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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 397 records · Page 22
All sourcesNASA NTRSDOE OSTI
NASA NTRS2014

Uncertainty in Model Predictions of Vibrio Vulnificus Response to Climate Variability and Change: A Chesapeake Bay Case Study

The effect that climate change and variability will have on waterborne bacteria is a topic of increasing concern for coastal ecosystems, including the Chesapeake Bay. Surface water temperature trends in the Bay indicate a warming pattern of roughly 0.3-0.4 C per decade over the past 30 years. It is unclear what impact future warming will have on pathogens currently found in the Bay, including Vibrio spp. Using historical environmental data, combined with three different statistical models of Vibrio vulnificus probability, we explore the relationship between environmental change and predicted Vibrio vulnificus presence in the upper Chesapeake Bay. We find that the predicted response of V. vulnificus probability to high temperatures in the Bay differs systematically between models of differing structure. As existing publicly available datasets are inadequate to determine which model structure is most appropriate, the impact of climatic change on the probability of V. vulnificus presence in the Chesapeake Bay remains uncertain. This result points to the challenge of characterizing climate sensitivity of ecological systems in which data are sparse and only statistical models of ecological sensitivity exist.

model predictions↗
DOE OSTI2017

Statistical Analysis of CO 2 Exposed Wells to Predict Long Term Leakage through the Development of an Integrated Neural-Genetic Algorithm

The objective of this project is to develop a computerized statistical model with the Integrated Neural-Genetic Algorithm (INGA) for predicting the probability of long-term leak of wells in CO 2 sequestration operations. This object has been accomplished by conducting research in three phases: 1) data mining of CO 2 -explosed wells, 2) INGA computer model development, and 3) evaluation of the predictive performance of the computer model with data from field tests. Data mining was conducted for 510 wells in two CO 2 sequestration projects in the Texas Gulf Coast region. They are the Hasting West field and Oyster Bayou field in the Southern Texas. Missing wellbore integrity data were estimated using an analytical and Finite Element Method (FEM) model. The INGA was first tested for performances of convergence and computing efficiency with the obtained data set of high dimension. It was concluded that the INGA can handle the gathered data set with good accuracy and reasonable computing time after a reduction of dimension with a grouping mechanism. A computerized statistical model with the INGA was then developed based on data pre-processing and grouping. Comprehensive training and testing of the model were carried out to ensure that the model is accurate and efficient enough for predicting the probability of long-term leak of wells in CO 2 sequestration operations. The Cranfield in the southern Mississippi was select as the test site. Observation wells CFU31F2 and CFU31F3 were used for pressure-testing, formation-logging, and cement-sampling. Tools run in the wells include Isolation Scanner, Slim Cement Mapping Tool (SCMT), Cased Hole Formation Dynamics Tester (CHDT), and Mechanical Sidewall Coring Tool (MSCT). Analyses of the obtained data indicate no leak of CO 2 cross the cap zone while it is evident that the well cement sheath was invaded by the CO 2 from the storage zone. This observation is consistent with the result predicted by the INGA model which indicates the well has a CO 2 leak-safe probability of 72%. This comparison implies that the developed INGA model is valid for future use in predicting well leak probability.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Alternating Conditional Expectations: Introducing a Non‐Parametric Statistical Method to Interpret Long‐Term Greenhouse Gas Flux Measurements Over Semi‐Arid and Wetland Ecosystems

Abstract We explore the potential of using a non‐parametric statistical method called Alternating Conditional Expectations, ACE, to quantify functional relationships in biogeosciences. Here, ACE is used to quantify the non‐linear and multi‐faceted responses of greenhouse gas fluxes to a set of biophysical forcings, when the shapes of those response surfaces are unknown. We evaluated the statistical method over two contrasting ecosystems and two contrasting time steps. One case involved quantifying the biophysical controls of water vapor and carbon dioxide (CO 2 ) fluxes over a semi‐arid oak savanna using daily integrated fluxes. The other case evaluated the responses of CO 2 and methane (CH 4 ) flux measurements to a set of biophysical forcings at a restored tidal wetland using thirty‐minute averages. The statistical model, based on 4 independent variables, explained up over 90% of the variation in daily integrated flux densities of water vapor and net carbon dioxide exchange at the savanna site. This fit was defined by distinct non‐linear responses to such drivers as gross primary production, photosynthetically active radiation, air temperature, vapor pressure deficit and soil moisture. At the tidal wetland site, we evaluated net carbon dioxide and methane fluxes with short‐term measurements to capture the influence of rising and falling tides and seasonality in biological activity. The statistical model defined the shape of the forcing of fluxes due to the roles of carbon exudates, water table depth, oxygen level in the water column, temperature and vegetation status. The statistical fits of the greenhouse gas fluxes were less precise than the savanna case. The fetch varies on a run‐to‐run basis as it is comprised of a heterogeneous mosaic of open water and vegetation. Furthermore, it is difficult to monitor the environmental conditions of the archaea and bacteria in the sediments that produce methane and carbon dioxide.

Environmental Sciences & Ecology↗
NASA NTRS2013

Spatial Statistical Data Fusion (SSDF)

As remote sensing for scientific purposes has transitioned from an experimental technology to an operational one, the selection of instruments has become more coordinated, so that the scientific community can exploit complementary measurements. However, tech nological and scientific heterogeneity across devices means that the statistical characteristics of the data they collect are different. The challenge addressed here is how to combine heterogeneous remote sensing data sets in a way that yields optimal statistical estimates of the underlying geophysical field, and provides rigorous uncertainty measures for those estimates. Different remote sensing data sets may have different spatial resolutions, different measurement error biases and variances, and other disparate characteristics. A state-of-the-art spatial statistical model was used to relate the true, but not directly observed, geophysical field to noisy, spatial aggregates observed by remote sensing instruments. The spatial covariances of the true field and the covariances of the true field with the observations were modeled. The observations are spatial averages of the true field values, over pixels, with different measurement noise superimposed. A kriging framework is used to infer optimal (minimum mean squared error and unbiased) estimates of the true field at point locations from pixel-level, noisy observations. A key feature of the spatial statistical model is the spatial mixed effects model that underlies it. The approach models the spatial covariance function of the underlying field using linear combinations of basis functions of fixed size. Approaches based on kriging require the inversion of very large spatial covariance matrices, and this is usually done by making simplifying assumptions about spatial covariance structure that simply do not hold for geophysical variables. In contrast, this method does not require these assumptions, and is also computationally much faster. This method is fundamentally different than other approaches to data fusion for remote sensing data because it is inferential rather than merely descriptive. All approaches combine data in a way that minimizes some specified loss function. Most of these are more or less ad hoc criteria based on what looks good to the eye, or some criteria that relate only to the data at hand.

Braverman, Amy J.↗
NASA NTRS1985

Use of observational and model-derived fields and regime model output statistics in mesoscale forecasting

Various empirical and statistical weather-forecasting studies which utilize stratification by weather regime are described. Objective classification was used to determine weather regime in some studies. In other cases the weather pattern was determined on the basis of a parameter representing the physical and dynamical processes relevant to the anticipated mesoscale phenomena, such as low level moisture convergence and convective precipitation, or the Froude number and the occurrence of cold-air damming. For mesoscale phenomena already in existence, new forecasting techniques were developed. The use of cloud models in operational forecasting is discussed. Models to calculate the spatial scales of forcings and resultant response for mesoscale systems are presented. The use of these models to represent the climatologically most prevalent systems, and to perform case-by-case simulations is reviewed. Operational implementation of mesoscale data into weather forecasts, using both actual simulation output and method-output statistics is discussed.

Forbes, G. S.↗
NASA NTRSDate not supplied

Multi-source Estimates of Land / Ocean Moisture Transport Variability over the Satellite Era

It is widely appreciated that atmospheric transport of water from the world’s oceans is a process key to planetary energy balance as well as Earth's habitability. What is not yet clear is the extent of variability in moisture transports, the relative importance of interdecadal variability versus climate change signals, and importantly, our ability to quantify these changes. This work assesses variations in moisture transport variability during the satellite era (~1980 to present) by comparing several different estimates. (i) The most direct estimate is the vertically integrated flux convergence of moisture from reanalyses which use observed wind and moisture information. (ii) One alternative estimate comes from P-ET over land taken from global hydrologic models constrained with precipitation and near-surface meteorology. Here we use an ensemble of six models. An adjunct to this method is to employ satellite derive ET (e.g., GLEAM or DOLCE). (iii) Complementary to this is E-P over the global oceans derived from satellite estimates of P such as TRMM, GPM and GPCP and SeaFlux V3 or J-OFURO3 estimates of E, all relying heavily upon microwave measurements. Transport between land and oceans must essentially balance at monthly scales, i.e., vanish globally. (iv) a fourth perspective comes from estimate of terrestrial RO + storage rate, delta S. G-RUN Ensemble which uses observed streamflow and P measurements to calibrate a statistical model provides the former while GRACE, GRACE-FO provide total water storage anomalies used to calculate storage rate changes. GRACE REC uses GRACE data to train a precipitation-driven statistical model to extend storage estimates before the GRACE era. (All of these alternatives to reanalysis estimates also consider the small atmospheric column water vapor contribution.) We examine the transport changes from these three different methodologies, their relative accuracies and discuss the origin of their differences. Regional trends in moisture flux divergence and their role in multi-decadal trends are considered. Interannual variability arising in connection with ENSO variability is a dominant signal, driven largely by P changes. Trends since 1980 include reductions in moisture delivery to the western U.S., eastern Brazil, and central Africa with recovery of moisture convergence to the Sahel and parts of eastern North America.

Franklin Robertson↗
NASA NTRS2011

Statistical Projection of Solar Cycle 24 for the Exposure Estimates

A solar cycle statistical model has been developed based on the accumulating cycle sunspot data to estimate future levels of the solar cycle activity. Since the current solar cycle 24 has progressed about three years, the cycle activity levels are estimated with an accurately defined solar minimum 24. Then, solar cycle 24 is projected with the cycle activity levels using the statistical model. The projection of solar cycle 24 is then coupled to space related quantities of interest to radiation protection, because the interplanetary plasma and radiation fields are modulated by the degree of disturbance in the solar surface and the radiation doses received by astronauts in interplanetary space are likewise influenced. The resultant projection of solar cycle 24 provides a basis for estimating exposure in future space missions, and projection errors can be corrected as the cycle progresses and observations become available because this model is shown to be self-correcting.

Kim, Myung-Hee↗
DOE OSTI2023

Neural networks for parameter estimation in intractable models

The goal is to use deep learning models to estimate parameters in statistical models when standard likelihood estimation methods are computationally infeasible. For instance, inference for max-stable processes is exceptionally challenging even with small datasets, but simulation is straightforward. Data from model simulations are used to train deep neural networks and learn statistical parameters from max-stable models. The proposed neural network-based method provides a competitive alternative to current approaches, as demonstrated by considerable accuracy and computational time improvements. Finally, it serves as a proof of concept for deep learning in statistical parameter estimation and can be extended to other estimation problems.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

Data assimilation for combustion ignition delay time simulation using schlieren image velocimetry

This study sought to improve the accuracy of simulating spray penetration and combustion ignition delay by means of data assimilation (DA). The simulations were conducted using the Reynolds-averaged Navier–Stokes (RANS) equations and assimilating the schlieren image data. In DA, an ensemble square root filter (EnSRF) was used to build the statistical model, making the simulation results more accurate without any change in the governing equations. Recognizing that the spray-cone injection angle has a large effect on penetration, we created ensemble members with different injection angles. And we applied the two-component velocity distribution calculated via SIV and updated both velocity and temperature by using a DA statistical model derived from RANS ensemble simulations. The ignition delay time is generally known to vary even under the same experimental conditions because it is influenced by many factors. In this study, we attempted the transient DA-assisted RANS simulation to predict the ignition delay time even when the temporal resolution and accuracy of the observation data ware insufficient. Our trials offer an example of how a combination of techniques can be effectively used to assimilate experimental data obtained under restricted conditions.

Combustion simulation↗
DOE OSTI2015

Spatial and Temporal Correlates of Greenhouse Gas Diffusion from a Hydropower Reservoir in the Southern United States

Emissions of CO 2 and CH 4 from freshwater reservoirs constitute a globally significant source of atmospheric greenhouse gases (GHGs), but knowledge gaps remain with regard to spatiotemporal drivers of emissions. We document the spatial and seasonal variation in surface diffusion of CO 2 and CH 4 from Douglas Lake, a hydropower reservoir in Tennessee, USA. Monthly estimates across 13 reservoir sites from January to November 2010 indicated that surface diffusions ranged from 236 to 18,806 mg m -2 day -1 for CO 2 and 0 to 0.95 mg m -2 day -1 for CH 4 . Next, we developed statistical models using spatial and physicochemical variables to predict surface diffusions of CO 2 and CH 4 . Models explained 22.7 and 20.9% of the variation in CO 2 and CH4 diffusions, respectively, and identified pH, temperature, dissolved oxygen, and Julian day as the most informative important predictors. These findings provide baseline estimates of GHG emissions from a reservoir in eastern temperate North America a region for which estimates of reservoir GHGs emissions are limited. Our statistical models effectively characterized non-linear and threshold relationships between physicochemical predictors and GHG emissions. Further refinement of such models will aid in predicting current GHG emissions in unsampled reservoirs and forecasting future GHG emissions.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Validation Metrics for Fixed Effects and Mixed-Effects Calibration

The modern scientific process often involves the development of a predictive computational model. To improve its accuracy, a computational model can be calibrated to a set of experimental data. A variety of validation metrics can be used to quantify this process. Some of these metrics have direct physical interpretations and a history of use, while others, especially those for probabilistic data, are more difficult to interpret. In this work, a variety of validation metrics are used to quantify the accuracy of different calibration methods. Frequentist and Bayesian perspectives are used with both fixed effects and mixed-effects statistical models. Through a quantitative comparison of the resulting distributions, the most accurate calibration method can be selected. Two examples are included which compare the results of various validation metrics for different calibration methods. It is quantitatively shown that, in the presence of significant laboratory biases, a fixed effects calibration is significantly less accurate than a mixed-effects calibration. This is because the mixed-effects statistical model better characterizes the underlying parameter distributions than the fixed effects model. The results suggest that validation metrics can be used to select the most accurate calibration model for a particular empirical model with corresponding experimental data.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2019

Spatial Variability of Winds and HRRR–NCEP Model Error Statistics at Three Doppler-Lidar Sites in the Wind-Energy Generation Region of the Columbia River Basin

Annually and seasonally averaged wind profiles from three Doppler lidars were gathered from sites in the Columbia River basin of east-central Oregon and Washington, a major region of wind-energy production, for the Second Wind Forecast Improvement Project (WFIP2) experiment. The profile data are used to quantify the spatial variability of wind flows in this area of complex terrain, to assess the HRRR-NCEP model's ability to capture spatial and temporal variability of wind profiles, and to evaluate model errors. Annually averaged measured wind speed differences over the 70-km extent of the lidar measurements reached 1 m s -1 within the wind-turbine rotor layer, and 2 m s -1 for 200-500 m AGL. Stronger wind speeds in the lowest 500 m occurred at sites higher in elevation, farther from the river, and farther west - closer to the Cascade Mountain barrier. Validating against the lidar data, the HRRR model underestimated strong wind speeds (>12 m s -1 ) and, consequently, their frequency of occurrence, especially at the two lowest-elevation sites, producing annual low biases in rotor-layer wind speed of 0.5 m s -1 . The RMSE between measured and modeled winds at all sites was about 3 m s -1 and did not degrade significantly with forecast lead time. The nature of the model errors was different for different seasons. Furthermore, although the three sites were located in the same basin terrain, the nature of the model errors was different at each site. Thus, if only one of the sites had been instrumented, different conclusions would have been drawn as to the major sources of model error, depending on where the measurements were made.

17 WIND ENERGY↗
NASA NTRS2021

Ecosystem age-class dynamics and distribution in the LPJ-wsl v2.0 global ecosystem model

Forest ecosystem processes follow classic responses with age, peaking production around canopy closure and declining thereafter. Although age dynamics might be more dominant in certain regions over others, demographic effects on net primary production (NPP) and heterotrophic respiration (Rh) are bound to exist. Yet, explicit representation of ecosystem demography is notably absent in many global ecosystem models. This is concerning because the global community relies on these models to regularly update our collective understanding of the global carbon cycle. This paper aims to present the technical developments of a computationally efficient approach for representing age-class dynamics within a global ecosystem model, the Lund–Potsdam–Jena – Wald, Schnee, Landschaft version 2.0 (LPJ-wsl v2.0) dynamic global vegetation model and to determine if explicit representation of demography influenced ecosystem stocks and fluxes at global scales or at the level of a grid cell. The modeled age classes are initially created by simulated fire and prescribed wood harvesting or abandonment of managed land, otherwise aging naturally until an additional disturbance is simulated or prescribed. In this paper, we show that the age module can capture classic demographic patterns in stem density and tree height compared to inventory data, and that simulated patterns of ecosystem function follow classic responses with age. We also present two scientific applications of the model to assess the modeled age-class distribution over time and to determine the demographic effect on ecosystem fluxes relative to climate. Simulations show that, between 1860 and 2016, zonal age distribution on Earth was driven predominately by fire, causing a 45- to 60-year difference in ages between older boreal (50–90° N) and younger tropical (23° S–23° N) ecosystems. Between simulation years 1860 and 2016, land-use change and land management were responsible for a decrease in zonal age by −6 years in boreal and by −21 years in both temperate (23–50° N) and tropical latitudes, with the anthropogenic effect on zonal age distribution increasing over time. A statistical model helped to reduce LPJ-wsl v2.0 complexity by predicting per-grid-cell annual NPP and Rh fluxes by three terms: precipitation, temperature, and age class; at global scales, R2 was between 0.95 and 0.98. As determined by the statistical model, the demographic effect on ecosystem function was often less than 0.10 kg C/sq. myr but as high as 0.60 kg C/sq. myr where the effect was greatest. In the eastern forests of North America, the simulated demographic effect was of similar magnitude, or greater than, the effects of climate; simulated demographic effects were similarly important in large regions of every vegetated continent. Simulated spatial datasets are provided for global ecosystem ages and the estimated coefficients for effects of precipitation, temperature and demography on ecosystem function. The discussion focuses on our finding of an increasing role of demography in the global carbon cycle, the effect of demography on relaxation times (resilience) following a disturbance event and its implications at global scales, and a finding of a 40 Pg C increase in biomass turnover when including age dynamics at global scales. Whereas time is the only mechanism that increases ecosystem age, any additional disturbance not explicitly modeled will decrease age. The LPJ-wsl v2.0 age module represents another step forward towards understanding the role of demography in global ecosystems.

LPJ-wsl↗
DOE OSTI2016

A NEW STATISTICAL PERSPECTIVE TO THE COSMIC VOID DISTRIBUTION

In this study, we obtain the size distribution of voids as a three-parameter redshift-independent log-normal void probability function (VPF) directly from the Cosmic Void Catalog (CVC). Although many statistical models of void distributions are based on the counts in randomly placed cells, the log-normal VPF that we obtain here is independent of the shape of the voids due to the parameter-free void finder of the CVC. We use three void populations drawn from the CVC generated by the Halo Occupation Distribution (HOD) Mocks, which are tuned to three mock SDSS samples to investigate the void distribution statistically and to investigate the effects of the environments on the size distribution. As a result, it is shown that void size distributions obtained from the HOD Mock samples are satisfied by the three-parameter log-normal distribution. In addition, we find that there may be a relation between the hierarchical formation, skewness, and kurtosis of the log-normal distribution for each catalog. We also show that the shape of the three-parameter distribution from the samples is strikingly similar to the galaxy log-normal mass distribution obtained from numerical studies. This similarity between void size and galaxy mass distributions may possibly indicate evidence of nonlinear mechanisms affecting both voids and galaxies, such as large-scale accretion and tidal effects. Considering the fact that in this study, all voids are generated by galaxy mocks and show hierarchical structures in different levels, it may be possible that the same nonlinear mechanisms of mass distribution affect the void size distribution.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2016

Proton radius from electron scattering data

Background: The proton charge radius extracted from recent muonic hydrogen Lamb shift measurements is significantly smaller than that extracted from atomic hydrogen and electron scattering measurements. The discrepancy has become known as the proton radius puzzle. Purpose: In an attempt to understand the discrepancy, we review high-precision electron scattering results from Mainz, Jefferson Lab, Saskatoon and Stanford. Methods: We make use of stepwise regression techniques using the F-test as well as the Akaike information criterion to systematically determine the predictive variables to use for a given set and range of electron scattering data as well as to provide multivariate error estimates. Results: Starting with the precision, low four-momentum transfer (Q 2 ) data from Mainz (1980) and Saskatoon (1974), we find that a stepwise regression of the Maclaurin series using the F-test as well as the Akaike information criterion justify using a linear extrapolation which yields a value for the proton radius that is consistent with the result obtained from muonic hydrogen measurements. Applying the same Maclaurin series and statistical criteria to the 2014 Rosenbluth results on GE from Mainz, we again find that the stepwise regression tends to favor a radius consistent with the muonic hydrogen radius but produces results that are extremely sensitive to the range of data included in the fit. Making use of the high-Q 2 data on G E to select functions which extrapolate to high Q 2 , we find that a Pad´e (N = M = 1) statistical model works remarkably well, as does a dipole function with a 0.84 fm radius, G E (Q 2 ) = (1 + Q 2 /0.66 GeV 2 ) -2 . Conclusions: Rigorous applications of stepwise regression techniques and multivariate error estimates result in the extraction of a proton charge radius that is consistent with the muonic hydrogen result of 0.84 fm; either from linear extrapolation of the extreme low-Q 2 data or by use of the Pad´e approximant for extrapolation using a larger range of data. Thus, based on a purely statistical analysis of electron scattering data, we conclude that the electron scattering result and the muonic hydrogen result are consistent. Lastly, it is the atomic hydrogen results that are the outliers.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2021

International collaboration framework for the calculation of performance loss rates: Data quality, benchmarks, and trends (towards a uniform methodology)

Abstract The IEA PVPS Task 13 group, experts who focus on photovoltaic performance, operation, and reliability from several leading R&D centers, universities, and industrial companies, is developing a framework for the calculation of performance loss rates of a large number of commercial and research photovoltaic (PV) power plants and their related weather data coming across various climatic zones. The general steps to calculate the performance loss rate are (i) input data cleaning and grading; (ii) data filtering; (iii) performance metric selection, corrections, and aggregation; and finally, (iv) application of a statistical modeling method to determine the performance loss rate value. In this study, several high‐quality power and irradiance datasets have been shared, and the participants of the study were asked to calculate the performance loss rate of each individual system using their preferred methodologies. The data are used for benchmarking activities and to define capabilities and uncertainties of all the various methods. The combination of data filtering, metrics (performance ratio or power based), and statistical modeling methods are benchmarked in terms of (i) their deviation from the average value and (ii) their uncertainty, standard error, and confidence intervals. It was observed that careful data filtering is an essential foundation for reliable performance loss rate calculations. Furthermore, the selection of the calculation steps filter/metric/statistical method is highly dependent on one another, and the steps should not be assessed individually.

14 SOLAR ENERGY↗
NASA NTRS2001

The AutoBayes Program Synthesis System: System Description

AUTOBAYES is a fully automatic program synthesis system for the statistical data analysis domain. Its input is a concise description of a data analysis problem in the form of a statistical model; its output is optimized and fully documented C/C++ code which can be linked dynamically into the Matlab and Octave environments. AUTOBAYES synthesizes code by a schema-guided deductive process. Schemas (i.e., code templates with associated semantic constraints) are applied to the original problem and recursively to emerging subproblems. AUTOBAYES complements this approach by symbolic computation to derive closed-form solutions whenever possible. In this paper, we concentrate on the interaction between the symbolic computations and the deductive synthesis process. A statistical model specifies for each problem variable (i.e., data or parameter) its properties and dependencies in the form of a probability distribution, A typical data analysis task is to estimate the best possible parameter values from the given observations or measurements. The following example models normal-distributed data but takes prior information (e.g., from previous experiments) on the data's mean value and variance into account.

Fischer, Bernd↗
DOE OSTI2015

SPINE: SParse eIgengene NEtwork linking gene expression clusters in Dehalococcoides mccartyi to perturbations in experimental conditions

We present a statistical model designed to identify the effect of experimental perturbations on the aggregate behavior of the transcriptome expressed by the bacterium Dehalococcoides mccartyi strain 195. Strains of Dehalococcoides are used in sub-surface bioremediation applications because they organohalorespire tetrachloroethene and trichloroethene (common chlorinated solvents that contaminate the environment) to non-toxic ethene. However, the biochemical mechanism of this process remains incompletely described. Additionally, the response of Dehalococcoides to stress-inducing conditions that may be encountered at field-sites is not well understood. The constructed statistical model captured the aggregate behavior of gene expression phenotypes by modeling the distinct eigengenes of 100 transcript clusters, determining stable relationships among these clusters of gene transcripts with a sparse network-inference algorithm, and directly modeling the effect of changes in experimental conditions by constructing networks conditioned on the experimental state. Based on the model predictions, we discovered new response mechanisms for DMC, notably when the bacterium is exposed to solvent toxicity. The network identified a cluster containing thirteen gene transcripts directly connected to the solvent toxicity condition. Transcripts in this cluster include an iron-dependent regulator (DET0096-97) and a methylglyoxal synthase (DET0137). To validate these predictions, additional experiments were performed. Continuously fed cultures were exposed to saturating levels of tetrachloethene, thereby causing solvent toxicity, and transcripts that were predicted to be linked to solvent toxicity were monitored by quantitative reverse-transcription polymerase chain reaction. Twelve hours after being shocked with saturating levels of tetrachloroethene, the control transcripts (encoding for a key hydrogenase and the 16S rRNA) did not significantly change. By contrast, transcripts for DET0137 and DET0097 displayed a 46.8±11.5 and 14.6±9.3 fold up-regulation, respectively, supporting the model. This is the first study to identify transcripts in Dehalococcoides that potentially respond to tetrachloroethene solvent-toxicity conditions that may be encountered near contamination source zones in sub-surface environments.

59 BASIC BIOLOGICAL SCIENCES↗