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At least 415 records · Page 23

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DOE OSTI2011

Fnr (EtrA) acts as a fine-tuning regulator of anaerobic metabolism in Shewanella oneidensis MR-1

EtrA in Shewanella oneidensis MR-1, a model organism for study of adaptation to varied redox niches, shares 73.6% and 50.8% amino acid sequence identity with the oxygen-sensing regulators Fnr in E. coli and Anr in Pseudomonas aeruginosa, respectively; however, its regulatory role of anaerobic metabolism in Shewanella spp. is not well understood. The expression of the nap genes, nrfA, cymA and hcp was significantly reduced in etrA deletion mutant EtrA7-1; however, limited anaerobic growth and nitrate reduction occurred, suggesting that multiple regulators control nitrate reduction in this strain. Dimethyl sulfoxide (DMSO) and fumarate reductase gene expression was down regulated at least 2-fold and the EtrA7-1 mutant grew poorly with fumarate and dimethyl sulfoxide (DMSO), suggesting both respiratory pathways are under EtrA control. Transcript analysis further suggested a role of EtrA in prophage activation and down regulation of genes implicated in aerobic metabolism. In contrast to previous studies that attributed a minor regulatory role to EtrA in Shewanella spp., this study demonstrates that EtrA acts as a global transcriptional regulator and confers physiological advantages to strain MR-1 under certain growth conditions. In conjunction with other regulators, EtrA fine-tunes the expression of genes involved in anaerobic metabolism in S. oneidensis strain MR-1.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

De novo transcriptome in roots of switchgrass ( Panicum virgatum L. ) reveals gene expression dynamic and act network under alkaline salt stress

Background: Soil salinization is a major limiting factor for crop cultivation. Switchgrass is a perennial rhizomatous bunchgrass that is considered an ideal plant for marginal lands, including sites with saline soil. Here we investigated the physiological responses and transcriptome changes in the roots of Alamo (alkaline-tolerant genotype) and AM314/MS-155 (alkaline-sensitive genotype) under alkaline salt stress. Results: Alkaline salt stress significantly affected the membrane, osmotic adjustment and antioxidant systems in switchgrass roots, and the ASTTI values between Alamo and AM-314/MS-155 were divergent at different time points. A total of 108,319 unigenes were obtained after reassembly, including 73,636 unigenes in AM-314/MS-155 and 65,492 unigenes in Alamo. A total of 10,219 DEGs were identified, and the number of upregulated genes in Alamo was much greater than that in AM-314/MS-155 in both the early and late stages of alkaline salt stress. The DEGs in AM-314/MS-155 were mainly concentrated in the early stage, while Alamo showed greater advantages in the late stage. These DEGs were mainly enriched in plant-pathogen interactions, ubiquitin-mediated proteolysis and glycolysis/gluconeogenesis pathways. We characterized 1480 TF genes into 64 TF families, and the most abundant TF family was the C2H2 family, followed by the bZIP and bHLH families. A total of 1718 PKs were predicted, including CaMK, CDPK, MAPK and RLK. WGCNA revealed that the DEGs in the blue, brown, dark magenta and light steel blue 1 modules were associated with the physiological changes in roots of switchgrass under alkaline salt stress. The consistency between the qRT-PCR and RNA-Seq results confirmed the reliability of the RNA-seq sequencing data. A molecular regulatory network of the switchgrass response to alkaline salt stress was preliminarily constructed on the basis of transcriptional regulation and functional genes. Conclusions: Alkaline salt tolerance of switchgrass may be achieved by the regulation of ion homeostasis, transport proteins, detoxification, heat shock proteins, dehydration and sugar metabolism. These findings provide a comprehensive analysis of gene expression dynamic and act network induced by alkaline salt stress in two switchgrass genotypes and contribute to the understanding of the alkaline salt tolerance mechanism of switchgrass and the improvement of switchgrass germplasm.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2013

A Trans -Acting Protein Effect Causes Severe Eye Malformation in the Mp Mouse

Mp is an irradiation-induced mouse mutation associated with microphthalmia, micropinna and hind limb syndactyly. We show that Mp is caused by a 660 kb balanced inversion on chromosome 18 producing reciprocal 3-prime gene fusion events involving Fbn2 and Isoc1. The Isoc1-Fbn2 fusion gene (Isoc1 Mp ) mRNA has a frameshift and early stop codon resulting in nonsense mediated decay. Homozygous deletions of Isoc1 do not support a significant developmental role for this gene. The Fbn2-Isoc1 fusion gene (Fbn2 Mp ) predicted protein consists of the N-terminal Fibrillin-2 (amino acids 1–2646, exons 1– 62) lacking the C-terminal furin-cleavage site with a short out-of-frame extension encoded by the final exon of Isoc1. The Mp limb phenotype is consistent with that reported in Fbn2 null embryos. However, severe eye malformations, a defining feature of Mp, are not seen in Fbn2 null animals. Fibrillin-2 Mp forms large fibrillar structures within the rough endoplasmic reticulum (rER) associated with an unfolded protein response and quantitative mass spectrometry shows a generalised defect in protein secretion in conditioned media from mutant cells. In the embryonic eye Fbn2 is expressed within the peripheral ciliary margin (CM). Mp embryos show reduced canonical Wnt-signalling in the CM – known to be essential for ciliary body development - and show subsequent aplasia of CM-derived structures. We propose that the Mp ‘‘worse-than-null’’ eye phenotype plausibly results from a failure in normal trafficking of proteins that are co-expressed with Fbn2 within the CM. The prediction of similar trans-acting protein effects will be an important challenge in the medical interpretation of human mutations from whole exome sequencing.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2014

Tissue-Specific RNA Expression Marks Distant-Acting Developmental Enhancers

Short non-coding transcripts can be transcribed from distant-acting transcriptional enhancer loci, but the prevalence of such enhancer RNAs (eRNAs) within the transcriptome, and the association of eRNA expression with tissue-specific enhancer activity in vivo remain poorly understood. Here, we investigated the expression dynamics of tissue-specific non-coding RNAs in embryonic mouse tissues via deep RNA sequencing. Overall, approximately 80% of validated in vivo enhancers show tissue-specific RNA expression that correlates with tissue-specific enhancer activity. Globally, we identified thousands of tissue-specifically transcribed non-coding regions (TSTRs) displaying various genomic hallmarks of bona fide enhancers. In transgenic mouse reporter assays, over half of tested TSTRs functioned as enhancers with reproducible activity in the predicted tissue. Together, our results demonstrate that tissue-specific eRNA expression is a common feature of in vivo enhancers, as well as a major source of extragenic transcription, and that eRNA expression signatures can be used to predict tissue-specific enhancers independent of known epigenomic enhancer marks.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

Modeling hepatitis C micro-elimination among people who inject drugs with direct-acting antivirals in metropolitan Chicago

Hepatitis C virus (HCV) infection is a leading cause of chronic liver disease and mortality worldwide. Direct-acting antiviral (DAA) therapy leads to high cure rates. However, persons who inject drugs (PWID) are at risk for reinfection after cure and may require multiple DAA treatments to reach the World Health Organization’s (WHO) goal of HCV elimination by 2030. Using an agent-based model (ABM) that accounts for the complex interplay of demographic factors, risk behaviors, social networks, and geographic location for HCV transmission among PWID, we examined the combination(s) of DAA enrollment (2.5%, 5%, 7.5%, 10%), adherence (60%, 70%, 80%, 90%) and frequency of DAA treatment courses needed to achieve the WHO’s goal of reducing incident chronic infections by 90% by 2030 among a large population of PWID from Chicago, IL and surrounding suburbs. We also estimated the economic DAA costs associated with each scenario. Our results indicate that a DAA treatment rate of >7.5% per year with 90% adherence results in 75% of enrolled PWID requiring only a single DAA course; however 19% would require 2 courses, 5%, 3 courses and <2%, 4 courses, with an overall DAA cost of $325 million to achieve the WHO goal in metropolitan Chicago. We estimate a 28% increase in the overall DAA cost under low adherence (70%) compared to high adherence (90%). Our modeling results have important public health implications for HCV elimination among U.S. PWID. Using a range of feasible treatment enrollment and adherence rates, we report robust findings supporting the need to address re-exposure and reinfection among PWID to reduce HCV incidence.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Bacterial amyloid curli acts as a carrier for DNA to elicit an autoimmune response via TLR2 and TLR9

Bacterial biofilms are associated with numerous human infections. The predominant protein expressed in enteric biofilms is the amyloid curli, which forms highly immunogenic complexes with DNA. Infection with curli-expressing bacteria or systemic exposure to purified curli-DNA complexes triggers autoimmunity via the generation of type I interferons (IFNs) and anti-double-stranded DNA antibodies. Here, we show that DNA complexed with amyloid curli powerfully stimulates Toll-like receptor 9 (TLR9) through a two-step mechanism. First, the cross beta-sheet structure of curli is bound by cell-surface Toll-like receptor 2 (TLR2), enabling internalization of the complex into endosomes. After internalization, the curli-DNA immune complex binds strongly to endosomal TLR9, inducing production of type I IFNs. Analysis of wild-type and TLR2-deficient macrophages showed that TLR2 is the major receptor that drives the internalization of curli-DNA complexes. Suppression of TLR2 internalization via endocytosis inhibitors led to a significant decrease in Ifnβ expression. Confocal microscopy analysis confirmed that the TLR2-bound curli was required for shuttling of DNA to endosomal TLR9. Structural analysis using small-angle X-ray scattering revealed that incorporation of DNA into curli fibrils resulted in the formation of ordered curli-DNA immune complexes. Curli organizes parallel, double-stranded DNA rods at an inter-DNA spacing that matches up well with the steric size of TLR9. We also found that production of anti-double-stranded DNA autoantibodies in response to curli-DNA was attenuated in TLR2- and TLR9-deficient mice and in mice deficient in both TLR2 and TLR9 compared to wild-type mice, suggesting that both innate immune receptors are critical for shaping the autoimmune adaptive immune response. We also detected significantly lower levels of interferon-stimulated gene expression in response to purified curli-DNA in TLR2 and TLR9 deficient mice compared to wild-type mice, confirming that TLR2 and TLR9 are required for the induction of type I IFNs. Finally, we showed that curli-DNA complexes, but not cellulose, were responsible elicitation of the immune responses to bacterial biofilms. This study defines the series of events that lead to the severe pro-autoimmune effects of amyloid-expressing bacteria and suggest a mechanism by which amyloid curli acts as a carrier to break immune tolerance to DNA, leading to the activation of TLR9, production of type I IFNs, and subsequent production of autoantibodies.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2022

AmeriFlux US-Act Acton Lake Flux Tower Site

This is the AmeriFlux version of the carbon flux data for the site US-Act Acton Lake Flux Tower Site. Site Description - This tower is located at Acton Lake, a eutrophic reservoir immediately surrounded by forest but draining an agricultural watershed in Hueston Woods State Park outside of Oxford, OH. The EC instrumentation was originally deployed 25 m from shore on a dock piling. In April of 2018 a lake tower was installed >200 m from the closest shoreline. The EC instrumentation was deployed on this aquatic tower on 7 May 2018.

Waldo, Sarah↗

DOE OSTI2010

American Recovery and Reinvestment Act (ARRA) Federal Energy Management Program Technical Assistance Project 282 Renewable Energy Opportunities at Fort Gordon, Georgia

This document provides an overview of renewable resource potential at Fort Gordon, based primarily upon analysis of secondary data sources supplemented with limited on-site evaluations. This effort focuses on grid-connected generation of electricity from renewable energy sources and also on ground source heat pumps for heating and cooling buildings. The effort was funded by the American Recovery and Reinvestment Act (ARRA) as follow-on to the 2005 Department of Defense (DoD) Renewables Assessment. The site visit to Fort Gordon took place on March 9, 2010.

15 GEOTHERMAL ENERGY↗

DOE OSTI2010

Comprehensive Energy Assessment: EE and RE Project Optimization Modeling for United States Pacific Command (USPACOM) American Recovery and Reinvestment Act (ARRA) FEMP Technical Assistance

This report summarizes a study and corresponding model development conducted in support of the United States Pacific Command (USPACOM) as part of the Federal Energy Management Program (FEMP) American Reinvestment and Recovery Act (ARRA). This research was aimed at developing a mathematical programming framework and accompanying optimization methodology in order to simultaneously evaluate energy efficiency (EE) and renewable energy (RE) opportunities. Once developed, this research then demonstrated this methodology at a USPACOM installation - Camp H.M. Smith, Hawaii. We believe this is the first time such an integrated, joint EE and RE optimization methodology has been constructed and demonstrated.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

DOE OSTI2010

American Recovery and Reinvestment Act (ARRA) Federal Energy Management Program Technical Assistance Project 281 Solar Hot Water Application Assessment for U.S. Army IMCOM-Southeast Region

The Energy Independence and Security Act of 2007 requires installations (EISA) to install solar systems of sufficient capacity to provide 30% of service hot water in new construction and renovations where cost-effective. However, installations are struggling with how to implement solar hot water, and while several installations are installing solar hot water on a limited basis, paybacks remain long. Pacific Northwest National Laboratory (PNNL) was tasked to address this issue to help determine how best to implement solar hot water projects. This documents discusses the results of that project.

Russo, Bryan J.↗

DOE OSTI2011

Post-Closure Report for Closed Resource Conservation and Recovery Act Corrective Action Units, Nevada National Security Site, Nevada, For Fiscal Year 2010

This report serves as the combined annual report for post-closure activities for the following closed Corrective Action Units (CAUs): (1) CAU 90, Area 2 Bitcutter Containment; (2) CAU 91, Area 3 U-3fi Injection Well; (3) CAU 92, Area 6 Decon Pond Facility; (4) CAU 110, Area 3 WMD U-3ax/bl Crater; and (5) CAU 112, Area 23 Hazardous Waste Trenches. The locations of the sites are shown in Figure 1. This report covers fiscal year 2010 (October 2009-September 2010). The post-closure requirements for these sites are described in Resource Conservation and Recovery Act Permit Number NEV HW0021 and summarized in each CAU-specific section in Section 1.0 of this report. Site inspections are conducted semiannually at CAUs 90 and 91 and quarterly at CAUs 92, 110, and 112. Additional inspections are conducted at CAU 92 if precipitation occurs in excess of 0.50 inches in a 24-hour period. Inspections include an evaluation of the condition of the units and identification of any deficiencies that may compromise the integrity of the units. The condition of covers, fencing, signs, gates, and locks is documented. In addition, soil moisture monitoring and subsidence surveys are conducted at CAU 110. The results of the inspections, summary of maintenance activities, results of vegetations surveys, and analysis of monitoring data are presented in this report. Copies of the inspection checklists are included as Appendix A. Field notes completed during each inspection are included in Appendix B. Photographs taken during the site inspections are included in Appendix C.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2011

RECOVERY ACT: DYNAMIC ENERGY CONSUMPTION MANAGEMENT OF ROUTING TELECOM AND DATA CENTERS THROUGH REAL-TIME OPTIMAL CONTROL (RTOC): Final Scientific/Technical Report

This final scientific report documents the Industrial Technology Program (ITP) Stage 2 Concept Development effort on Data Center Energy Reduction and Management Through Real-Time Optimal Control (RTOC). Society is becoming increasingly dependent on information technology systems, driving exponential growth in demand for data center processing and an insatiable appetite for energy. David Raths noted, 'A 50,000-square-foot data center uses approximately 4 megawatts of power, or the equivalent of 57 barrels of oil a day1.' The problem has become so severe that in some cases, users are giving up raw performance for a better balance between performance and energy efficiency. Historically, power systems for data centers were crudely sized to meet maximum demand. Since many servers operate at 60%-90% of maximum power while only utilizing an average of 5% to 15% of their capability, there are huge inefficiencies in the consumption and delivery of power in these data centers. The goal of the 'Recovery Act: Decreasing Data Center Energy Use through Network and Infrastructure Control' is to develop a state of the art approach for autonomously and intelligently reducing and managing data center power through real-time optimal control. Advances in microelectronics and software are enabling the opportunity to realize significant data center power savings through the implementation of autonomous power management control algorithms. The first step to realizing these savings was addressed in this study through the successful creation of a flexible and scalable mathematical model (equation) for data center behavior and the formulation of an acceptable low technical risk market introduction strategy leveraging commercial hardware and software familiar to the data center market. Follow-on Stage 3 Concept Development efforts include predictive modeling and simulation of algorithm performance, prototype demonstrations with representative data center equipment to verify requisite performance and continued commercial partnering agreement formation to ensure uninterrupted development, and deployment of the real-time optimal control algorithm. As a software implementable technique for reducing power consumption, the RTOC has two very desirable traits supporting rapid prototyping and ultimately widespread dissemination. First, very little capital is required for implementation. No major infrastructure modifications are required and there is no need to purchase expensive capital equipment. Second, the RTOC can be rolled out incrementally. Therefore, the effectiveness can be proven without a large scale initial roll out. Through the use of the Impact Projections Model provided by the DOE, monetary savings in excess of $100M in 2020 and billions by 2040 are predicted. In terms of energy savings, the model predicts a primary energy displacement of 260 trillion BTUs (33 trillion kWh), or a 50% reduction in server power consumption. The model also predicts a corresponding reduction of pollutants such as SO2 and NOx in excess of 100,000 metric tonnes assuming the RTOC is fully deployed. While additional development and prototyping is required to validate these predictions, the relative low cost and ease of implementation compared to large capital projects makes it an ideal candidate for further investigation.

24 POWER TRANSMISSION AND DISTRIBUTION↗

DOE OSTI2012

Recovery Act - PEM Fuel Cell Systems Providing Emergency Reserve and Backup Power (Final Technical Report)

The STI product is the Final Technical Report from ReliOn, Inc. for contract award DE-EE0000487: Recovery Act PEM Fuel Cell Systems Providing Emergency Reserve and Backup Power. The program covered the turnkey deployment of 431 ReliOn fuel cell systems at 189 individual sites for AT&T and PG&E with ReliOn functioning as the primary equipment supplier and the project manager. The Final Technical Report provides an executive level summary, a comparison of the actual accomplishments vs. the goals and objectives of the project, as well as a summary of the project activity from the contract award date of August 1, 2009 through the contract expiration date of December 31, 2011. Two photos are included in the body of the report which show hydrogen storage and bulk hydrogen refueling technologies developed as a result of this program.

08 HYDROGEN↗

DOE OSTI2013

1.5D Quasilinear Model for Alpha Particle-TAE Interaction in ARIES ACT-I

We study the TAE interaction with alpha particle fusion products in ARIES ACT-I using the 1.5D quasilinear model. 1.5D uses linear analytic expressions for growth and damping rates of TAE modes evaluated using TRANSP profiles to calculates the relaxation of pressure profiles. NOVA-K simulations are conducted to validate the analytic dependencies of the rates, and to normalize their absolute value. The low dimensionality of the model permits calculating loss diagrams in large parameter spaces.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

DOE OSTI2013

American Recovery and Reinvestment Act: North Fork Skokomish Powerhouse at Cushman No. 2 Dam

The objective of this project was to add generating capacity on an in-stream flow release at Tacoma Power's Cushman hydroelectric project, Cushman No. 2 Dam, FERC Project P-460. The flow that is being used to generate additional electricity was being discharged from a valve at the base of the dam without recovery of the energy. A second objective to the project was to incorporate upstream fish passage by use of a fish collection structure attached to the draft tubes of the hydroelectric units. This will enable reintroduction of native anadromous fish above the dams which have blocked fish passage since the late 1920's. The project was funded in part by the American Recovery and Reinvestment Act through the Department of Energy, Office of Energy, Efficiency and Renewable Energy, Wind and Water Power Program.

13 HYDRO ENERGY↗

DOE OSTI2013

Impacts Analyses Supporting the National Environmental Policy Act Environmental Assessment for the Resumption of Transient Testing Program

Environmental and health impacts are presented for activities associated with transient testing of nuclear fuel and material using two candidate test reactors. Transient testing involves irradiation of nuclear fuel or materials for short time-periods under high neutron flux rates. The transient testing process includes transportation of nuclear fuel or materials inside a robust shipping cask to a hot cell, removal from the shipping cask, pre-irradiation examination of the nuclear materials, assembly of an experiment assembly, transportation of the experiment assembly to the test reactor, irradiation in the test reactor, transport back to the hot cell, and post-irradiation examination of the nuclear fuel or material. The potential for environmental or health consequences during the transportation, examination, and irradiation actions are assessed for normal operations, off-normal (accident) scenarios, and transportation. Impacts to the environment (air, soil, and groundwater), are assessed during each phase of the transient testing process. This report documents the evaluation of potential consequences to the general public. This document supports the Environmental Assessment (EA) required by the U.S. National Environmental Policy Act (NEPA) (42 USC Subsection 4321 et seq.).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2013

National Environmental Policy Act Hazards Assessment for the TREAT Alternative

This document provides an assessment of hazards as required by the National Environmental Policy Act for the alternative of restarting the reactor at the Transient Reactor Test (TREAT) facility by the Resumption of Transient Testing Program. Potential hazards have been identified and screening level calculations have been conducted to provide estimates of unmitigated dose consequences that could be incurred through this alternative. Consequences considered include those related to use of the TREAT Reactor, experiment assembly handling, and combined events involving both the reactor and experiments. In addition, potential safety structures, systems, and components for processes associated with operating TREAT and onsite handling of nuclear fuels and experiments are listed. If this alternative is selected, a safety basis will be prepared in accordance with 10 CFR 830, “Nuclear Safety Management,” Subpart B, “Safety Basis Requirements.”

21 SPECIFIC NUCLEAR REACTORS AND ASSOCIATED PLANTS↗

DOE OSTI2014

National Environmental Policy Act Hazards Assessment for the TREAT Alternative

99 GENERAL AND MISCELLANEOUS↗