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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 163 records · Page 9
All sourcesNASA NTRSDOE OSTI
DOE OSTI2017

Antigenicity-defined conformations of an extremely neutralization-resistant HIV-1 envelope spike

Here, the extraordinary genetic diversity of the HIV-1 envelope spike [Env; trimeric (gp160) 3 , cleaved to (gp120/gp41) 3 ] poses challenges for vaccine development. Envs of different clinical isolates exhibit different sensitivities to antibody-mediated neutralization. Envs of difficult-to-neutralize viruses are thought to be more stable and conformationally homogeneous trimers than those of easy-to-neutralize viruses, thereby providing more effective concealment of conserved, functionally critical sites. In this study we have characterized the antigenic properties of an Env derived from one of the most neutralization-resistant HIV-1 isolates, CH120.6. Sequence variation at neutralizing epitopes does not fully account for its exceptional resistance to antibodies. The full-length, membrane-bound CH120.6 Env is indeed stable and conformationally homogeneous. Its antigenicity correlates closely with its neutralization sensitivity, and major changes in antigenicity upon CD4 engagement appear to be restricted to the coreceptor site. The CH120.6 gp140 trimer, the soluble and uncleaved ectodomain of (gp160) 3 , retains many antigenic properties of the intact Env, consistent with a conformation close to that of Env spikes on a virion, whereas its monomeric gp120 exposes many nonneutralizing or strain-specific epitopes. Thus, trimer organization and stability are important determinants not only for occluding many epitopes but also for conferring resistance to neutralization by all but a small set of antibodies. Env preparations derived from neutralization-resistant viruses may induce irrelevant antibody responses less frequently than do other Envs and may be excellent templates for developing soluble immunogens.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Targeted DNA insertion in plants

Conventional methods of DNA sequence insertion into plants, using Agrobacterium -mediated transformation or microprojectile bombardment, result in the integration of the DNA at random sites in the genome. These plants may exhibit altered agronomic traits as a consequence of disruption or silencing of genes that serve a critical function. Also, genes of interest inserted at random sites are often not expressed at the desired level. For these reasons, targeted DNA insertion at suitable genomic sites in plants is a desirable alternative. In this paper we review approaches of targeted DNA insertion in plant genomes, discuss current technical challenges, and describe promising applications of targeted DNA insertion for crop genetic improvement.

Dong, Oliver Xiaoou↗
DOE OSTI2026

Depth of nutrient uptake by deep-rooted plants is regulated by water availability

The capacity of some plants to access water and nutrients at depths greater than one meter is a critical functional trait that confers resistance to drought and impacts both belowground and shallow soil processes. Here, we report water and strontium isotopic data from an alpine meadow transect showing the correlation between water and nutrient acquisition depths. The isotopic compositions of Sr ( 87 Sr/ 86 Sr ratio) and water in rock and soil, and in plant leaf tissues, reveal that deeper-rooted plants acquire a higher proportion of water, Sr, and cation nutrients that are derived from the saprolite, a zone of silicate weathering, than shallow-rooted grass. A three-decade dendrochemical record reveals that reductions of wet precipitation drive deep-rooted plants to acquire cation nutrients from deeper saprolite or bedrock regions. Thus, the depth of cation nutrient acquisition by deep-rooted plant species at this site is tightly coupled with, and likely determined by, water availability in soil, saprolite, and bedrock. The enhanced uptake of cations as well as water from deeper saprolite zones could impact the rate of bedrock weathering and watershed chemistry during drought.

biogeochemistry↗
DOE OSTI2023

An open-source framework for simulation-based testing of buildings control strategies

Here this paper presents a simulation framework for evaluating building control strategies (BCSs), developed with VOLTTRON, an opensource platform that integrates data, devices, and systems for sensing and control applications, and is based on co-simulation interfaces. It realizes an integrated environment for both testing and deploying BCSs, thereby eliminating the need for having a dedicated implementation of BCS for testing. For the first time, this framework provides critical functionalities, including scalable communication management and time-drive simulation advance, i.e., advancing the simulation based on clock time. We applied this framework to evaluating two BCSs from ASHRAE Guideline 36-2008 and ASHRAE Standard 90.1-2019. The evaluation results show that those BCSs primarily benefit the heating operation by reducing gas usage but yield insignificant savings in electricity consumption. The results also emphasize the importance of tuning the parameters of the BCSs to achieve better performances.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2010

OVERVIEW OF THE KEPLER SCIENCE PROCESSING PIPELINE

The Kepler Mission Science Operations Center (SOC) performs several critical functions including managing the {approx}156,000 target stars, associated target tables, science data compression tables and parameters, as well as processing the raw photometric data downlinked from the spacecraft each month. The raw data are first calibrated at the pixel level to correct for bias, smear induced by a shutterless readout, and other detector and electronic effects. A background sky flux is estimated from {approx}4500 pixels on each of the 84 CCD readout channels, and simple aperture photometry is performed on an optimal aperture for each star. Ancillary engineering data and diagnostic information extracted from the science data are used to remove systematic errors in the flux time series that are correlated with these data prior to searching for signatures of transiting planets with a wavelet-based, adaptive matched filter. Stars with signatures exceeding 7.1{sigma} are subjected to a suite of statistical tests including an examination of each star's centroid motion to reject false positives caused by background eclipsing binaries. Physical parameters for each planetary candidate are fitted to the transit signature, and signatures of additional transiting planets are sought in the residual light curve. The pipeline is operational, finding planetary signatures and providing robust eliminations of false positives.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2018

Investigating mycobacterial topoisomerase I mechanism from the analysis of metal and DNA substrate interactions at the active site

Here, we have obtained new crystal structures of Mycobacterium tuberculosis topoisomerase I, including structures with ssDNA substrate bound to the active site, with and without Mg 2+ ion present. Significant enzyme conformational changes upon DNA binding place the catalytic tyrosine in a pre-transition state position for cleavage of a specific phosphodiester linkage. Meanwhile, the enzyme/DNA complex with bound Mg 2+ ion may represent the post-transition state for religation in the enzyme's multiple-step DNA relaxation catalytic cycle. The first observation of Mg 2+ ion coordinated with the TOPRIM residues and DNA phosphate in a type IA topoisomerase active site allows assignment of likely catalytic role for the metal and draws a comparison to the proposed mechanism for type IIA topoisomerases. The critical function of a strictly conserved glutamic acid in the DNA cleavage step was assessed through site-directed mutagenesis. The functions assigned to the observed Mg 2+ ion can account for the metal requirement for DNA rejoining but not DNA cleavage by type IA topoisomerases. This work provides new structural insights into a more stringent requirement for DNA rejoining versus cleavage in the catalytic cycle of this essential enzyme, and further establishes the potential for selective interference of DNA rejoining by this validated TB drug target.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Where does the carbon go?–Plant carbon allocation under climate change

The ability of terrestrial vegetation to both take up and release carbon and water makes understanding climate change effects on plant function critical. These effects could alter the impacts and feedbacks of vegetation on climate and either slow down or accelerate climatic warming (Bonan 2008). In conclusion, studies on plant responses to increased atmospheric CO 2 concentration and elevated temperatures have become abundant in the last 20 years (for reviews, see Way and Oren 2010, Franks et al. 2013).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

A gene desert required for regulatory control of pleiotropic Shox2 expression and embryonic survival

ABSTRACT The Shox2 homeodomain transcriptional regulator is known for its critical functions during mouse embryogenesis, enabling accurate development of limbs, craniofacial structures, neural populations and the cardiac conduction system. At the genomic level, the Shox2 gene is flanked by an extensive gene desert, a continuous non-coding genomic region spanning over 500 kilobases that contains a multitude of evolutionarily conserved elements with predicted cis -regulatory activities. However, the transcriptional enhancer potential of the vast majority of these elements in combination with the biological necessity of the gene desert have not yet been explored. Using transgenic reporter assays in mouse embryos to validate an extensive set of stringent epigenomic enhancer predictions, we identify several novel gene desert enhancers with distinct tissue-specific activities in Shox2 expressing tissues. 4C-seq chromatin conformation capture further uncovers a repertoire of gene desert enhancers with overlapping activities in the proximal limb, in a compartment essential for Shox2 -mediated stylopod formation. Leveraging CRISPR/Cas9 to delete the gene desert region contained in the Shox2 topologically associated domain (TAD), we demonstrate that this complex cis -regulatory platform is essential for embryonic survival and required for control of region-specific Shox2 expression in multiple developing tissues. While transcription of Shox2 in the embryonic limb is only moderately affected by gene desert loss, Shox2 expression in craniofacial and cardiac domains is nearly abolished. In particular, Shox2 transcripts in the sinus venosus (SV) encompassing the sinoatrial node (SAN) were depleted in embryos lacking the gene desert, likely accounting for the embryonic lethality due to Shox2 -dependency of the SAN pacemaker. Finally, we discover a 1.5kb SV enhancer within the deleted gene desert region, which may act as a genomic module controlling the development of the cardiac conduction system. In summary, our results identify a gene desert indispensable for pleiotropic patterning and highlight the importance of these extensive regulatory landscapes for embryonic development and viability.

Abassah-Oppong, Samuel↗
DOE OSTI2020

Phase Switching as the Origin of Large Piezoelectric Response in Organic-Inorganic Perovskites: A First-Principles Study

Piezoelectrics are critical functional components of many practical applications such as sensors, ultrasonic transducers, actuators, medical imaging, telecommunications. So far, the best performing piezoelectrics are ferroelectric ceramics, many of which are toxic, heavy, hard, and cost-ineffective. Recently, a groundbreaking discovery of extraordinarily large piezoelectric coefficients in the family of organic-inorganic perovskites gave a hope for a cheaper, environmentally friendly, inexpensive, light-weight and flexible alternative. However, the origin of such response in organic-inorganic ferroelectrics whose spontaneous polarization is an order of magnitude smaller than for inorganic counterparts remains unclear. In this study we employ first-principles simulations to predict that the mechanism associated with large piezoelectric constants is of extrinsic origin and associated with switching between the stable phase and previously overlooked energetically competitive metastable phase that can be stabilized by the external stress. Here, the phase switching changes the polarization direction and, therefore, gives origin to large piezoelectric response, similar to PbZr$_{1-x}$Ti$_x$O$_3$ near morphotropic phase boundary. Existence of such metastable phases is likely to manifest as the dynamical molecular disorder above the Curie temperature and, therefore, could be intrinsic to the entire family of organic-inorganic ferroelectrics with such disorder.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca 2+ -calmodulin

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca 2+ -CaM, but no assignment of these features has been made. In addition, Ca 2+ -CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 Å resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca 2+ -CaM. Density-modified electron-density maps enabled the accurate assignment of Ca 2+ -CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using low-contour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca 2+ -CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca 2+ -CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca 2+ -CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal.

Lin, Jiusheng↗
DOE OSTI2018

A High Performance Computational Framework for Dynamic Security Assessment under Uncertainty

Dynamic security assessment (DSA) is a critical function to evaluate power grids’ capability to survive the transition caused by a set of disturbances to an acceptable steady-state condition. Its computational burden is heavy. With the challenges brought by renewable energy and new smart grid technologies, DSA under uncertainty has to be considered to study the impact of forecast errors on DSA simulation, which further increases the computational burden. To address this challenge, this paper presents a high performance computational framework to support DSA simulation user uncertainty. The computational framework aims to provide a seamless workflow that links data from high performance computing, statistical analysis, to visualization so that a problem can be easily expressed in a way compatible with different functions. It also enables software compatibility such that application development can be more efficient. Case study results of the ESCA60 system and a western U.S. size system show the advantages and efficiency of the computational framework.

dynamic security assessment, high performance comp↗
DOE OSTI2020

Robust Distribution System Load Restoration With Time-Dependent Cold Load Pickup

Service restoration is one of the critical functions to enable the future self-healing distribution system. To restore the distribution system in a timely and reliable manner, the realistic system operating conditions need to be accurately characterized. Here, two main factors that have great impacts on distribution system restoration (DSR) in practice are investigated. First, cold load pickup (CLPU), generally caused by thermostatically controlled loads (TCLs), is a common phenomenon after an outage and shaped by the outage duration. However, the time-dependent behaviors of CLPU are rarely considered in literature. In this paper, the operating state evolution of TCLs after an outage is analyzed to characterize time-dependent CLPU. And the time-dependent CLPU is analytically embedded in DSR to accurately represent the actual behaviors of the restored loads. Second, it is difficult to predict loads that fluctuate during DSR due to the lack of real-time measurement data. Accordingly, a robust DSR based on the information gap decision theory (IGDT) is proposed to address this challenge, fully considering the uncertainty of CLPU. The proposed models are tested in IEEE 13-node and 123-node test feeders. Simulation results demonstrate that the time-dependent CLPU model and the uncertainty modeling of CLPU can accurately capture the actual behaviors of loads with TCLs after an outage, which greatly improves DSR decisions in practice.

24 POWER TRANSMISSION AND DISTRIBUTION↗
DOE OSTI2025

Structural architecture of TolQ-TolR inner membrane protein complex from opportunistic pathogen Acinetobacter baumannii

Gram-negative bacteria harness the proton motive force (PMF) within their inner membrane (IM) to uphold cell envelope integrity, an indispensable aspect for both division and survival. The IM TolQ-TolR complex is the essential part of the Tol-Pal system, serving as a conduit for PMF energy transfer to the outer membrane. Here we present cryo–electron microscopy reconstructions ofAcinetobacter baumanniiTolQ in apo and TolR-bound forms at atomic resolution. The apo TolQ configuration manifests as a symmetric pentameric pore, featuring a transmembrane funnel leading toward a cytoplasmic chamber. In contrast, the TolQ-TolR complex assumes a proton nonpermeable stance, characterized by the TolQ pentamer’s flexure to accommodate the TolR dimer, where two protomers undergo a translation-based relationship. Our structure-guided analysis and simulations support the rotor-stator mechanism of action, wherein the rotation of the TolQ pentamer harmonizes with the TolR protomers’ interplay. These findings broaden our mechanistic comprehension of molecular stator units empowering critical functions within the Gram-negative bacterial cell envelope.

Science & Technology - Other Topics↗
DOE OSTI2021

Global Diversity and Biogeography of the Zostera marina Mycobiome

Seagrasses are marine flowering plants that provide critical ecosystem services in coastal environments worldwide. Marine fungi are often overlooked in microbiome and seagrass studies, despite terrestrial fungi having critical functional roles as decomposers, pathogens, or endophytes in global ecosystems. Here, we characterize the distribution of fungi associated with the seagrass Zostera marina, using leaves, roots, and rhizosphere sediment from 16 locations across its full biogeographic range. Using high-throughput sequencing of the ribosomal internal transcribed spacer (ITS) region and 18S rRNA gene, we first measured fungal community composition and diversity. We then tested hypotheses of neutral community assembly theory and the degree to which deviations suggested that amplicon sequence variants (ASVs) were plant selected or dispersal limited. Finally, we identified a core mycobiome and investigated the global distribution of differentially abundant ASVs. We found that the fungal community is significantly different between sites and that the leaf mycobiome follows a weak but significant pattern of distance decay in the Pacific Ocean. Generally, there was evidence for both deterministic and stochastic factors contributing to community assembly of the mycobiome, with most taxa assembling through stochastic processes. The Z. marina core leaf and root mycobiomes were dominated by unclassified Sordariomycetes spp., unclassified Chytridiomycota lineages (including Lobulomycetaceae spp.), unclassified Capnodiales spp., and Saccharomyces sp. It is clear from the many unclassified fungal ASVs and fungal functional guilds that knowledge of marine fungi is still rudimentary. Further studies characterizing seagrass-associated fungi are needed to understand the roles of these microorganisms generally and when associated with seagrasses. Fungi have important functional roles when associated with land plants, yet very little is known about the roles of fungi associated with marine plants, like seagrasses. In this study, we report the results of a global effort to characterize the fungi associated with the seagrass Zostera marina across its full biogeographic range. Although we defined a putative global core fungal community, it is apparent from the many fungal sequences and predicted functional guilds that had no matches to existing databases that general knowledge of seagrass-associated fungi and marine fungi is lacking. This work serves as an important foundational step toward future work investigating the functional ramifications of fungi in the marine ecosystem.

ITS2↗
DOE OSTI2017

Middle East Respiratory Syndrome Coronavirus Nonstructural Protein 16 Is Necessary for Interferon Resistance and Viral Pathogenesis

ABSTRACT Coronaviruses (CoVs) encode a mixture of highly conserved and novel genes, as well as genetic elements necessary for infection and pathogenesis, raising the possibility of common targets for attenuation and therapeutic design. In this study, we focused on highly conserved nonstructural protein 16 (NSP16), a viral 2' O -methyltransferase (2' O -MTase) that encodes critical functions in immune modulation and infection. Using reverse genetics, we disrupted a key motif in the conserved KDKE motif of Middle East respiratory syndrome CoV (MERS-CoV) NSP16 (D130A) and evaluated the effect on viral infection and pathogenesis. While the absence of 2' O -MTase activity had only a marginal impact on propagation and replication in Vero cells, dNSP16 mutant MERS-CoV demonstrated significant attenuation relative to the control both in primary human airway cell cultures and in vivo . Further examination indicated that dNSP16 mutant MERS-CoV had a type I interferon (IFN)-based attenuation and was partially restored in the absence of molecules of IFN-induced proteins with tetratricopeptide repeats. Importantly, the robust attenuation permitted the use of dNSP16 mutant MERS-CoV as a live attenuated vaccine platform protecting from a challenge with a mouse-adapted MERS-CoV strain. These studies demonstrate the importance of the conserved 2' O -MTase activity for CoV pathogenesis and highlight NSP16 as a conserved universal target for rapid live attenuated vaccine design in an expanding CoV outbreak setting. IMPORTANCE Coronavirus (CoV) emergence in both humans and livestock represents a significant threat to global public health, as evidenced by the sudden emergence of severe acute respiratory syndrome CoV (SARS-CoV), MERS-CoV, porcine epidemic diarrhea virus, and swine delta CoV in the 21st century. These studies describe an approach that effectively targets the highly conserved 2' O -MTase activity of CoVs for attenuation. With clear understanding of the IFN/IFIT (IFN-induced proteins with tetratricopeptide repeats)-based mechanism, NSP16 mutants provide a suitable target for a live attenuated vaccine platform, as well as therapeutic development for both current and future emergent CoV strains. Importantly, other approaches targeting other conserved pan-CoV functions have not yet proven effective against MERS-CoV, illustrating the broad applicability of targeting viral 2' O -MTase function across CoVs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Changes in environmental and engineered conditions alter the plasma membrane lipidome of fractured shale bacteria

ABSTRACT Microorganisms that persist in fractured shale reservoirs cause several problems including secreting foul gases and forming biofilms. Current biocontrol measures often fail due to limited knowledge of their in situ activities. The plasma membrane protects the cell, mediates many of its critical functions, and responds to intracellular cues and ecological perturbations through physicochemical modifications. As such, it provides valuable insight into the physiological adaptation of microorganisms in disturbed environmental systems. Here, we (i) demonstrate how changes in salinity and hydraulic retention time (HRT) influence the plasma membrane intact polar lipid (IPL) chemistry of model bacterium, Halanaerobium congolense WG10, and mixed microbial consortia enriched from shale-produced fluids and (ii) elucidate adjustments in membrane IPL chemistry during biofilm growth relative to planktonic cells. We incubated H. congolense WG10 in chemostats under three salinities (7%, 13%, and 20% NaCl), operated under three HRTs (19.2, 24, and 48 h), and in drip flow biofilm reactors under the same salinity gradients. Also, mixed microbial consortia in produced fluids were enriched in triplicate chemostat vessels under three HRTs (19.2, 24, and 72 h) and biofilm reactors. Lipids were analyzed by ultra high performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). Our results show that phosphatidylglycerols, cardiolipins, and phosphatidylethanolamines were predominantly enriched in planktonic H. congolense WG10 cells grown at hypersalinity (20%) compared to optimum (13%). In addition, several zwitterionic phosphatidylcholines and phosphatidylethanolamines were higher in abundance during biofilm growth. These observations suggest that microbial adaptation and biofilm formation in fractured shale are enabled by strategic plasma membrane IPL chemistry adjustments. IMPORTANCE Microorganisms inadvertently introduced into the shale reservoir during fracturing face multiple stressors including brine-level salinities and starvation. However, some anaerobic halotolerant bacteria adapt and persist for long periods of time. They produce hydrogen sulfide, which sours the reservoir and corrodes engineering infrastructure. In addition, they form biofilms on rock matrices, which decrease shale permeability and clog fracture networks. These reduce well productivity and increase extraction costs. Under stress, microbes remodel their plasma membrane to optimize its roles in protection and mediating cellular processes such as signaling, transport, and energy metabolism. Hence, by observing changes in the membrane lipidome of model shale bacteria, Halanaerobium congolense WG10, and mixed consortia enriched from produced fluids under varying subsurface conditions and growth modes, we provide insight that advances our knowledge of the fractured shale biosystem. We also offer data-driven recommendations for improving biocontrol efficacy and the efficiency of energy recovery from unconventional formations.

03 NATURAL GAS↗
DOE OSTI2014

LCMSNet v. 3.0

LCMSnet communicates with, controls and orchestrates devices for high pressure liquid chromatography. In developing cutting edge chromatographic methods it was apparent that components from different manufacturers were required. Autosamplers, valves, and pumps all had to be controlled and configured to run unattended and in the highest throughput possible. The power of LCMSnet is the ability so build methods in a simple step by step fashion and then the software uses a scheduling algorithm to run the devices as efficiently as possible without crashing critical functions. This latest iteration of the software allows for modeling of the valves and incorporates logic that will report if a fluid path is undesirable. LCMSnet has reduced method development time from days to minutes and allows the ability to check configurations before any valves or pumps are connected.

Source record↗
DOE OSTI2025

Electric Grid Simulator For Human Factor Research

The developed code simulates real-time monitor and control for west area of IEEE 118-bus system. The 24-hour load profile for each bus is derived by scaling the system’s rated load in the PSSE sav file according to the California Independent System Operator’s Day-ahead load forecast for May 1, 2024. This simulator performs several critical functions: (1) Calculating time-series power flow every 4 seconds; (2) Updating and dispatching AGC signals every minute; (3) Conducting N-1 contingency analysis every 5 minutes. Additionally, the simulator can trip lines and subsequently update and dispatch AGC signals, running power flow analysis after each tripping event.

Huang, Jianqiao [Idaho National Laboratory (INL), ↗