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Title: Intercellular Genomics of Subsurface Microbial Colonies

Abstract

This report summarizes progress in the second year of this project. The objective is to develop methods and software to predict the spatial configuration, properties and temporal evolution of microbial colonies in the subsurface. To accomplish this, we integrate models of intracellular processes, cell-host medium exchange and reaction-transport dynamics on the colony scale. At the conclusion of the project, we aim to have the foundations of a predictive mathematical model and software that captures the three scales of these systems – the intracellular, pore, and colony wide spatial scales. In the second year of the project, we refined our transcriptional regulatory network discovery (TRND) approach that utilizes gene expression data along with phylogenic similarity and gene ontology analyses and applied it successfully to E.coli, human B cells, and Geobacter sulfurreducens. We have developed a new Web interface, GeoGen, which is tailored to the reconstruction of microbial TRNs and solely focuses on Geobacter as one of DOE’s high priority microbes. Our developments are designed such that the frameworks for the TRND and GeoGen can readily be used for other microbes of interest to the DOE. In the context of modeling a single bacterium, we are actively pursuing both steady-state and kineticmore » approaches. The steady-state approach is based on a flux balance that uses maximizing biomass growth rate as its objective, subjected to various biochemical constraints, for the optimal values of reaction rates and uptake/release of metabolites. For the kinetic approach, we use Karyote, a rigorous cell model developed by us for an earlier DOE grant and the DARPA BioSPICE Project. We are also investigating the interplay between bacterial colonies and environment at both pore and macroscopic scales. The pore scale models use detailed representations for realistic porous media accounting for the distribution of grain size whereas the macroscopic models employ the Darcy-type flow equations and up-scaled advective-diffusive transport equations for chemical species. We are rigorously testing the relationship between these two scales by evaluating macroscopic parameters using the volume averaging methodology applied to pore scale model results.« less

Authors:
 [1];  [1];  [1];  [1]
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  1. Indiana Univ., Bloomington, IN (United States)
Publication Date:
Research Org.:
Indiana Univ., Bloomington, IN (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
899328
Report Number(s):
DOE/ER/25676-2
DOE Contract Number:
FG02-05ER25676
Resource Type:
Technical Report
Country of Publication:
United States
Language:
English
Subject:
58 GEOSCIENCES; 54 ENVIRONMENTAL SCIENCES; 60 APPLIED LIFE SCIENCES; geobacter; porous media; reaction-transport modeling; fluid flow; transcriptional regulatory networks; genomics; kinetic modeling

Citation Formats

Ortoleva, Peter, Tuncay, Kagan, Gannon, Dennis, and Meile, Christof. Intercellular Genomics of Subsurface Microbial Colonies. United States: N. p., 2007. Web. doi:10.2172/899328.
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Ortoleva, Peter, Tuncay, Kagan, Gannon, Dennis, & Meile, Christof. Intercellular Genomics of Subsurface Microbial Colonies. United States. doi:10.2172/899328.
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Ortoleva, Peter, Tuncay, Kagan, Gannon, Dennis, and Meile, Christof. Wed . "Intercellular Genomics of Subsurface Microbial Colonies". United States. doi:10.2172/899328. https://www.osti.gov/servlets/purl/899328.
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@article{osti_899328,
title = {Intercellular Genomics of Subsurface Microbial Colonies},
author = {Ortoleva, Peter and Tuncay, Kagan and Gannon, Dennis and Meile, Christof},
abstractNote = {This report summarizes progress in the second year of this project. The objective is to develop methods and software to predict the spatial configuration, properties and temporal evolution of microbial colonies in the subsurface. To accomplish this, we integrate models of intracellular processes, cell-host medium exchange and reaction-transport dynamics on the colony scale. At the conclusion of the project, we aim to have the foundations of a predictive mathematical model and software that captures the three scales of these systems – the intracellular, pore, and colony wide spatial scales. In the second year of the project, we refined our transcriptional regulatory network discovery (TRND) approach that utilizes gene expression data along with phylogenic similarity and gene ontology analyses and applied it successfully to E.coli, human B cells, and Geobacter sulfurreducens. We have developed a new Web interface, GeoGen, which is tailored to the reconstruction of microbial TRNs and solely focuses on Geobacter as one of DOE’s high priority microbes. Our developments are designed such that the frameworks for the TRND and GeoGen can readily be used for other microbes of interest to the DOE. In the context of modeling a single bacterium, we are actively pursuing both steady-state and kinetic approaches. The steady-state approach is based on a flux balance that uses maximizing biomass growth rate as its objective, subjected to various biochemical constraints, for the optimal values of reaction rates and uptake/release of metabolites. For the kinetic approach, we use Karyote, a rigorous cell model developed by us for an earlier DOE grant and the DARPA BioSPICE Project. We are also investigating the interplay between bacterial colonies and environment at both pore and macroscopic scales. The pore scale models use detailed representations for realistic porous media accounting for the distribution of grain size whereas the macroscopic models employ the Darcy-type flow equations and up-scaled advective-diffusive transport equations for chemical species. We are rigorously testing the relationship between these two scales by evaluating macroscopic parameters using the volume averaging methodology applied to pore scale model results.},
doi = {10.2172/899328},
journal = {},
number = ,
volume = ,
place = {United States},
year = {Wed Feb 14 00:00:00 EST 2007},
month = {Wed Feb 14 00:00:00 EST 2007}
}
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Technical Report:
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DOI:  10.2172/899328
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