In Fiscal Year 2001, DOEs Offices of Biological and Environmental
Research (BER) and Advanced Scientific Computing Research (ASCR) called
for new research that was to become the predecessor of the Genomic Science program. These research solicitations, Microbial Cell Project
and Advanced Modeling and Simulation of Biological Systems,
called for research that would use experimentation and computation to
lead to a more comprehensive understanding of the functioning of microbes
as complete biological systems. The following projects were funded from
these solicitations and are part of the Genomic Science program.
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Jim Fredrickson (PNNL), Jizhong Zhou
(ORNL) and Eugene Kolker (BIATECH), Environmental
Sensing, Metabolic Response and Regulatory Networks in the Respiratory
Versitile Bacterium Shewanella, to initiate the Shewanella
Federation, a multi-investigator and multi-lab consortium to
characterize the biology of the fully sequenced bacterium Shewanella
oneidensis MR-1. This microbe is widespread in the environment
and has metabolic capacities allowing it to "handle" (reduce
or oxidize) many of the metals of major concern to DOE due to
their presence at contaminated
DOE sites. The research will use innovative technologies to: 1) analyze
the proteome and transcriptome (using Mass Spec and microarray
methods);
2) localize the proteins in the cell envelope (using various microscope
approaches); 3) characterize the biochemistry and physiology,
using
optical methods to examine protein/protein interactions (in collaboration
with Shimon Weiss at UCLA); and 4) model cell networks (in collaboration
with Bernhard Palsson, UCSD).
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Harley McAdams (Stanford), Global Characterization
of Genetic Regulatory Circuitry Controlling Adaptive Metabolic Pathways,
to study Caulobacter crescentus, an important organism
for bioremediation. The 5 main thrusts are: 1) to identify genome
circuits involved in growth; 2) to study the physiology of cells in
biofilms; 3) to study signal transduction networks; 4) to combine
these experiments with computational programs to predict metabolic
and regulatory pathways and operons and to construct a regulatory
map to identify networks that control growth cell cycle, biofilm formation
and response to stress; and 5) to model, using this vast array of
information generated about the biology of C. crescentus, its
biology. DOEs Office of Basic Energy Sciences is also helping to
fund this project.
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Derek Lovley (U Mass Amherst), A Conceptual
and In Silico Model of the Dissimilatory Metal-Reducing Microorganism,
Geobacter Sulforeducens, to study the energetics and metabolism
of Geobacter sulfurreducens, a model organism for various Geobacter
species and other iron-reducing microbes. Geobacter species dominate
subsurface sites in which iron reduction occurs. The project will
model central metabolism, electron transport, growth under nutrient-limiting
conditions, regulatory mechanisms, and environmental responses in
G. sulfurreducens. The long term goal is to develop a predictive
in silico model of these processes.
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Michael Daly (Uniformed Services University
of the Health Sciences), The Dynamics of Cellular Processes in Deinococcus
Radiodurans, to study the multiple cellular components of
the responses of the highly radiation-resistant microbe, Deinococcus
radiodurans, to acute and chronic radiation exposure. This project
will use computational and experimental approaches including whole
cell mass spectrometry (MS) and DNA arrays. The organism focused
on, Deinococcus radiodurans is capable of resisting enormous
doses of radiation and the mechanisms behind this ability are as yet
uncharacterized.
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Robert Tabita (Ohio State), The Rhodopseudomonas
Palustris Microbial Cell Project, to study Rhodopseudomonas
palustris, a model purple nonsulfur photosynthetic bacterium.
This bacterium is remarkably versatile in the ways in which it can
grow. The genome sequence is complete and the annotation is nearing
completion. A genetic system is available. This group will carry
out research to characterize the biochemical and physiological processes
as well as functional proteomic analyses using expression profiling
with transcriptional micro-array analysis, intracellular localization
and computational cell process modeling. The combination of genomics,
proteomics, DNA array technology, bacterial "two hybrid"
systems, and directed and random mutagenesis constitutes a global
approach to the biology of R. palustris.
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Timothy Donohue (University of Wisconsin-Madison),
The Molecular Basis for Metabolic and Energetic Diversity, to
analyze and model the flux of carbon, nitrogen and "reducing
power" of the versatile microorganism, the alpha proteobacterium
Rhodobacter sphaeroides strain 2.4.1. A main goal is to understand
the complex regulation system in this versatile bacterium and the
expected complexity of the genome.
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John Leigh (University of Washington), Global
Regulation in the Methane Producing Archaeon Methanococcus maripaludis,
to study Methanococcus maripaludis, a methane producing microbe
of considerable promise for understanding biomass conversion. The
focus will be on understanding its physiology (using microarrays)
and its regulatory systems (using mutagenesis of candidate regulatory
genes), especially those pertinent to methane production. Funding
for this project is provided by DOEs Office of Basic Energy Sciences.
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Willem Vermaas (Arizona State University),
An Integrative Approach to Energy, Carbon, and Redox Metabolism
in
the Cyanobacterium Synechocystis, to study Synechocystis
sp. PCC 6803, the first photosynthetic organism whose genome
was completely sequenced. The main approach will be to exploit the
library
of targeted gene deletion mutants that are available (with more becoming
available) to study photosynthesis and electron transport pathways.
This will be combined with other proteomic, metabolic, and intracellular
localization information to build a metabolic model. Funding for
this
project is provided by DOEs Office of Basic Energy Sciences.
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Norman Dovichi (University of Washington),
The Single-Cell Proteome Project: Ultrasensitive Proteome Analysis
of Deinococcus Radiodurans, to develop capillary analysis
technologies to permit the monitoring of changes in protein expression
in single cells using fluorescence and pushing the resolution by an
order of magnitude over what it presently is; in short, to build a
"better microscope" for tracking gene expression in single
cells following environmental challenges (e.g., exposure to radiation).
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Kenneth Downing (LBNL), Electron Tomography
of Microbial Cells, to study the use of electron tomography to
image the inside of a microbial cell by freezing intact microbial
cells in a way that preserves one layer of liquid water molecules
above their membranes (permitting survival and viability). EM images
and computer reconstruction are then be used to derive 3D images of
internal cell constituents.
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Gary Andersen (LLNL), Pangenomic Analysis
Using RDA, to pursue advanced protein-protein interaction systems
for use to characterize the protein machines within Caulobacter
crescentus (in collaboration with Harley McAdams, Stanford). This
project will build a cellular protein interaction map using a protein-fragment
complementation assay that offers advantages over the yeast two-hybrid
system.
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David Case (Scripps Research Institute), Biomolecular
Simulation Using Amber and CHARMM, to build on the existing CHARMM
and Amber simulation packages, adapting them in novel ways to massively
parallel architectures and high-performance CPUs.
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Peter Ortoleva (Indiana University), Cyber
Cell: Automated Physico-Chemical Cell Model Development Through Information
Technology, to integrate the comprehensive reaction-transport-genetic
cell simulator, Cyber-Cell, with experimental data, resulting in an
automated model development methodology. The model will be developed
and tested using data on E. coli.
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Andrey Rzhetsky (Columbia University),
Computational Analysis and Simulation of Bacterial Molecular Networks,
to enhance our ability to predict and control bacterial phenotypic
behavior by proper manipulation of genomic information and environmental
stimuli. Such bacterial phenotypic behavior can be steered towards
DOE-relevant activities such as environmental remediation and restoration
of contaminated environments.
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Albert Laszio Barabasi (University of
Notre Dame), Organization of Complex Metabolic Networks, to develop
semi-quantitative models that capture the structure and function of
the E. coli metabolism. The investigators plan to complement
the purely topologic, pathway based methodologies with dynamical information
quantifying how the different components of E. coli metabolism
work together under varying conditions. The approach emphasizes topological
characterization of the networks, and statistical characterization
of the fluctuation of metabolites, leading to experimentally testable
predictions. The modeling approach will combine stoichiometric and
regulatory information.
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Julie Mitchell, (University of California,
San Diego), Parallel Protein Docking and Interaction Dynamics with
Adaptive Meash Solutions to the Poisson-Boltzmann Equation, to
improve tools for determination of the structures of protein complexes
through docking with an energy function of high quality. Particular
emphasis is given to electrostatic interactions, and much of the work
involves needed improvements to approaches in current use through
application of accurate solutions to the Poisson-Boltzmann equation.
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Michael Colvin (Lawrence Livermore National
Laboratory), Advanced Molecular Simulations of E. Coli Polymerase
III, to use advanced molecular simulation methods on terascale
computers to improve understanding of bacterial multicomponent protein
machines. The research will involve performing dynamical simulations
of E. coli DNA polymerase III biochemical processes using classical
and quantum mechanical force fields and object-oriented implementations
of these algorithms that efficiently use massively parallel computers.
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Haluk Resat (Pacific Northwest National Laboratory),
Computational Approaches and Framework for Microbial Cell Simulations,
to develop a wide-ranging set of computational tools in support of
intracellular model building. These tools will be applied to build
computable representations of the core energy and material pathways
in Rhodobacter sphaeroides genome sequenced and being assembled
at present. R. sphaeroidess is of interest and relevant for applying
and validating newly developed biological modeling tools as (1) the
structure, function and regulation of its photosynthetic systems are
among the best characterized (2) it provides, in a single organism,
access to the entire range of metabolic lifestyles, their coupling
and regulation.
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T.P. Straatsma (Pacific Northwest National
Laboratory), Molecular Modeling of Complex Enzymatic reactions: The
Respiratory Enzyme Flavocytochrome c3 Fumarate Reductase of Shewanella
frigidimarina, to carry out highly detailed simulations
of complex reaction mechanisms in bacterial enzymes such as a flavocytochrome.
Research involves ongoing development of a program that permits such
simulations, and specific application to the study of metal ion reduction
through an electron transfer process. The tools developed will be
useful to many researchers.
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Christopher Schilling (Genomatica, Inc.),
Development of the Next Generation of Genome-scale Constraints-Based
Cellular Models, to carry out a top-down approach to metabolic
modeling, that begins with a stoichiometric network model and successively
constrains the set of admissible solutions with conditions that are
derived, for instance, from thermodynamics resulting, ideally, in
a unique solution that is the true solution.
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Eugene Kolker (BIATECH),
Interdisciplinary Study of Shewanella putrefaciens MR-1's
Metabolism and Metal Reduction, to study S. putrefaciens MR-1
in an attempt to delineate the organisms response to environmental
perturbation.
MR-1 is a suitable organism for this study because it can function
in aerobic conditions, reduces metals, has a well-defined biochemistry
and a sequenced genome.
