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Fiscal
Year 2000 Awards| Fellow's Name | Host Institution | Research Area/Training Plan | NSF Award # |
| Title of Research and Training Plan |
| Abstract |
| Lauren Ancel | Princeton University | Evolution of Developmental Mechanisms | 0074505 |
| Evolvability and Modularity of Molecules, Viruses and Regulatory Networks |
| Plastogenetic congruence, a correlation between environment-induced and mutation-induced phenotypes, has been shown by computational studies of RNA secondary structure evolution. This correlation, where phenotypes produced by an RNA sequence under thermodynamic fluctuation mirror those produced by genetic mutation, has profound evolutionary implications as RNA sequences undergo environmental canalization towards more thermodynamically stable structures. Assuming that the rule of plastogenetic congruence is followed, phenotypes that are resistant to environmental changes must also resistant to mutation-induced changes and the ensuing novel phenotypes. |
| Jennifer Dunne | San Francisco State University | Ecology | 0074521 |
| A Web-Based Combinatorial Approach to the Effects of Biodiversity Loss on Complex Ecological Networks. |
| Ecological research into biodiversity loss is limited by what experiments can actually be conducted and by the underlying theory which is complex, making it difficult to separate the many interacting processes. This project applies global optimization techniques and network analyses to high quality food-web data to simulate effects of small to large biodiversity losses on complex communities. Systematic deletion of combinations of species in empirical and model food-webs are being used to generate theory that distinguishes effects of reducing species richness from effects of eliminating particular species' functions on ecosystems. |
| Avijit Ghosh | Cornell University | Molecular Biophysics | 0074494 |
| Mechanisms into the folding of Arc Repressor: A theoretical study |
| In this project, a theoretical investigation into the mechanism of the folding of Arc Repressor using developments in the study of kinetics and dynamics of protein systems is being developed. A Master Equation for describing the folding kinetics of protein models (recently demonstrated by Scheraga), as well as the stochastic path approach of Elber, will be used in a corroborative way to elucidate the particular kinetic mechanism of the well-studied Arc Repressor. While the emphasis of this research is on application of existing models of protein folding of Arc Repressor, specific theoretical extensions will be developed both with regard to numerical methods and optimizations and with alternative formulations of the model itself. |
| Christine Howell | University of Missouri -Saint Louis |
Ecology | 0074482 |
| Evaluating Alternative Biodiversity Conservation Hypotheses: A test of the Coarse-Filter Paradigm |
| GIS and computer modeling are used in this study to develop a coarse-filter computer model for conservation reserve network planning in Ecuador. The model will generate multiple alternative "biodiversity reserve hypotheses" with variable sets of increasing complexity and spatial resolution. The efficacy of the model will then be evaluated with extensive biotic inventory databases for birds and plants. |
| Matthew Jacobson | Columbia University | Molecular Biophysics | 0074464 |
| Systematic Evaluation of Algorithms/Models for Protein Structure Prediction Using a Database of Cyclic Oligopeptide NMR Data |
| While many computational algorithms and models exist for simulation of protein folding, there is a distinct need for statistical measures of their accuracy and efficiency. This project assembles a database of Nuclear Magnetic Resonance (NMR) data of cyclic oligopeptides. These are proteins which are small enough to be computationally tractable but retain key features of protein structure and thus allow analysis of intermolecular and intramolecular forces as well as sampling algorithms for identifying stable conformations. Algorithms whose accuracy have been validated through this research are then employed to predict the structure of previously uncharacterized cyclic peptides. |
| Lewis Lukens | University of Wisconsin | Integrated Plant Biology | 0074484 |
| An Analysis of genetic architecture, gene expression, and phenotypic variation within resynthesized Brassica napus polyploids |
| The goal of this study is to investigate the phenomenon of polyploidization (fusion of two genomes into one) in flowering plants, via resynthesizing fifty lines of the natural polypoid Brassica napus from its diploid progenitors Brassica rapa and Brassica oleracea. Changes in genomic architecture, gene expression, and phenotype between the diploid parents, the progeny of the resynthesized B. napus, and the fourth generation offspring of the resynthesized plants are being examined. These experiments will determine the nature of the changes within individual, resynthesized polyploid genomes and whether or not these changes are shared among independently derived polyploids. Such changes will be identified by comparisons of gene expression using Northern blots and DNA microarrays. |
| Peter Midford | University of Arizona | Systematic Biology and Animal Behavior |
0074524 |
| Comparative Methods and Data Representation for Structured Traits, Including Temporal Sequences in Behavior, Morphology and Development |
| Many traits of organisms, especially in behavior, morphology, and development exhibit structured relationships with other traits. Examples of structuring include temporal sequences in behavior and development and whole-part relationships in morphology. This project develops software to apply phylogenetically informed comparative methods to traits in structured relationships. Developing these methods and their underlying representations is an important step in integrating diverse phenotypic data. |
| Susan Moegenburg | Smithsonian Institution | Ecology | 0074499 |
| Reconstructing Biogeography: Tree Species as a Novel Explanation for North American Bird Population Declines |
| One of the most visible environmental problems in eastern North America is the decline of many populations of breeding birds. While deforestation and loss of habitat have been identified as the causes for some species, they do not explain the population decline of the remainder. Important factors, such as quality of breeding habitat, have not been sufficiently studied. This research examines the alternative hypothesis that historical changes in forest composition, such as the decline of previously dominant tree species, is contributing to changes in bird populations due to species' preferences for particular trees. Examination of morphology (bill, leg, foot, wing, and tail dimensions) of various bird species allows characterization of their preferences for specific trees and in turn provides a means to identify correlations between tree species and bird species population decline. |
| Charles Nunn | University of Virginia | Ecological and Evolutionary
Physiology |
0074483 |
| Phylogenetic Comparative Methods to Analyze Host-Parasite Trait Evolution |
| The aim of this research is to develop comparative methods to test for correlated evolution. Previous investigations of host-parasite evolution have provided analyses of the congruence of the phylogenetic trees of hosts and parasites, yet have failed to characterize and describe correlative/causal effects on trait evolution. The aims of this research are 1. To use simulation techniques to identify the statistical consequences of different levels of host-parasite tree congruence on comparative studies of trait evolution, via computer simulation 2. Develop a system that minimizes statistical bias and inconsistency when host-parasite trees are not fully congruent, and 3. Apply these methods to real-world datasets to test hypotheses for host-parasite trait evolution in primates and carnivores. This research will contribute greatly to knowledge of evolution. |
| Marjorie Oleksiak | University of Missouri -Kansas City |
Eukaryotic Genetics | 0074520 |
| Analysis of Microarray Data to Identify Adaptive Promoters |
| This bioinformatic study will examine sequence variation in proximal promoters of genes involved with metabolic processes, and distinguish "useful" variations (i.e. variations associated with adaptation) from random variations that have no functional significance. Comparisons of microarray analyses of genes expressed in cardiac tissue of different populations of teleost Fundulus, which exhibit different cardiac metabolisms, can identify genes linked to metabolic processes. In Fundulus, genes whose transcription is altered (increased) by transcription factor SP1 will also be identified by using microarray technology, as these genes are preceded by promoter sequences that bind SP1. The subset of genes that are 1. Associated with cardiac metabolism, and 2. Affected by presence and concentration of SP1, will be further examined to determined which variations are adaptive. |
| Susan Perkins | University of Edinburgh | Evolution of Development | 0074512 |
| Evolutionary Rate and Pattern in Developmentally-regulated Genes in Malaria and Related Parasites |
| Malaria parasites (Plasmodium) and some other members of their phylum, Apicomplexa, have nuclear ribsomal DNA with an unusual organization. Unlike most other eukaryotes, these protozoans have only a few, independently-evolving rDNA loci, and at least in malaria, these genes may be expressed only at specific times in the parasites' development. The goal of this research is to identify when in the evolutionary history of this phylum the peculiar organization of these genes arose as well as to examine in detail the rate and pattern of the evolution of these genes. Evolutionary genomics, structural biology, and the use of large databases of sequence data are among the bioinformatic approaches being used. |
| Karin Pfennig | University of Texas at Austin |
Ecological and Evolutionary
Physiology |
0074508 |
| The evolution of species recognition and mate choice: a neural network approach |
| The aim of this research is to model mate choice behavior via use of artificial neural networks that will model cognitive function. The proposed research investigates a well known problem in evolutionary biology: the evolution of species recognition that both accompanies and influences speciation itself, i.e. the manner in which the signal recipient (usually female) evolves, and how this change affects evolution of the signaler (typically male). The model neural networks are being tested against the behavior of spadefoot frogs and will determine if species recognition by the female will result in stabilizing the male phenotype or, rather, drive it in a specific direction. |
| Molly Przeworski | University of Oxford | Population Biology | 0074466 |
| Maximum likelihood estimates of the rate of occurrence of selected sweeps and of the time to the last selective event in the history of a sample |
| The rapid fixation of strongly favored mutations, or selective sweeps, is thought to be a common mechanism by which adaptive evolution occurs. For example, humans and chimpanzees differ by only 2% on the DNA level, yet it is this minute genotypic difference that confers enormous differences in phenotype, such as enhanced communication (speech) and cognition. It is suggested that this fact can be attributed to the occurrence of selective sweeps/directional selection of genes that already existed rather than creation of novel genes unique to humans. This research aims to use computationally-intensive full likelihood methods to estimate the rate of occurrence of adaptive fixations and the time to the last favored substitution in order to identify these genes in humans. |
| Leslie Rissler | University of California
at Berkeley |
Population Biology | 0074509 |
| A Comparative Phylogeographic Approach to Studying Biodiversity |
| Evolutionary and geographical factors influencing patterns of amphibian biodiversity are investigated by analyzing, within three different genera (Ensatina, Taricha, and Batrochoseps), multiple codistributed species for phylogeographic concordance. In addition, comparisons of current and historic population level processes across species provide strong inferences on factors impacting genetic divergence in zones of secondary contact. By combining spatial and genetic information across multiple species and populations, a more thorough understanding of the forces affecting speciation and regional biodiversity will result. |
| John Schienman | State University of New York
at Albany |
Population Biology | 0074488 |
| The Role of Alu Elements in Regulatory Evolution: Bioinformatic and Experimental Study |
| About 10% of the human genome is composed of Alu elements, which are primate-specific SINES (short interspersed elements)--sequences of DNA thought to have been retroposed into the primate genome during evolutionary history. The human lineage has thousands of recent Alu insertions that are not found in other hominoids. Alu sequences have all been shown to have transcription factor binding sites. The aim of this study is to test, via molecular techniques and bioinformatic studies, the hypothesis that Alus preferentially insert predominantly near male germ cell transcribed genes. The resulting analyses of human-specific SINES will help identify candidate genes that may be expressed differently in humans compared to other hominoids. |
| Paul Spellman | University of California Berkeley |
Animal Developmental Mechanisms | 0074472 |
| Characterization of Transcriptional Networks by Comprehensive Target Identification in Drosolphila |
| This study proposes to identify transcriptional targets of sequence-specific transcription factors in Drosophila, via in-vivo assays using approximately 50 transcription factors . The goal is the identification of genes whose transcription produces the complex developmental patterns that occur, as well as the resulting diversity in cell function that is necessary to create complex organisms. Further, these data should facilitate attempts at computational modeling of transcription factor networks on a scale that previously has not been possible. |
| Karen Stocks | University of California at San Diego |
Ecology | 0074498 |
| Development of a Biogeographical Information System for Seamounts |
| Seamounts, which are volcanic peaks found within the ocean and rise 1000 feet above the ocean floor (yet not breaking the surface), exist in a variety of locations and latitudes, and may be highly representative of several aspects of biodiversity. This project creates an oceanographic information system by aggregating global biogeographic data from seamounts into a database/GIS system which is used to map and explain patterns of seamount biodiversity and will be freely accessible over the internet to aid research, management, and education. |
| John Uy | University of California Santa Barbara |
Animal Behavior |
0074504
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Signal Evolution and Speciation in the Common Paradise
Kingfisher Complex
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The means by which changes in mating signals lead to
the formation of new species remain an unresolved issue in biology.
The proposed research addresses this question via study of populations
of the paradise kingfisher (T.galatea). These populations exhibit different
plumage traits and may represent early stages of speciation. Using Geographic
Information System, molecular genetics, and spectrographs, this study
will determine how differences in environmental conditions, through
induction of changes in plumage traits between populations, leads to
reproductive isolation of a given population and, in turn, speciation.
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| Jeffrey Wall | Harvard University | Population Genetics |
0074503
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Using Current DNA Polymorphism Data to Make Inferences
about Past Human Demography
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Statistical analyses and extensive computer simulations
are being used to determine what models of human demography are compatible
with existing DNA polymorphism data. These methods can answer important
and interesting questions about human populations such as when did they
start to expand in size and which groups are closely related to each
other. The methods are generally applicable to population studies.
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| Charles Whitfield | University of Illinois | Behavioral Neuroscience |
0074467
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Analysis
of Global Gene Expression in the Social and Genetic Determination of
Behavioral Diversity in the Bee Colony
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Division
of labor in the honey bee colony (Apis mellifera) is dependent on variation
in the behavior of the colony's individual workers. Worker behavior
varies as a function of an individual worker's age, interactions with
other colony members, social environment, and inherited genetic factors.
To address the relationship between genes and behavior, this research
uses DNA microarrays to test whether variation in gene expression in
the brain is a mechanism that underlies behavioral diversity in the
honey bee colony.
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| Last Modified: June 14'01 |