dynamical processes increase, or decrease, the persistence of metapopulations and local populations of the two interacting species.


Edward Schuur University of California
Irvine
Ecosystem Studies 9974215
"The Response of Soil Carbon Turnover and Storage to Global Climate Change: A Systhesis of Modeling and Radiocarbon Data"
Dynamic modeling is a powerful approach to understanding carbon accumulation and turnover in terrestrial soils. This study combines carbon turnover estimates from radiocarbon measurements from a range of sites with modeling simulations to validate model predictions of the exchange of carbon between soils and the atmosphere in response to global climate change.


Janet Siefert Rice University Systematic Biology 9974214
"Tracking the Evolution of Cellular Processes Using Molecular Geneology"
This project is in two parts. The first entails 'phylogeny mapping'. This incorporates the phylogenetic framework of small subunit ribosomal RNA (ssu rRNA) as a scaffold on which homologous cellular processes such as metabolic processes, genes, or morphological description are mapped. The second involves producing a model for a rate of evolution based on empirical in vitro evolution data and modified versions of existing programs that incorporate fossil evidence for known divergence times in a pair of sequences. This model will be applied to the results of the phylogeny mapping in an effort to place a relative time on internal nodes of the ssu rRNA tree topology. Results of will include new analysis tools of interest to the bioinformatics community as well as providing new strategies for accessing and analyzing sequence data. Some of these programs will be useful beyond the scope of bioinformatics. In addition, fundamental answers concerning the evolution of cellular processes will lend new insights into the process by which life originated.


Eleanor Steinberg University of Montana Population Biology 9974243
"Natural Selection 'in the wild:' Use of a High-Density Linkage Map to Detect loci Affecting Fitness in Pink Salmon"
It focuses on extending and developing computational tools to analyze an extensive dataset resulting from a large-scale release and return genetic study of pink salmon (Oncorhynchus gorbuscha). Genotypes at approximately 50 loci from 50 families (bred using wild-caught parents) are being analyzed with reference to a high-density linkage map to identify quantitative trait loci (QTLs) controlling phenotypes influencing marine survival in this commercially important and biologically interesting anadromous species.


Jerry Tsai University of Washington Biophysics 9974195
"Data Mining Recurrent 3D Interaction for Pretein Structure Prediction"
Data mining of the Protein Data Bank (PDB) is being used to identify recurrent non-local interactions (salt bridges, hydrogen bonds, and hydrophobic contacts) in three dimensions (3D) between two segments of structure greater than 15 amino acids apart. The resulting databases of 3D interactions will be used for protein structure prediction.


Jason Wolf Washington University Eukaryotic Genetics 9974193
"Methods for Characterizing the Effect of Maternal Genes on the Expression of Early Developmental Traits in Offspring"
Genes expressed in mothers often influence the expression of traits in their offspring. These so-called maternal effects are ubiquitous but have traditionally been ignored in studies of genetic architecture (e.g., QTL analysis). Methods are being developed to incorporate maternal effects into QTL analyses and apply these methods to examine the genetics of development in the mouse.


Last Modified: Nov. 18 '99 Nov 19, '99