Fiscal Year 2000 Awards

Division of Biological Infrastructure

Postdoctoral Research Fellowships in Microbial Biology

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

Michael Atkins   Systematic Biology 0074371
Study of Ancyromonas as a Possible Ancestor to All Metazoa, Fungi, and Choanoflagellates
Preliminary analysis of 18S rDNA sequences from the flagellate genus Ancyromonas suggests it is descended from the specific common ancestor of multicellular metazoa and fungi. Additional phylogenetically-informative genes from species of Ancyromonas are being sequenced and analyzed to determine if there is an extant unicellular ancestor to this group. Morphology and ultrastructure of Ancyromonas species also are being studied and compared with metazoan and fungal species to determine the extent of shared characteristics suggestive of common ancestry. Fluorescent in-situ probe hybridization (FISH) technology is used to look for undiscovered species of this globally-distributed genus in an effort to find and culture unique species for this and future study.

Farida Attar Medical College of Ohio Population Biology 0074382
Evolution of Life History Characters in a Arbovirus
Vesicular Stomatitis Virus (VSV) has been chosen for this study not only because it is similar to important human pathogens, e.g., measles, influenza, poliovirus, HIV, hepatitis A, B and C, but its genomic information is stored in RNA instead of DNA. RNA replication is error-prone, and therefore many mutations are constantly produced that allow extremely rapid evolution and offer an opportunity to study specific aspects of virus evolution and general issues of population genetics. A combination of comparative, mathematical, experimental, and molecular studies are being used to ask how the life histories of parasites adapt to different hosts and how these life history traits and trade-offs between the traits change in response to natural selection in the laboratory. The answers will significantly enhance our understanding of the patterns and diversity of life cycles in parasites.

Daniel Buckley University of Connecticut Metabolic Biochemistry 0074404
Anaerobic Methane Oxidizers in Marine Microbial Mats
Anaerobic methane oxidation (AMOX), a sink for greenhouse gas methane, is a microbially-mediated process of global ecological significance. This research investigates the biology of microorganisms responsible for AMOX in marine microbial mats by using microelectrodes in conjunction with 16S rRNA-based techniques to monitor the organisms as they occur in their natural environments. The data acquired from this research helps to determine if AMOX is mediated by a syntropic relationship between two microbial groups or by a single microbial group possessing an unknown biochemical pathway.

Jayna Ditty Texas A&M University Metabolic Biochemistry 0074386
Characterization of a Second Circadian Oscillator in Synechococcus sp. Strain PCC 7942
The single-celled cyanobacterium Synechococcus sp. srain PCC 7942 has a circadian pacemaker or "clock" consisting of at least three genes (kaiA, kaiB, and kaiC) that has an endogenous period of 25 hours. A second mutant clock with a 27.5-hour period has been shown in the sigC mutant of Synechococcus. While experiments have shown kaiA in this mutant to oscillate with the 27.5 hour period, kaiB exhibits the wild-type 25 hour periodicity, leading to the hypothesis that there is an unforeseen oscillator (UFO) present that is overruled under wild-type conditions by the master Kai oscillator. This research physiologically characterizes the 27.5-hour oscillation of strain PCC 7942 by examining its temperature compensation and ability to phase reset. In addition, the molecular basis of the 27.5-hour UFO and its effects on synechococcal circadian gene expression is investigated.

Caryn Evilia Thomas Jefferson University Biochemistry of Gene Expression 0074388
Elements Required for Protein Synthesis in Archaea
This research focuses on post-transcriptional modifications of the archaeon Methanococcus jannaschii. This research provides an understanding of the role of tRNA modifications in the archaeal adaptation to extreme environments. A variety of approaches are used to identify modifications that are important for tRNAs in protein synthesis. The archaeal mechanism of protein synthesis and its differentiation from those of Eubacteria and Eukarya will be investigated.

Christine Foreman Montana State University Ecosystem Studies 0074372
Microbial linkages among ecocystem components in the McMurdo Dry Valleys in Antarctica
These valleys provide a unique environment to study biocomplexity in extreme environments. This research links microbial community structure and function with physical and biogeochemical processes in the lakes, streams, and terrestrial systems using a suite of biochemical and molecular biological techniques.

Sandra Haddad University of Georgia Metabolic Biochemistry 0074398
Integrated Studies of Biodegradation in Rhodococcus and Acinetobacter
This research studies aerobic biodegradation of aromatic hydrocarbons in Rhodococcus sp. strain 19070 and Acinetobacter sp. strain ADP1 and may facilitate the development of effective bioremediation strategies. Rhodococcus is an environmentally important microorganism but is difficult to study because genetic techniques are not well developed for it; however, Acinetobacter can be used to overcome this difficulty. Since the first step in environmental degradation of many pollutants is the cleavage of a benzene ring, the primary focus of this research is the purification and characterization of the enzyme benzoate dioxygenase from Rhodococcus. The biodegradative pathway is being elucidated using mutants and complementation studies.

Cynthia Haseltine University of California Davis Microbial Genetics 0074380
Mechanism of Homologous Recombination in Archaea
This research examines general recombination mechanisms in the hyperthermophilic archaeal microbe Solfolobus solfataricus. Functional homologues to eukaryotic recombination proteins are being heterologously produced and are used to reconstitute archaeal recombination in-vitro. In-vivo gene disruption and mutant rescue studies will complement the in-vitro data and demonstrate functional homology of proteins produced by S. solfataricus to those produced in yeasts. Homologous recombination is a universal process in which genetic information is exchanged between separate strands of DNA, introducing new linkages and genetic sequences.

Karin Jackson University of Maryland Biotechnology Inst. Microbial Genetics 0074397
Role of Gene Control Mechanisms in Microbial Methane Production
The primary goal of this study is to identify and characterize the mechanism for genetic regulatory control of methanogenesis, which has a pivotal role in the global carbon cycle. A combination of physiological and genetic approaches is being used to investigate the control networks that mediate expression of a catabolic gene encoding carbon monoxide dehydrogenase in the methanogen Methanosarcina actevorans.

Janet Lamb University of Rochester Biochemistry of Gene Expression 0074374

Identification of Novel Pseudomonas aeruginosa Quorum Sensing Genes
Monitoring of surroundings by quorum sensing in Pseudomonas aeruginosa, a gram-negative bacterium, plays an important role in its ability to grow in a wide variety of conditions. The two best studied quorum-sensing systems are the las and rhl systems. This research utilizes a fluorescence activated cell sorter (FACS)-based approach to identify novel genes positively and negatively regulated by the las and/or rhl system. Temporal induction or repression of the identified genes is examined during the growth cycle, and regulatory factors dictating the induction and/or repression of these genes are identified. In addition, the functions of these genes are examined via insertional activation and observation of the phenotypic changes.

Elizabeth McGraw Yale University Population Biology 0074396
Evolution of Wolbachia pipientis Substitution Rates and Phenotypic Variants
This research seeks to measure the rate and mode of evolutionary change in Wolbachia, a bacterium that lives intracellularly in multiple tissues of various arthropods, and identify the selective forces that mediate persistence of different Wolbachia phenotypic variants in populations. Specifically, the aims are to address 1. Whether or not modification and rescue variants of Wolbachia are maintained in populations as part of an evolutionary cycling scenario, and 2. If the rate and pattern of Wolbachia evolution suggest a small effective population size for the symbiont.

Deborah Millikan University of Hawaii Animal Development 0074383
Motility-related Symbiotic Determinants in Vibro fischeri
The interaction between microbe and host is a dynamic process that requires phenotypic changes by both partners and likely the coordinated regulation of specific genes for the success of this association. The symbiotic interaction between the luminous bacterium Vibrio fischeri and the bobtail squid Euprymna scolopes is a model system for investigating the role of bacterial motility in the colonization of animal tissue. While V. fischeri cells present in seawater must be motile to migrate to the initial site of colonization in the juvenile squid, a role for motility in the colonization of specific locations within the animal has not been investigated. This research 1. Experimentally identifies colonization stage-specific regulation of motility genes and 2. Explores, via two approaches, the ability of V. fischeri to coordinately regulate motility genes with other colonization factors. The first approach is to examine symbiotic capacity of V. fischeri mutants that exhibit an altered motility phenotype, while the second approach is to experimentally investigate the role of the bacterium's polar flagellum, which is thought to play a role in gene regulation within the bacteria. The results of the proposed work will likely serve as a model that provides an improved understanding of the role of motility and co-regulated symbiotic factors in bacterial host interactions.

Dale Pelletier Stanford University Microbial Genetics 0074387
Molecular Biology of Anaerobic Ethylbenzene Oxidation
The goal of this research is to advance the understanding of the processes involved in the microbial metabolism of aromatic hydrocarbons under anaerobic conditions. Recent biochemical investigation of anaerobic ethylbenzene degradation with the denitrifying bacterium Azoarcus sp. strain EB1 has led to a proposed pathway for ethylbenzene mineralization. DNA microarray analysis and 2-dimensional gel electrophoresis experiments are used to identify genes differentially expressed during anaerobic growth of Azoarcus. These experiments will lead to identification and functional analysis of genes involved in ethylbenzene mineralization, with special consideration of the gene associated with ethylbenzene dehydrogenase (a novel enzyme found within Azoarcus which catalyzes the removal of a hydride from an aromatic hydrocarbon, initiating anaerobic ethylbenzene oxidation). The genetic tools developed here, in addition to furthering knowledge of hydrocarbon metabolism, will also be helpful in identifying environmental factors involved in regulation of ethylbenzene degradation and will help to maximize the potential use of these organisms for bioremediation applications.

Daniel Rozen University of Dundee Plant & Microbial Development 0074378
Evolution of Morphological Variation Across Dictyostelid Social Amoebae
While most microbes live solitary lives, a few groups have evolved more complex multicellular strategies. The multicellular structures of one such group, the Dictyostelids, are extremely variable both in size and overall morphology. This work examines the evolution of morphological diversity across Dictyostelid species using a comparative approach. Three questions are addressed: To what extent are mechanisms that affect size and pattern conserved across solitary amoebas (SA's)? What specific molecular changes underlie the divergent morphologies observed across SA species? What is the molecular evolutionary history of genes involved in SA fruiting body size and pattern formation? This research provides insight into the evolutionary origins of their morphological variation and begins to address the evolution of these social organisms from solitary ones.

Elise Sullivan Rutgers University Metabolic Biochemistry 0047363
The Use of Benzoyl-CoA Reductase Genes in the Benzoate Pathway as an Indicator of Anaerobic Bacterial Degradation of Monoaromatic Hydrocarbon Pollutants
A key feature of monoaromatic compound metabolism by anaerobic bacteria is the enzyme benzoyl-CoA reductase, a protein previously thought to be highly conserved among anaerobes. This research examines the diveristy of this important enzyme. Then, the mechanisms by which benzoate degradation takes place are being characterized 1. Via biochemical analysis and 2. Mutagenesis-to determine which genes are involved in the process. Finally, Terminal Restriction Fragment Length Polymorphism analysis is being used to determine the abundance and diversity of these genes in the environment. This study will help assess the appropriateness of reductase genes as indicators of a bacterial community's capacity for bioremediation of aromatic hydrocarbons in polluted environments.

David Valentive Stanford University Metabolic Biochemistry 0074368
Experimental Studies of Hydrogen-producing Bacteria
Hydrogen is a key intermediate in anaerobic environments and is maintained at low concentration by microbial competition. This research uses a novel hydrogen-removal system to study the physiology and bioenergetics of obligately hydrogen-producing bacteria in pure culture. Studies focus on metabolism of important substrates, i.e., acetate, benzoate, amino acids, and glycolate. Enrichment and isolation procedures for anaerobic bacteria are also being developed. Hydrogen metabolism in bacteria is not well-understood but plays an important role in microbial diversity in the environment.

Doyle Ward University of California Berkeley Molecular Biochemistry 0074391
Understanding Bacterial Injection of DNA into Other Cells
The bacterium Agrobacterium tumefaciens injects DNA into plant cells via a type IV transporter "syringe", transforming the plant and creating a more favorable habitat for itself. Type IV transporters are multi-protein, bacterial membrane-associated complexes that attach to the recipient cell and bring it into close proximity with the host. They have not been well studied. This research examines the protein-protein interactions involved in type IV transporters using yeast two-hybrid assays and will construct a high-resolution protein map and determine the specific amino acid residues required for interaction. The functional significance of the peptide interactions will be confirmed in-vivo, and conservation of the peptide functions in other transporter systems will be examined. This research may be valuable to genetic engineering for industrial and agricultural uses, as well as identification of targets for disease intervention.

Cheryl Whistler University of Hawaii Animal Development 0074400
The role of the GacA/S Sensory System of the Marine Bacterium Vibrio fischeri During Symbiotic Association of the Bacterium with its Animal Host, the Hawaiian Bobtail Squid
This research explores how the symbiotic bacterium, V. fischeri, regulates association with its squid host, Euprymna scolopes. A sensory system, GacA/S which is involved in the virulence of pathogens, is experimentally mutated and the resulting symbiotic traits of the bacterium are assessed. The mutant bacterium is evaluated for its ability to associate with and influence normal development of the squid.

Alexandra Worden Scripps Institution of Oceanography Ecological and Evolutionary Physiology 0074392
Diversity and Physiology of Extemely Small Algae

Extremely small algae, otherwise known as picoeukaryotes (0.2-2micrometers), have been recorded as abundant in the worlds oceans since the early 1980s. Unfortunately little is known about them probably due to the fact that they are not well suited to characterization by microscopy or flow cytometry. The proposed work will explore both the diversity and physiology of these unique organisms. Diversity will be assessed in a marine ecosystem using phylogenetic libraries based on the 18S rRNA gene. In addition, two newly isolated strains will be characterized both phylogenetically and morphologically. In order to gain a better understanding of the physiology of these organisms, and their ability to co-exist with photosynthetic prokaryotic counterparts, preferences and mechanisms for nitrogen utilization will assessed. Growth under different nitrogen conditions will be measured and the molecular genetics of their nitrate transporters characterized. A full length cDNA will be generated and employed for the development of an antibody to the nitrate transporter for further elucidation of cellular response to changing nitrogen conditions. This type of approach should allow a high degree of sensitivity in analyzing growth regulating environmental factors.