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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 775 records · Page 43
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

COM1 , a factor of alternative non‐homologous end joining, lagging behind the classic non‐homologous end joining pathway in rice somatic cells

SUMMARY The role of rice ( Oryza sativa ) COM1 in meiotic homologous recombination (HR) is well understood, but its part in somatic double‐stranded break (DSB) repair remains unclear. Here, we show that for rice plants COM1 conferred tolerance against DNA damage caused by the chemicals bleomycin and mitomycin C, while the COM1 mutation did not compromise HR efficiencies and HR factor (RAD51 and RAD51 paralogues) localization to irradiation‐induced DSBs. Similar retarded growth at the post‐germination stage was observed in the com1‐2 mre11 double mutant and the mre11 single mutant, while combined mutations in COM1 with the HR pathway gene ( RAD51C ) or classic non‐homologous end joining (NHEJ) pathway genes ( KU70 , KU80 , and LIG4 ) caused more phenotypic defects. In response to γ‐irradiation, COM1 was loaded normally onto DSBs in the ku70 mutant, but could not be properly loaded in the MRE11 RNAi plant and in the wortmannin‐treated wild‐type plant. Under non‐irradiated conditions, more DSB sites were occupied by factors (MRE11, COM1, and LIG4) than RAD51 paralogues (RAD51B, RAD51C, and XRCC3) in the nucleus of wild‐type; protein loading of COM1 and XRCC3 was increased in the ku70 mutant. Therefore, quite differently to its role for HR in meiocytes, rice COM1 specifically acts in an alternative NHEJ pathway in somatic cells, based on the Mre11–Rad50–Nbs1 (MRN) complex and facilitated by PI3K‐like kinases. NHEJ factors, not HR factors, preferentially load onto endogenous DSBs, with KU70 restricting DSB localization of COM1 and XRCC3 in plant somatic cells.

Xu, Zhan↗
DOE OSTI2016

TU-H-CAMPUS-JeP1-05: Dose Deformation Error Associated with Deformable Image Registration Pathways

Purpose: To evaluate errors associated with using different deformable image registration (DIR) pathways to deform dose from planning CT (pCT) to cone-beam CT (CBCT). Methods: Deforming dose is controversial because of the lack of quality assurance tools. We previously proposed a novel metric to evaluate dose deformation error (DDE) by warping dose information using two methods, via dose and contour deformation. First, isodose lines of the pCT were converted into structures and then deformed to the CBCT using an image based deformation map (dose/structure/deform). Alternatively, the dose matrix from the pCT was deformed to CBCT using the same deformation map, and then the same isodose lines of the deformed dose were converted into structures (dose/deform/structure). The doses corresponding to each structure were queried from the deformed dose and full-width-half-maximums were used to evaluate the dose dispersion. The difference between the FWHM of each isodose level structure is defined as the DDE. Three head-and-neck cancer patients were identified. For each patient, two DIRs were performed between the pCT and CBCT, either deforming pCT-to-CBCT or CBCT-to-pCT. We evaluated the errors associated by using either of these pathways to deform dose. A commercially available, Demons based DIR was used for this study, and 10 isodose levels (20% to 105%) were used to evaluate the errors in various dose levels. Results: The prescription dose for all patients was 70 Gy. The mean DDE for CT-to-CBCT deformation was 1.0 Gy (range: 0.3–2.0 Gy) and this was increased to 4.3 Gy (range: 1.5–6.4 Gy) for CBCT-to-CT deformation. The mean increase in DDE between the two deformations was 3.3 Gy (range: 1.0–5.4 Gy). Conclusion: The proposed DDF was used to quantitatively estimate dose deformation errors caused by different pathways to perform DIR. Deforming dose using CBCT-to-CT deformation produced greater error than CT-to-CBCT deformation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Structural dissection of ergosterol metabolism reveals a pathway optimized for membrane phase separation

Sterols are among the most abundant lipids in eukaryotic cells yet are synthesized through notoriously long metabolic pathways. It has been proposed that the molecular evolution of such pathways must have required each step to increase the capacity of its product to condense and order phospholipids. Here, we carry out a systematic analysis of the ergosterol pathway that leverages the yeast vacuole’s capacity to phase separate into ordered membrane domains. In the post-synthetic steps specific to ergosterol biosynthesis, we find that successive modifications act to oscillate ordering capacity, settling on a level that supports phase separation while retaining fluidity of the resulting domains. Simulations carried out with each intermediate showed how conformers in the sterol’s alkyl tail are capable of modulating long-range ordering of phospholipids, which could underlie changes in phase behavior. Our results indicate that the complexity of sterol metabolism could have resulted from the need to balance lipid interactions required for membrane organization.

Science & Technology - Other Topics↗
DOE OSTI2025

Revealing atomic-scale switching pathways in van der Waals ferroelectrics

Two-dimensional (2D) van der Waals (vdW) materials hold the potential for ultrascaled ferroelectric (FE) devices due to their silicon compatibility and robust polarization down to atomic scale. However, the inherently weak vdW interactions enable facile sliding between layers, introducing complexities beyond those encountered in conventional ferroelectric materials and presenting substantial challenges in uncovering intricate switching pathways. Here, we combine atomic-resolution imaging under in situ electrical biasing conditions with first-principles calculations to unravel the atomic-scale switching mechanisms in SnSe, a vdW group IV monochalcogenide. Our results uncover the coexistence of a consecutive 90° switching pathway and a direct 180° switching pathway from antiferroelectric (AFE) to FE order in this vdW system. Atomic-scale investigations and strain analysis reveal that the switching processes simultaneously induce interlayer sliding and compressive strain, while the lattice remains coherent despite the presence of multidomain structures. These findings elucidate vdW ferroelectric switching dynamics at atomic scale and lay the foundation for the rational design of 2D ferroelectric nanodevices.

Li, Xinyan [Rice University, Houston, TX (United S↗
DOE OSTI2019

Oxidative Pathways of Deoxyribose and Deoxyribonate Catabolism

Deoxyribose is one of the building blocks of DNA and is released when cells die and their DNA degrades. We identified a bacterium that can grow with deoxyribose as its sole source of carbon even though its genome does not contain any of the known genes for breaking down deoxyribose. By growing many mutants of this bacterium together on deoxyribose and using DNA sequencing to measure the change in the mutants’ abundance, we identified multiple protein-coding genes that are required for growth on deoxyribose. Based on the similarity of these proteins to enzymes of known function, we propose a 6-step pathway in which deoxyribose is oxidized and then cleaved. Diverse bacteria use a portion of this pathway to break down a related compound, deoxyribonate, which is a waste product of metabolism. Our study illustrates the utility of large-scale bacterial genetics to identify previously unknown metabolic pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Mechanistic Insights into Oxygen Reduction Reaction on Metal Cathode Over BaZrO 3 -Based Electrolyte under Moist Atmosphere: Interfacial Interactions and Reaction Pathways

The oxygen reduction reaction (ORR) is a critical process that often governs the overall performance of electrochemical systems such as proton conducting solid oxide fuel cells. Despite its significance, the current understanding about the ORR, especially when it involves H 2 O is still limited. In this study, the proton involved ORR (PI-ORR) on metal cathode (e.g., Pt) over BaZrO 3 (BZO) electrolyte is investigated using density functional theory (DFT) under moist atmosphere. Two scenarios are considered: one at relatively high temperature (900 K) in the presence of oxygen vacancy in BZO substrate and one at relatively low temperature (700 K) without oxygen vacancy. We systematically explored oxygen vacancy effects on adsorption sites and proton transfer pathways, calculated energy profiles and Gibbs free energies for elementary steps along the O 2 dissociated and the O 2 concerted reaction pathways. We also evaluated H 2 O impacts on intermediate oxygen species (*O and *OH) through Ab Initio molecular dynamics. These analyses revealed pathway-dependent reaction mechanisms and hydration effects at triple-phase boundary, advancing fundamental understanding of PI-ORR in metal cathode/Ba-based electrolyte systems for energy applications.

08 - HYDROGEN↗
DOE OSTI2024

Feature Pathway Graphs using Random Forest Regressors

SAND2025-04671O Feature Pathway Graphs using Random Forest Regressors is a software tool that uses machine learning to determine pathways of influence between features in data sets. It can be used as a surrogate method for casual discovery. The output creates pathway graphs between features of interest. Sandia National Laboratories is a multimission laboratory managed and operated by National Technology & Engineering Solutions of Sandia, LLC, a wholly owned subsidiary of Honeywell International Inc., for the U.S. Department of Energy’s National Nuclear Security Administration under contract DE-NA0003525.

Peterson, Matthew↗
DOE OSTI2016

An Electrostatic Funnel in the GABA-Binding Pathway

The γ-aminobutyric acid type A receptor (GABA A -R) is a major inhibitory neuroreceptor that is activated by the binding of GABA. The structure of the GABA A -R is well characterized, and many of the binding site residues have been identified. However, most of these residues are obscured behind the C-loop that acts as a cover to the binding site. Thus, the mechanism by which the GABA molecule recognizes the binding site, and the pathway it takes to enter the binding site are both unclear. Through the completion and detailed analysis of 100 short, unbiased, independent molecular dynamics simulations, we have investigated this phenomenon of GABA entering the binding site. In each system, GABA was placed quasi-randomly near the binding site of a GABA A -R homology model, and atomistic simulations were carried out to observe the behavior of the GABA molecules. GABA fully entered the binding site in 19 of the 100 simulations. The pathway taken by these molecules was consistent and non-random; the GABA molecules approach the binding site from below, before passing up behind the C-loop and into the binding site. This binding pathway is driven by long-range electrostatic interactions, whereby the electrostatic field acts as a ‘funnel’ that sweeps the GABA molecules towards the binding site, at which point more specific atomic interactions take over. These findings define a nuanced mechanism whereby the GABA A -R uses the general zwitterionic features of the GABA molecule to identify a potential ligand some 2 nm away from the binding site.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Filling gaps in bacterial catabolic pathways with computation and high-throughput genetics

To discover novel catabolic enzymes and transporters, we combined high-throughput genetic data from 29 bacteria with an automated tool to find gaps in their catabolic pathways. GapMind for carbon sources automatically annotates the uptake and catabolism of 62 compounds in bacterial and archaeal genomes. For the compounds that are utilized by the 29 bacteria, we systematically examined the gaps in GapMind’s predicted pathways, and we used the mutant fitness data to find additional genes that were involved in their utilization. We identified novel pathways or enzymes for the utilization of glucosamine, citrulline, myo-inositol, lactose, and phenylacetate, and we annotated 299 diverged enzymes and transporters. We also curated 125 proteins from published reports. For the 29 bacteria with genetic data, GapMind finds high-confidence paths for 85% of utilized carbon sources. In diverse bacteria and archaea, 38% of utilized carbon sources have high-confidence paths, which was improved from 27% by incorporating the fitness-based annotations and our curation. GapMind for carbon sources is available as a web server ( http://papers.genomics.lbl.gov/carbon ) and takes just 30 seconds for the typical genome.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

The NRF2-KEAP1 Pathway Is an Early Responsive Gene Network in Arsenic Exposed Lymphoblastoid Cells

Inorganic arsenic (iAs), a major environmental contaminant, has risen as an important health problem worldwide. More detailed identification of the molecular mechanisms associated with iAs exposure would help to establish better strategies for prevention and treatment. Although chronic iAs exposures have been previously studied there is little to no information regarding the early events of exposure to iAs. To better characterize the early mechanisms of iAs exposure we conducted gene expression studies using sublethal doses of iAs at two different time-points. The major transcripts differentially regulated at 2 hrs of iAs exposure included antioxidants, detoxificants and chaperones. Moreover, after 12 hrs of exposure many of the down-regulated genes were associated with DNA replication and S phase cell cycle progression. Interestingly, the most affected biological pathway by both 2 or 12 hrs of iAs exposure were the Nrf2-Keap1 pathway, represented by the highly up-regulated HMOX1 transcript, which is transcriptionally regulated by the transcription factor Nrf2. Additional Nrf2 targets included SQSTM1 and ABCB6, which were not previously associated with acute iAs exposure. Signaling pathways such as interferon, B cell receptor and AhR route were also responsive to acute iAs exposure. Since HMOX1 expression increased early (20 min) and was responsive to low iAs concentrations (0.1 mM), this gene could be a suitable early biomarker for iAs exposure. In addition, the novel Nrf2 targets SQSTM1 and ABCB6 could play an important and previously unrecognized role in cellular protection against iAs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2014

Systems Level Analysis and Identification of Pathways and Networks Associated with Liver Fibrosis

Toxic liver injury causes necrosis and fibrosis, which may lead to cirrhosis and liver failure. Despite recent progress in understanding the mechanism of liver fibrosis, our knowledge of the molecular-level details of this disease is still incomplete. The elucidation of networks and pathways associated with liver fibrosis can provide insight into the underlying molecular mechanisms of the disease, as well as identify potential diagnostic or prognostic biomarkers. Towards this end, we analyzed rat gene expression data from a range of chemical exposures that produced observable periportal liver fibrosis as documented in DrugMatrix, a publicly available toxicogenomics database. We identified genes relevant to liver fibrosis using standard differential expression and co-expression analyses, and then used these genes in pathway enrichment and protein-protein interaction (PPI) network analyses. We identified a PPI network module associated with liver fibrosis that includes known liver fibrosis-relevant genes, such as tissue inhibitor of metalloproteinase-1, galectin-3, connective tissue growth factor, and lipocalin-2. We also identified several new genes, such as perilipin-3, legumain, and myocilin, which were associated with liver fibrosis. We further analyzed the expression pattern of the genes in the PPI network module across a wide range of 640 chemical exposure conditions in DrugMatrix and identified early indications of liver fibrosis for carbon tetrachloride and lipopolysaccharide exposures. Although it is well known that carbon tetrachloride and lipopolysaccharide can cause liver fibrosis, our network analysis was able to link these compounds to potential fibrotic damage before histopathological changes associated with liver fibrosis appeared. These results demonstrated that our approach is capable of identifying early-stage indicators of liver fibrosis and underscore its potential to aid in predictive toxicity, biomarker identification, and to generally identify disease-relevant pathways.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Biophysical and biochemical studies support TP0094 as a phosphotransacetylase in an acetogenic energy-conservation pathway in Treponema pallidum

The mechanisms of energy generation and carbon-source utilization in the syphilis spirochete Treponema pallidum have remained enigmatic despite complete genomic sequence information. Whereas the bacterium harbors enzymes for glycolysis, the apparatus for more efficient use of glucose catabolites, namely the citric-acid cycle, is apparently not present. Yet, the organism’s energy needs likely exceed the modest output from glycolysis alone. Recently, building on our structure-function studies of T . pallidum lipoproteins, we proposed a “flavin-centric” metabolic lifestyle for the organism that partially resolves this conundrum. As a part of the hypothesis, we have proposed that T . pallidum contains an acetogenic energy-conservation pathway that catabolizes D-lactate, yielding acetate, reducing equivalents for the generation and maintenance of chemiosmotic potential, and ATP. We already have confirmed the D-lactate dehydrogenase activity in T . pallidum necessary for this pathway to operate. In the current study, we focused on another enzyme ostensibly involved in treponemal acetogenesis, phosphotransacetylase (Pta). This enzyme is putatively identified as TP0094 and, in this study, we determined a high-resolution (1.95 Å) X-ray crystal structure of the protein, finding that its fold comports with other known Pta enzymes. Further studies on its solution behavior and enzyme activity confirmed that it has the properties of a Pta. These results are consistent with the proposed acetogenesis pathway in T . pallidum , and we propose that the protein be referred to henceforth as TpPta.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2013

A Systems Biology Platform for Characterizing Regulatory and Metabolic Pathways that Influence and Control Microbial Hydrogen Production

In this project, we created a novel systems biology technology platform and resources that can be used to reverse engineer and analyze gene regulatory networks and metabolic pathways that influence and control microbial hydrogen production. We constructed genome-scale transcriptional regulatory and metabolic models using automated model reconstruction methods, and subsequently integrated the regulatory and metabolic models for computational analysis. We devised novel algorithms for inferring putative regulatory architectures of metabolic pathways based on their topology, and for integrating gene expression information in flux balance analysis (FBA) models towards computing dynamical changes in metabolic objectives. From a metabolic engineering perspective, we improved and applied a method for predicting optimal environmental conditions and genetic modifications towards maximal productions of multiple desired metabolic outputs. We also developed and tested an improved flux balance approach for predicting the response of metabolic networks to genetic perturbations, proving that errors in model predictions are approaching the limit of experimental uncertainty. We also used the metabolic and regulatory models to identify relevant metabolic processes and pathways involved in hydrogen production. Below we provide a summary and details of our achievements.

Collins, James J.↗
DOE OSTI2015

Pathway Aggregation in the Risk Assessment of Proliferation Resistance and Physical Protection (PR&PP) of Nuclear Energy Systems

The framework for Proliferation Resistance and Physical Protection (PR & PP) evaluation is to define a set of challenges, to obtain the system responses, and to assess the outcomes. The assessment of outcomes heavily relies on pathways, defined as sequences of events or actions that could potentially be followed by a State or a group of individuals in order to achieve a proliferation objective, with the defined threats as initiating events. There may be large number of segments connecting pathway stages (e.g. acquisition, processing, and fabrication for PR) which can lead to even larger number of pathways or scenarios through possible different combinations of segment connections, each with associated probabilities contributing to the overall risk. Clustering of these scenarios in specified stage attribute intervals is important for their tractable analysis and outcome assessment. A software tool for scenario generation and clustering (OSUPR) is developed that utilizes the PRCALC code developed at the Brookhaven National Laboratory for scenario generation and the K- means, mean shift and adaptive mean shift algorithms as possible clustering schemes. The results of the study using the Example Sodium Fast Breeder as an example system show that clustering facilitates the probabilistic or deterministic analysis of scenarios to identify system vulnerabilities and communication of the major risk contributors to stakeholders. The results of the study also show that the mean shift algorithm has the most potential for assisting the analysis of the scenarios generated by PRCALC.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2016

Cradle-to-Grave Lifecycle Analysis of U.S. Light Duty Vehicle-Fuel Pathways: A Greenhouse Gas Emissions and Economic Assessment of Current (2015) and Future (2025-2030) Technologies

This study provides a comprehensive lifecycle analysis (LCA), or cradle-to-grave (C2G) analysis, of the cost and greenhouse gas (GHG) emissions of a variety of vehicle-fuel pathways, as well as the levelized cost of driving (LCD) and cost of avoided GHG emissions. This study also estimates the technology readiness levels (TRLs) of key fuel and vehicle technologies along the pathways. The C2G analysis spans a full portfolio of midsize light-duty vehicles (LDVs), including conventional internal combustion engine vehicles (ICEVs), flexible fuel vehicles (FFVs), hybrid electric vehicles (HEVs), plug-in hybrid electric vehicles (PHEVs), battery electric vehicles (BEVs), and fuel cell electric vehicles (FCEVs). In evaluating the vehicle-fuel combinations, this study considers both low-volume and high-volume “CURRENT TECHNOLOGY” cases (nominally 2015) and a high-volume “FUTURE TECHNOLOGY” lower-carbon case (nominally 2025–2030). For the CURRENT TECHNOLOGY case, low-volume vehicle and fuel production pathways are examined to determine costs in the near term.

29 ENERGY PLANNING, POLICY, AND ECONOMY↗
DOE OSTI2016

Cradle-to-Grave Lifecycle Analysis of U.S. Light-Duty Vehicle-Fuel Pathways: A Greenhouse Gas Emissions and Economic Assessment of Current (2015) and Future (2025–2030) Technologies

This study provides a comprehensive life-cycle analysis (LCA), or cradle-to-grave (C2G) analysis, of the cost and greenhouse gas (GHG) emissions of a variety of vehicle-fuel pathways, as well as the levelized cost of driving (LCD) and cost of avoided GHG emissions. This study also estimates the technology readiness levels (TRLs) of key fuel and vehicle technologies along the pathways. The C2G analysis spans a full portfolio of midsize light-duty vehicles (LDVs), including conventional internal combustion engine vehicles (ICEVs), flexible fuel vehicles (FFVs), hybrid electric vehicles (HEVs), plug-in hybrid electric vehicles (PHEVs), battery electric vehicles (BEVs), and fuel cell electric vehicles (FCEVs). In evaluating the vehicle-fuel combinations, this study considers both low-volume and high-volume “CURRENT TECHNOLOGY” cases (nominally 2015) and a high-volume “FUTURE TECHNOLOGY” lower-carbon case (nominally 2025–2030). For the CURRENT TECHNOLOGY case, low-volume vehicle and fuel production pathways are examined to determine costs in the near term.

02 PETROLEUM↗
DOE OSTI2016

RECOVERY ACT - Thylakoid Assembly and Folded Protein Transport by the Tat Pathway

Assembly of functional photosystems complete with necessary intrinsic (membrane-bound) and extrinsic proteins requires the function of at least 3 protein transport pathways in thylakoid membranes. Our research focuses on one of those pathways, a unique and essential protein transport pathway found in the chloroplasts of plants, bacteria, and some archaebacteria, the Twin arginine translocation (Tat) system. The chloroplast Tat (cpTat) system is thought to be responsible for the proper location of ~50% of thylakoid lumen proteins, several of which are necessary for proper photosystem assembly, maintenance, and function. Specifically, cpTat systems are unique because they transport fully folded and assembled proteins across ion tight membranes using only three membrane components, Tha4, Hcf106, and cpTatC, and the protonmotive force generated by photosynthesis. Despite the importance of the cpTat system in plants, the mechanism of transport of a folded precursor is not well known. Our long-term goal is to investigate the role protein transport systems have on organelle biogenesis, particularly the assembly of membrane protein complexes in thylakoids of chloroplasts. The objective of this proposal is to correlate structural changes in the membrane-bound cpTat component, Tha4, to the mechanism of translocation of folded-precursor substrates across the membrane bilayer by using a cysteine accessibility and crosslinking approach. Our central hypothesis is that the precursor passes through a proteinaceous pore of assembled Tha4 protomers that have undergone a conformational or topological change in response to transport. This research is predicated upon the observations that Tha4 exists in molar excess in the membrane relative to the other cpTat components; its regulated assembly to the precursor-bound receptor; and our data showing oligomerization of Tha4 into very large complexes in response to transport. Our rationale for these studies is that understanding cpTat system mechanism in chloroplasts will lead to a better understanding of the biogenesis of photosynthetic membranes potentially providing a means to engineer photosynthetic complexes into synthetic membranes for energy production. We are especially well prepared to undertake this project because we have developed a novel functional replacement assay, which was used to demonstrate a correlation of Tha4 oligomerization to transport. Thylakoids of plant chloroplasts provide a very robust, reliable assay to gain mechanistic detail about cpTat systems, providing most of the biochemical analyses to date. We plan to test our central hypothesis and accomplish the overall objective of this proposal by (1) Identifying the cpTat component(s) that interact with the mature domain of precursor during transport, (2) Determining the organization of the cpTat translocon, and (3) Comparing Tha4 topology in thylakoids during active transport and at rest. The proposed studies are innovative due to our ability to correlate structural changes in cpTat protein complexes during the transport of precursor. At the completion of this project, we expect to know the cpTat component(s) that interacts directly with the mature domain of the precursor, important because it is not known which components comprise the pore for passage of the mature domain. We also expect to know the arrangement of the components in the cpTat transport complex through direct interaction between Tha4 and the other CpTat components, a key point to establishing the mechanism of translocation. Lastly, we expect to correlate topological changes of Tha4 with precursor transport, key to establishing Tha4's role in the transport process. The successful completion of these studies is expected to have an important impact in understanding chloroplast biogenesis and assembly of photosynthetic complexes in plants and photosynthetic bacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Computational Modeling of Fluctuations in Energy and Metabolic Pathways of Methanogenic Archaea

The methanogenic archaea, anaerobic microbes that convert CO2 and H2 and/or other small organic fermentation products into methane, play an unusually large role in the global carbon cycle. As they perform the final step in the anaerobic breakdown of biomass, methanogens are a biogenic source of an estimated one billion tons methane each year. Depending on the location, produced methane can be considered as either a greenhouse gas (agricultural byproduct), sequestered carbon storage (methane hydrate deposits), or a potential energy source (organic wastewater treatment). These microbes therefore represent an important target for biotechnology applications. Computational models of methanogens with predictive power are useful aids in the adaptation of methanogenic systems, but need to connect processes of wide-ranging time and length scales. In this project, we developed several computational methodologies for modeling the dynamic behavior of entire cells that connects stochastic reaction-diffusion dynamics of individual biochemical pathways with genome-scale modeling of metabolic networks. While each of these techniques were in the realm of well-defined computational methods, here we integrated them to develop several entirely new approaches to systems biology. The first scientific aim of the project was to model how noise in a biochemical pathway propagates into cellular phenotypes. Genetic circuits have been optimized by evolution to regulate molecular processes despite stochastic noise, but the effect of such noise on a cellular biochemical networks is currently unknown. An integrated stochastic/systems model of Escherichia coli species was created to analyze how noise in protein expression gives—and therefore noise in metabolic fluxes—gives rise to multiple cellular phenotype in isogenic population. After the initial work developing and validating methods that allow characterization of the heterogeneity in the model organism E. coli, the project shifted toward investigations of the methanogen Methanosarcina acetivorans. By integrating an unprecedented transcriptomics dataset for growth of the methanogen on many substrates with an in silico model, heterogeneity in metabolic pathway usage and methane production were examined. This lent insight into the physiological requirements of the organism under different environmental conditions and uncovered the unique regulatory role that mRNA half-life has in shaping metabolic flux distributions in this organism.

59 BASIC BIOLOGICAL SCIENCES↗