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At least 649 records · Page 36
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Alternative splicing: transcriptional regulatory network in agroforestry

Alternative splicing (AS) in plants plays a key role in regulating the expression of numerous transcripts from a single gene in a regulatory pathway. Variable concentrations of growth regulatory hormones and external stimuli trigger alternative splicing to switch among different growth stages and adapt to environmental stresses. In the AS phenomenon, a spliceosome causes differential transcriptional modifications in messenger RNA (mRNAs), resulting in partial or complete retention of one or more introns as compared to fully spliced mRNA. Differentially expressed proteins translated from intron-retaining messenger RNA (mRNA ir ) perform vital functions in the feedback mechanism. At the post-transcriptional level, AS causes the remodeling of transcription factors (TFs) by the addition or deletion of binding domains to activate and/or repress transcription. In this study, we have summarized the specific role of AS in the regulation of gene expression through repression and activation of the transcriptional regulatory network under external stimuli and switch among developmental stages.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Iron at the Air-Sea Interface (Final Report)

Workshop: Seventy-four scientists from twenty-three countries registered to participate and to present their experimental, modeling, and remote sensing studies related to atmospheric supply and speciation of aerosol iron (Fe), its contribution to the dissolved Fe inventory of the ocean, and its potential impacts on primary production and CO 2 uptake. Due to travel restrictions related to the ongoing pandemic, the meeting was conducted in a hybrid mode. The in-person portion of the meeting was held in Asheville, North Carolina and the online participants were able to join using two streaming platforms. The objective of this workshop was to address the most urgent open science questions for improved quantification of Fe at the air-sea interface. Iron is required for the growth of phytoplankton. The availability of iron can limit the growth of phytoplankton and thus the overall productivity of the marine ecosystem. Therefore, the atmospheric supply of iron to the surface oceans may play a key role in regulating biological productivity, atmospheric carbon dioxide (CO 2 ) concentrations, and possibly climate.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Independent Review of Groundwater Remediation Strategy for Hexavalent Chromium and RDX Groundwater Plumes at Los Alamos National Laboratory (Rev. 1)

Site operations at the Los Alamos National Laboratory (LANL) resulted in the release of oxidized chromium, Cr(VI), into Sandia Canyon from cooling tower effluent from 1956 until 1972. The chromium traveled with the surface water approximately 3 miles downstream before migrating below ground surface. Chromium concentrations exceed 50 μg/L in the upper portion of the aquifer. Another LANL groundwater plume of concern is associated with RDX (Royal Demolition Explosives, 1,3,5-trinitro-1,3,5-triazine). Between 1951 and 1996, RDX was released to the mesa-top facilities' process water outfall, adjacent and underlying soils, and alluvial sediments, along with surface water in Cañon de Valle. Between 2000 and 2010, two remedial actions were deployed, removing much of the near-surface RDX, however, recharge due to precipitation has transported RDX into the perched-intermediate zone and into the regional aquifer. The report documents an independent technical review by scientists from the Department of Energy (DOE) Network of National Laboratories for Environmental Management and Stewardship (NNLEMS) to provide recommendations for potential near term actions to address and optimize remediation for both the Cr(VI) and RDX plumes. The proposed near-term remedial actions include design of pump and treat systems for Cr(VI) and monitoring and study for natural attenuation for RDX. The review assesses existing data, conceptual and numerical modeling, and it recommends a technical integration process to support identifying and implementing strategic, effective and efficient remedies. The DOE Environmental Management Los Alamos Field Office (EM-LA) and their cleanup contractor Newport News Nuclear-BWTX, LLC Los Alamos (N3B) provided the information required for the review. Interviews were also conducted with regulators to obtain the full spectrum of technical, regulatory and scientific perspectives. The independent review team was impressed by the capabilities, experiences, innovativeness, and insightfulness of the technical representatives from both the regulator, the New Mexico Environment Department (NMED) and N3B. Incorporation of vadose zone flow pathways in the conceptual site model (CSM) and configuring the numerical modeling for the site was generally state-of-the-practice (or better). This could be considered state-of-the-art by addressing uncertainties related to spatial extent of hydraulic windows. The reviews from the regulators were thorough and often provided useful concepts for consideration and future/study resolutions. The overarching consensus recommendation of independent review team is that the LANL groundwater plumes should be addressed in context of the emerging "management of complex sites" paradigm.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2020

Engineering regulatory networks for complex phenotypes in E. coli

Regulatory networks describe the hierarchical relationship between transcription factors, associated proteins, and their target genes. Regulatory networks respond to environmental and genetic perturbations by reprogramming cellular metabolism. Here we design, construct, and map a comprehensive regulatory network library containing 110,120 specific mutations in 82 regulators expected to perturb metabolism. We screen the library for different targeted phenotypes, and identify mutants that confer strong resistance to various inhibitors, and/or enhanced production of target compounds. These improvements are identified in a single round of selection, showing that the regulatory network library is universally applicable and is convenient and effective for engineering targeted phenotypes. The facile construction and mapping of the regulatory network library provides a path for developing a more detailed understanding of global regulation in E. coli , with potential for adaptation and use in less-understood organisms, expanding toolkits for future strain engineering, synthetic biology, and broader efforts.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Scoping Review of Global Offshore Geologic Carbon Storage Activities

This technical report documents an inventory of offshore geologic carbon storage (GCS) sites globally, with a focus on existing, operating international sites and those characterized in the United States, indicating the type and variety of GCS efforts. Regional overviews provide a high level understanding of basin-scale geology and history of GCS globally. Key aspects documented in this review include geological formation types, depth, play style, project size, timeline, existing infrastructure, environmental challenges, and potential risks. This review also includes a summary of the regulatory frameworks globally, as well as environmental, social, and commercial considerations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Approach to Startup Inventory for Viable Commercial Power Plant

Summary • FPP realization within the next 10-15 years will require dedicated efforts to improve DIR, burn fraction, fueling efficiency, and/or processing times. • Modest improvements from either the fuel cycle side or plasma physics side should be possible with considered allocation of R&D funding. • Current gaps in particular include blanket extraction at scale, improved efficiency in isotope separation and detritiation, and maximizing DIR efficiency. • Total costs for FPP construction and commissioning depend heavily on site regulation, so decreases in required SI and OI can lead to large decreases in capital outlay. • Some subsystems in the fuel cycle are required from a environmental management perspective but are both energetically expensive and time consuming, particularly water detritiation. • Low inventories but high capital and operational costs mean a centralized water detritiation plant could greatly improve likelihood of deployment of multiple FPPs on the same time scale.

MALONE, COLLIN↗
NASA NTRS1997

A low molecular weight artificial RNA of unique size with multiple probe target regions

Artificial RNAs (aRNAs) containing novel sequence segments embedded in a deletion mutant of Vibrio proteolyticus 5S rRNA have previously been shown to be expressed from a plasmid borne growth rate regulated promoter in E. coli. These aRNAs accumulate to high levels and their detection is a promising tool for studies in molecular microbial ecology and in environmental monitoring. Herein a new construct is described which illustrates the versatility of detection that is possible with aRNAs. This 3xPen aRNA construct carries a 72 nucleotide insert with three copies of a unique 17 base probe target sequence. This aRNA is 160 nucleotides in length and again accumulates to high levels in the E. coli cytoplasm without incorporating into ribosomes. The 3xPen aRNA illustrates two improvements in detection. First, by appropriate selection of insert size, we obtained an aRNA which provides a unique and hence, easily quantifiable peak, on a high resolution gel profile of low molecular weight RNAs. Second, the existence of multiple probe targets results in a nearly commensurate increase in signal when detection is by hybridization. These aRNAs are naturally amplified and carry sequence segments that are not found in known rRNA sequences. It thus may be possible to detect them directly. An experimental step involving RT-PCR or PCR amplification of the gene could therefore be avoided.

Non-NASA Center↗
NASA NTRS2005

Low Noise Exhaust Nozzle Technology Development

NASA and the U.S. aerospace industry have been assessing the economic viability and environmental acceptability of a second-generation supersonic civil transport, or High Speed Civil Transport (HSCT). Development of a propulsion system that satisfies strict airport noise regulations and provides high levels of cruise and transonic performance with adequate takeoff performance, at an acceptable weight, is critical to the success of any HSCT program. The principal objectives were to: 1. Develop a preliminary design of an innovative 2-D exhaust nozzle with the goal of meeting FAR36 Stage III noise levels and providing high levels of cruise performance with a high specific thrust for Mach 2.4 HSCT with a range of 5000 nmi and a payload of 51,900 lbm, 2. Employ advanced acoustic and aerodynamic codes during preliminary design, 3. Develop a comprehensive acoustic and aerodynamic database through scale-model testing of low-noise, high-performance, 2-D nozzle configurations, based on the preliminary design, and 4. Verify acoustic and aerodynamic predictions by means of scale-model testing. The results were: 1. The preliminary design of a 2-D, convergent/divergent suppressor ejector nozzle for a variable-cycle engine powered, Mach 2.4 HSCT was evolved, 2. Noise goals were predicted to be achievable for three takeoff scenarios, and 3. Impact of noise suppression, nozzle aerodynamic performance, and nozzle weight on HSCT takeoff gross weight were assessed.

Majjigi, R. K.↗
NASA NTRS2000

Modeling Stratospheric Constituents: Reactive Species That Regulate Ozone

Photochemical loss of stratospheric ozone occurs primarily by catalytic cycles whose rates are limited by the concentration of OH, HO2, NO2, ClO, and/or BrO as well as the concentration of either atomic oxygen or of ozone itself. Once the concentrations of these gases are established, the photochemical loss rate of O3 depends on the rate coefficient of only a handful of key reactions. We have developed a method for testing our understanding of stratospheric ozone photochemistry by comparing measured and modeled concentrations of reactive hydrogen, nitrogen, chlorine and bromine radicals using a photochemical steady state model constrained by observed concentrations of long-lived precursors (e.g., NO(y), Cl(y), Br(y), O3, H2O, CH4) and environmental parameters such as ozone column, reflectivity, and aerosol surface area. We will show based on analyses of observations obtained by aircraft, balloon, and satellite platforms during the POLARIS campaign that our overall understanding of the processes that regulate these radical species is very good. The most notable current discrepancies are the tendency to underestimate observed NO2 by 15 to 30% for air masses that experience near continuous solar illumination over a 24 hour period and the tendency to underestimate observed OH and H02 by about 10 to 20% during midday and by much larger amounts at high solar zenith angle (SZA > 85). Possible resolutions to these discrepancies will be discussed. This study was carried out in close collaboration with many members of the POLARIS science team.

Salawitch, Ross J.↗
NASA NTRS1997

Gravity, light and plant form

Plants have evolved highly sensitive and selective mechanisms that detect and respond to various aspects of their environment. As a plant develops, it integrates the environmental information perceived by all of its sensory systems and adapts its growth to the prevailing environmental conditions. Light is of critical importance because plants depend on it for energy and, thus, survival. The quantity, quality and direction of light are perceived by several different photosensory systems that together regulate nearly all stages of plant development, presumably in order to maintain photosynthetic efficiency. Gravity provides an almost constant stimulus that is the source of critical spatial information about its surroundings and provides important cues for orientating plant growth. Gravity plays a particularly important role during the early stages of seedling growth by stimulating a negative gravitropic response in the primary shoot that orientates it towards the source of light, and a positive gravitropic response in the primary root that causes it to grow down into the soil, providing support and nutrient acquisition. Gravity also influences plant form during later stages of development through its effect on lateral organs and supporting structures. Thus, the final form of a plant depends on the cumulative effects of light, gravity and other environmental sensory inputs on endogenous developmental programs. This article is focused on developmental interactions modulated by light and gravity.

NASA Discipline Plant Biology↗
DOE OSTI2022

The fluid definition of the ‘waters of the United States’: Non-uniform effects of regulation on US wetland protections

Recent revisions to the definition of the ‘waters of the United States’ (WOTUS) have considerably altered how wetlands are federally regulated under the Clean Water Act. The two most recent modifications to WOTUS, the Clean Water Rule (CWR) and the Navigable Waters Protection Rule (NWPR), represent two opposing approaches to the federal wetland policy. The impacts of these two rules on the regulation of wetlands have as of yet been poorly characterized at broad spatial scales. Using New York State (NYS) as a case study, we evaluated the jurisdictional statuses of more than 253 000 wetlands under the CWR and the NWPR to assess the landscape-scale effects of WOTUS re-definitions. Here, we found that statewide and within each of NYS's hydrologic regions, the NWPR protects fewer wetlands and less total wetland area than the CWR. The efficacy of the two regulations varied considerably in space across NYS, highlighting the need for comprehensive, nationwide assessments of wetland policy outcomes. We also observed that both rules produced non-uniform patterns in jurisdiction across a range of landscape positions and wetland sizes, preferentially protecting large wetlands close to the stream network. This effect was particularly pronounced under the NWPR, which excludes all geographically isolated wetlands from protection. Our findings in NYS emphasize the existence of unique patterns in protected wetlands across spatial scales, highlighting the value in applying geospatial analyses to evaluate environmental policy.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Aligned FTICR-MS, Respiration, and Biochemical Transformation Data from Columbia River Sediment Incubations Associated with: “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism”

Columbia River hyporheic zone sediments from the Hanford Site 300 Area in eastern Washington were incubated in a full factorial design with different organic matter (OM) amendments. The aim of the experiment was to test the influence of OM thermodynamics on aerobic respiration across different organic carbon pools and concentrations. This dataset is comprised of (1) a csv with high resolution characterization of dissolved organic matter via 12 Tesla Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) analyzed through the Environmental Molecular Sciences Laboratory (EMSL; https://www.pnnl.gov/environmental-molecular-sciences-laboratory), (2) a csv with sample IDs, replicates, amendments, dissolved oxygen (DO) measurements, and sampling time points, (3) a csv with sample IDs, replicates, respiration rates, FTICR summary metrics, and relative abundance of chemical classes; and (4) a csv with the number of chemical transformations in each sample replicate (microcosm). The data are associated with the publication “Carbon Limitation Leads to Thermodynamic Regulation of Aerobic Metabolism” published in ES&T Letters (Garayburu-Caruso et al., 2020). Please use the data package’s DOI to cite the data package. We ask that you acknowledge the U.S. Department of Energy (DOE) Biological and Environmental Research (BER) Subsurface Biogeochemical Research (SBR) program when using the data. All data are free to be used for any purpose, such as for manuscripts, presentations, and grant proposals. There is no obligation to include data package authors as co-authors.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Organic compounds alter the preference and rates of heavy metal adsorption on ferrihydrite

The availability of heavy metals in terrestrial environments is largely controlled by their interactions with minerals and organic matter, with iron minerals having a particularly strong role in heavy metal fate. Because soil organic matter contains a variety of compounds that differ in their chemical properties, the underlying impact organic matter-soil mineral associations bestow on heavy metal binding is still unresolved. Here, we systematically examine the binding of Cd, Zn and Ni by a suite of organic-ferrihydrite assemblages, chosen to account for various compound chemistries within soil organic matter. We posited that organic compound functionality would dictate the extent of association with the organic-ferrihydrite assemblages. Increased heavy metal binding to the assemblages was observed and attributed to the introduction of additional binding sites by the organic functional groups with differing metal affinities. Furthermore, the relative increase depended on the metal's Lewis acidity and followed the order Cd > Zn > Ni, whereas the reverse order was obtained for metal binding by pristine ferrihydrite (Ni > Zn > Cd). Citric acid-, aspartic acid- and cysteine-ferrihydrite assemblages also enhanced the metal binding rate. X-ray absorption spectroscopy revealed that the organic coating contributed significantly to Zn binding by the assemblages, despite relatively low organic surface coverage. Our findings provide valuable information on the nature of heavy metal-organic-mineral interactions and metal adsorption processes regulating their bioavailability and transport.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Hg Accumulation by Single-Cell Sulfate-Reducing Bacteria Methylating Mercury

Methylmercury (MeHg) is a potent neurotoxin that poses risks to ecosystems and human health. MeHg is produced by microbes following saturating-like kinetics. We hypothesize that this saturation reflects a limited intracellular mercury (Hg) accumulation. Here, in this study, we investigated Hg accumulation in Pseudodesulfovibrio hydrargyri BerOc1, a sulfate-reducing model strain able to methylate Hg. Cells were incubated with 0.5 and 2 μM of mercury (HgCl 2 ), and mercury localization was studied using synchrotron-based nano-X-ray fluorescence and high-resolution analytical electron microscopy. For both concentrations, Hg was detected in the bacterial cytosol, in addition to extracellular (Hg, S)-containing nanoparticles. Intracellular Hg levels were slightly higher at 2 μM than at 0.5 μM (1.61 vs 1.40 pg.mm –2 ), suggesting a regulated accumulation. However, the population exhibited heterogeneity in Hg accumulation, particularly at the highest Hg exposure, with some cells being Hg hyperaccumulators. Correlative imaging between Hg localization and cell viability revealed that these hyperaccumulating cells were non-active. Our results suggest that active cells regulate Hg accumulation. From an analytical perspective, a minor subpopulation of hyperaccumulating cells can bias bulk measurements and should be considered in interpreting Hg accumulation in microorganisms. Environmentally, these cells can impact Hg cycling by acting as a metal sink.

Intracellular accumulation↗
DOE OSTI2021

TROPOMI NO 2 in the United States: A Detailed Look at the Annual Averages, Weekly Cycles, Effects of Temperature, and Correlation With Surface NO 2 Concentrations

Abstract Observing the spatial heterogeneities of NO 2 air pollution is an important first step in quantifying NO X emissions and exposures. This study investigates the capabilities of the Tropospheric Monitoring Instrument (TROPOMI) in observing the spatial and temporal patterns of NO 2 pollution in the continental United States. The unprecedented sensitivity of the sensor can differentiate the fine‐scale spatial heterogeneities in urban areas, such as emissions related to airport/shipping operations and high traffic, and the relatively small emission sources in rural areas, such as power plants and mining operations. We then examine NO 2 columns by day‐of‐the‐week and find that Saturday and Sunday concentrations are 16% and 24% lower respectively, than during weekdays. We also analyze the correlation of daily maximum 2‐m temperatures and NO 2 column amounts and find that NO 2 is larger on the hottest days (>32°C) as compared to warm days (26°C–32°C), which is in contrast to a general decrease in NO 2 with increasing temperature at moderate temperatures. Finally, we demonstrate that a linear regression fit of 2019 annual TROPOMI NO 2 data to annual surface‐level concentrations yields relatively strong correlation ( R 2 = 0.66). These new developments make TROPOMI NO 2 satellite data advantageous for policymakers and public health officials, who request information at high spatial resolution and short timescales, in order to assess, devise, and evaluate regulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Hyporheic Oxygen Dynamics in the East River, Colorado: Insights From an In–Situ, High Frequency Time Series During Two Distinct Flow Seasons

Dissolved oxygen (DO) is critical for aquatic ecosystems, however, few studies have focused on the long-term DO dynamics in hyporheic zones, which are a function of both transport (hydrologic exchange between river and hyporheic zone) and uptake by biogeochemical reactions or respiration. We explore the dynamics of temperature and DO at 10, 20, and 35 cm depth beneath the East River, Colorado, from July–October 2017 (relatively normal water year) and April to October 2018 (comparatively low flow year), enabled by distinctive, in-situ, high frequency (Δt = 5 min) sensors that provided continuous time-series from the undisturbed study site over 14 months. We expect that hyporheic DO, which has a regular daily fluctuation pattern, is supplied by the surface water (at all times we estimate downwelling) and that diurnal hyporheic DO temporal patterns should be aligned with diurnal hyporheic temperature patterns. However, this was not found to be the case. Hyporheic DO becomes depleted briefly at 20 and 35 cm depths in 2017, and at all three hyporheic depths for extended periods in 2018. Whereas diurnal temperature fluctuations have consistent timings of maxima and minima, hyporheic DO rarely has as regular a pattern, and daily ranges are inconsistent. Rainfall events caused some of these changes to diurnal hyporheic DO patterns without repeatable effects. Antecedent snowpack conditions influence streamflow dynamics and therefore hyporheic DO dynamics in this alpine river. These results also point to the strong and variable influence of hyporheic microbial communities regulating hyporheic DO.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Adapted laboratory evolution of Thermotoga sp. strain RQ7 under carbon starvation

Abstract Objective Adaptive laboratory evolution (ALE) is an effective approach to study the evolution behavior of bacterial cultures and to select for strains with desired metabolic features. In this study, we explored the possibility of evolving Thermotoga sp. strain RQ7 for cellulose-degrading abilities. Results Wild type RQ7 strain was subject to a series of transfers over six and half years with cellulose filter paper as the main and eventually the sole carbon source. Each transfer was accompanied with the addition of 50 μg of Caldicellulosiruptor saccharolyticus DSM 8903 genomic DNA. A total of 331 transfers were completed. No cellulose degradation was observed with the RQ7 cultures. Thirty three (33) isolates from six time points were sampled and sequenced. Nineteen (19) of the 33 isolates were unique, and the rest were duplicated clones. None of the isolates acquired C. saccharolyticus DNA, but all accumulated small-scale mutations throughout their genomes. Sequence analyses revealed 35 mutations that were preserved throughout the generations and another 15 mutations emerged near the end of the study. Many of the affected genes participate in phosphate metabolism, substrate transport, stress response, sensory transduction, and gene regulation.

54 ENVIRONMENTAL SCIENCES↗