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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 361 records · Page 20
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

The Role of Groundwater Withdrawals on River Regulation: Example From the Columbia River Basin

The Columbia River Basin (CRB) is heavily regulated by more than 250 dams on its river system while depending significantly on groundwater withdrawals in certain sub-basins. Neglecting groundwater withdrawals in hydrologic models of the basin could result in inaccurate predictions of its water budget and thus mislead water management decisions in the basin. This work aims to understand the impacts of groundwater pumping on the spatiotemporal patterns of modeling regulated streamflow in the CRB using a modified version of the Variable Infiltration Capacity (VIC) model integrated with a water management component that accounts for groundwater withdrawals, irrigation demands, and reservoir operation (VIC-GIRR). The VIC-GIRR simulations showed that considering additional groundwater withdrawals would alleviate the stress of irrigation water deficit in the Snake River Basin with an average reduction of 10 km 3 /year. Such a reduction in water deficit resulted in slight streamflow increase over the CRB with maximum increase up to 40% during dry period in certain locations. We also note that the implementation of groundwater withdrawal does not, however, improve the overall model performance in long-term averaged streamflow and storage predictions. Our results highlight the efforts needed to examine additional important processes in representing the interactions between water withdrawals and reservoir operations. Such efforts will aid in better simulation of multi-reservoir system and improve effectiveness for agricultural productivity, power generation, flood control, and navigation purposes.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

How Does Flow Alteration Propagate Across a Large, Highly Regulated Basin? Dam Attributes, Network Context, and Implications for Biodiversity

Abstract Large dams are a leading cause of river ecosystem degradation. Although dams have cumulative effects as water flows downstream in a river network, most flow alteration research has focused on local impacts of single dams. Here we examined the highly regulated Colorado River Basin (CRB) to understand how flow alteration propagates in river networks, as influenced by the location and characteristics of dams as well as the structure of the river network—including the presence of tributaries. We used a spatial Markov network model informed by 117 upstream‐downstream pairs of monthly flow series (2003–2017) to estimate flow alteration from 84 intermediate‐to‐large dams representing >83% of the total storage in the CRB. Using Least Absolute Shrinkage and Selection Operator regression, we then investigated how flow alteration was influenced by local dam properties (e.g., purpose, storage capacity) and network‐level attributes (e.g., position, upstream cumulative storage). Flow alteration was highly variable across the network, but tended to accumulate downstream and remained high in the main stem. Dam impacts were explained by network‐level attributes (63%) more than by local dam properties (37%), underscoring the need to consider network context when assessing dam impacts. High‐impact dams were often located in sub‐watersheds with high levels of native fish biodiversity, fish imperilment, or species requiring seasonal flows that are no longer present. These three biodiversity dimensions, as well as the amount of dam‐free downstream habitat, indicate potential to restore river ecosystems via controlled flow releases. Our methods are transferrable and could guide screening for dam reoperation in other highly regulated basins.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Submersed Macrophyte Density Regulates Aquatic Greenhouse Gas Emissions

Abstract Shallow freshwater ecosystems emit large amounts of greenhouse gases (GHGs), such as carbon dioxide (CO 2 ) and methane (CH 4 ), yet emissions are highly variable. The role that aquatic macrophytes play in regulating aquatic GHG emissions is uncertain despite their ability to dominate shallow waterbodies. Here, we studied the effects of submersed macrophyte (Ceratophyllum demersum) density on CO 2 and CH 4 concentrations and fluxes. We conducted a 61‐days experiment using mesocosms containing one of the followingC.demersumdensity treatments: 0, 10, 20, or 30 individual shoots (n = 3). We found that high densityC.demersumhad the highest CO 2 and CH 4 surface water concentrations and emissions while there was no significant difference in CH 4 in the low and medium densities and no plant control. The high density treatment lost biomass over the course of the experiment, indicating die‐off and additions of organic matter to the sediment. High organic matter loading and low dissolved oxygen likely stimulated GHG production in the high density treatment. Our results emphasize that submersed macrophyte density and periods of growth and dieback are important in regulating GHG emissions, which may help explain why shallow waterbodies are high yet variable sources of GHGs to the atmosphere.

Environmental Sciences & Ecology↗
DOE OSTI2020

Rationale for reconsidering current regulations restricting use of hybrids in orange juice

Huanglongbing (HLB) is a disease that has devastated the Florida citrus industry, threatens the entire U.S. citrus industry, and globally is rapidly spreading. Florida’s citrus production is 90% sweet orange, which is quite sensitive to HLB. The heavy reliance on sweet orange for Florida citrus production makes the industry especially vulnerable to diseases that are damaging to this type of citrus. Furthermore, 90% of Florida oranges are used in producing orange juice that is defined by a federal regulation known as the “orange juice standard”, specifying that at least 90% of “orange juice” must be derived from Citrus sinensis. Genomic analyses definitively reveal that sweet orange is not a true species, but just one of many introgression hybrids of C. reticulata and C. maxima, with phenotypic diversity resulting from accumulated mutations in this single hybrid, the “sweet orange”. No other fruit industry is limited by law to such a narrow genetic base. Fortunately, there are new citrus hybrids displaying reduced sensitivity to HLB, and in some cases they produce juice, alone or in blends, that consumers would recognize as “orange juice”. Reconsidering current regulations on orange juice standards may permit use of such hybrids in “orange juice”, providing greater latitude for commercialization of these hybrids, leading to higher-quality orange juice and a more sustainable Florida orange juice industry.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Feedback regulation of crystal growth by buffering monomer concentration

Abstract Crystallization is a ubiquitous means of self-assembly that can organize matter over length scales orders of magnitude larger than those of the monomer units. Yet crystallization is notoriously difficult to control because it is exquisitely sensitive to monomer concentration, which changes as monomers are depleted during growth. Living cells control crystallization using chemical reaction networks that offset depletion by synthesizing or activating monomers to regulate monomer concentration, stabilizing growth conditions even as depletion rates change, and thus reliably yielding desired products. Using DNA nanotubes as a model system, here we show that coupling a generic reversible bimolecular monomer buffering reaction to a crystallization process leads to reliable growth of large, uniformly sized crystals even when crystal growth rates change over time. Buffering could be applied broadly as a simple means to regulate and sustain batch crystallization and could facilitate the self-assembly of complex, hierarchical synthetic structures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Arabidopsis calcium-dependent protein kinase 3 regulates actin cytoskeleton organization and immunity

Pattern-triggered immunity and effector-triggered immunity are two primary forms of innate immunity in land plants. The molecular components and connecting nodes of pattern-triggered immunity and effector-triggered immunity are not fully understood. Here, we report that the Arabidopsis calcium-dependent protein kinase CPK3 is a key regulator of both pattern-triggered immunity and effector-triggered immunity. In vitro and in vivo phosphorylation assays, coupled with genetic and cell biology-based analyses, show that actin-depolymerization factor 4 (ADF4) is a physiological substrate of CPK3, and that phosphorylation of ADF4 by CPK3 governs actin cytoskeletal organization associated with pattern-triggered immunity. CPK3 regulates stomatal closure induced by flg22 and is required for resistance to Pst DC3000. Our data further demonstrates that CPK3 is required for resistance to Pst DC3000 carrying the effector AvrPphB. These results suggest that CPK3 is a missing link between cytoskeleton organization, pattern-triggered immunity and effector-triggered immunity.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Machine learning uncovers independently regulated modules in the Bacillus subtilis transcriptome

The transcriptional regulatory network (TRN) of Bacillus subtilis coordinates cellular functions of fundamental interest, including metabolism, biofilm formation, and sporulation. Here, we use unsupervised machine learning to modularize the transcriptome and quantitatively describe regulatory activity under diverse conditions, creating an unbiased summary of gene expression. We obtain 83 independently modulated gene sets that explain most of the variance in expression and demonstrate that 76% of them represent the effects of known regulators. The TRN structure and its condition-dependent activity uncover putative or recently discovered roles for at least five regulons, such as a relationship between histidine utilization and quorum sensing. The TRN also facilitates quantification of population-level sporulation states. As this TRN covers the majority of the transcriptome and concisely characterizes the global expression state, it could inform research on nearly every aspect of transcriptional regulation in B. subtilis.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Allosteric regulation of glycogen breakdown by the second messenger cyclic di-GMP

Streptomyces are our principal source of antibiotics, which they generate concomitant with a complex developmental transition from vegetative hyphae to spores. c-di-GMP acts as a linchpin in this transition by binding and regulating the key developmental regulators, BldD and WhiG. Here we show that c-di-GMP also binds the glycogen-debranching-enzyme, GlgX, uncovering a direct link between c-di-GMP and glycogen metabolism in bacteria. Further, we show c-di-GMP binding is required for GlgX activity. We describe structures of apo and c-di-GMP-bound GlgX and, strikingly, their comparison shows c-di-GMP induces long-range conformational changes, reorganizing the catalytic pocket to an active state. Glycogen is an important glucose storage compound that enables animals to cope with starvation and stress. Our in vivo studies reveal the important biological role of GlgX in Streptomyces glucose availability control. Overall, we identify a function of c-di-GMP in controlling energy storage metabolism in bacteria, which is widespread in Actinobacteria.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Structural insights into strigolactone catabolism by carboxylesterases reveal a conserved conformational regulation

Phytohormone levels are regulated through specialized enzymes, participating not only in their biosynthesis but also in post-signaling processes for signal inactivation and cue depletion. Arabidopsis thaliana (At) carboxylesterase 15 (CXE15) and carboxylesterase 20 (CXE20) have been shown to deplete strigolactones (SLs) that coordinate various growth and developmental processes and function as signaling molecules in the rhizosphere. Here, we elucidate the X-ray crystal structures of AtCXE15 (both apo and SL intermediate bound) and AtCXE20, revealing insights into the mechanisms of SL binding and catabolism. The N-terminal regions of CXE15 and CXE20 exhibit distinct secondary structures, with CXE15 characterized by an alpha helix and CXE20 by an alpha/beta fold. These structural differences play pivotal roles in regulating variable SL hydrolysis rates. Our findings, both in vitro and in planta, indicate that a transition of the N-terminal helix domain of CXE15 between open and closed forms facilitates robust SL hydrolysis. The results not only illuminate the distinctive process of phytohormone breakdown but also uncover a molecular architecture and mode of plasticity within a specific class of carboxylesterases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Non-coding structural variants disrupt FOXG1 transcriptional regulation in early neurodevelopment

The FOXG1 transcription factor is a crucial regulator of embryonic brain development. Pathogenic FOXG1 variants cause FOXG1 syndrome. Although structural variants in the non-coding region downstream of FOXG1 have been reported in 38 individuals with similar characteristics, the regulatory pathomechanisms remain unknown. Here, we identify two non-coding structural variants in individuals with FOXG1 syndrome-like features, allowing us to delineate a ~ 124 kb commonly affected regulatory region. Using epigenomic profiling and in vivo enhancer assays, we characterize and validate regulatory elements within the commonly affected regulatory region and wider FOXG1 TAD. We see strong activation of previously validated forebrain enhancers, and identify an enhancer cluster and progenitor-specific enhancer region that are strongly activated during forebrain-directed neural progenitor cell differentiation, a process in which FOXG1 is an important regulator. Perturbation of these elements results in varying degrees of reduced FOXG1 transcription in forebrain neural progenitor cells and in population shifts within these cells, while removal of the TAD boundary leads to aberrant expression of the neighbouring PRKD1 gene. Our findings characterize enhancer and architectural elements essential for proper FOXG1 transcription during neurodevelopment, therefore improving variant interpretation in this region.

Hamerlinck, Lisa↗
DOE OSTI2024

Redox regulation of m 6 A methyltransferase METTL3 in β-cells controls the innate immune response in type 1 diabetes

Type 1 Diabetes (T1D) is characterized by the destruction of pancreatic ß-cells. Several observations have renewed the interest in ß-cell RNA sensors and editors. Here, in this study, we report that N 6 -methyladenosine (m 6 A) is an adaptive ß-cell safeguard mechanism that controls the amplitude and duration of the antiviral innate immune response at T1D onset. m 6 A writer methyltransferase 3 (METTL3) levels increase drastically in ß-cells at T1D onset but rapidly decline with disease progression. m 6 A-sequencing revealed the m 6 A hypermethylation of several key innate immune mediators including OAS1, OAS2, OAS3, and ADAR1 in human islets and EndoC-ßH1 cells at T1D onset. METTL3 silencing enhanced OAS levels by increasing its mRNA stability. Consistently, in vivo gene therapy, to prolong Mettl3 overexpression specifically in ß-cells, delayed diabetes progression in the non-obese diabetic (NOD) mouse model of T1D. Mechanistically, the accumulation of reactive oxygen species blocked upregulation of METTL3 in response to cytokines, while physiological levels of nitric oxide enhanced its expression. Furthermore, for the first time to our knowledge, we report that the cysteines in position C276 and C326 in the zinc finger domains of the METTL3 protein are sensitive to S-nitrosylation (SNO) and are significant for the METTL3-mediated regulation of OAS mRNA stability in human ß-cells. Collectively, we report that m 6 A regulates ß-cells to control the innate immune response during the onset of T1D in humans.

2'-5'-oligoadenylate synthetase↗
DOE OSTI2025

Multiplexed profiling of transcriptional regulators in plant cells

Transcriptional regulators play key roles in plant growth, development and environmental responses; however, understanding how their regulatory activity is encoded at the protein level has been hindered by a lack of multiplexed large-scale methods to characterize protein libraries in planta. Here we present enrichment of nuclear trans-elements reporter assay in plants with sequencing (ENTRAP-seq), a high-throughput method that introduces protein-coding libraries into plant cells to drive a nuclear magnetic sorting-based reporter, enabling multiplexed measurement of regulatory activity from thousands of protein variants. Using ENTRAP-seq and machine learning, we screen 1,495 plant viruses and identify hundreds of putative transcriptional regulatory domains found in structural proteins and enzymes not associated with gene regulation. In addition, we combine ENTRAP-seq with machine-guided design to engineer the activity of a plant transcription factor in a semirational fashion. Our findings demonstrate how scalable protein function assays deployed in planta will enable the characterization of natural and synthetic coding diversity in plants.

Alamos, Simon↗
DOE OSTI2021

Fusion and fission events regulate endosome maturation and viral escape

Endosomes are intracellular vesicles that mediate the communication of the cell with its extracellular environment. They are an essential part of the cell’s machinery regulating intracellular trafficking via the endocytic pathway. Many viruses, which in order to replicate require a host cell, attach themselves to the cellular membrane; an event which usually initiates uptake of a viral particle through the endocytic pathway. In this way viruses hijack endosomes for their journey towards intracellular sites of replication and avoid degradation without host detection by escaping the endosomal compartment. Recent experimental techniques have defined the role of endosomal maturation in the ability of enveloped viruses to release their genetic material into the cytoplasm. Endosome maturation depends on a family of small hydrolase enzymes (or GTPases) called Rab proteins, arranged on the cytoplasmic surface of its membrane. Here, we model endosomes as intracellular compartments described by two variables (its levels of active Rab5 and Rab7 proteins) and which can undergo coagulation (or fusion) and fragmentation (or fission). The key element in our approach is the “per-cell endosomal distribution” and its dynamical (Boltzmann) equation. The Boltzmann equation allows us to derive the dynamics of the total number of endosomes in a cell, as well as the mean and the standard deviation of its active Rab5 and Rab7 levels. We compare our mathematical results with experiments of Dengue viral escape from endosomes. The relationship between endosomal active Rab levels and pH suggests a mechanism that can account for the observed variability in viral escape times, which in turn regulate the viability of a viral intracellular infection.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structure of the master regulator Rns reveals an inhibitor of enterotoxigenic Escherichia coli virulence regulons

Enteric infections caused by the gram-negative bacteria enterotoxigenic Escherichia coli (ETEC), Vibrio cholerae, Shigella flexneri, and Salmonella enterica are among the most common and affect billions of people each year. These bacteria control expression of virulence factors using a network of transcriptional regulators, some of which are modulated by small molecules as has been shown for ToxT, an AraC family member from V. cholerae. In ETEC the expression of many types of adhesive pili is dependent upon the AraC family member Rns. We present here the 3 Å crystal structure of Rns and show it closely resembles ToxT. Rns crystallized as a dimer via an interface similar to that observed in other dimeric AraC’s. Furthermore, the structure of Rns revealed the presence of a ligand, decanoic acid, that inhibits its activity in a manner similar to the fatty acid mediated inhibition observed for ToxT and the S. enterica homologue HilD. Together, these results support our hypothesis that fatty acids regulate virulence controlling AraC family members in a common manner across a number of enteric pathogens. Furthermore, for the first time this work identifies a small molecule capable of inhibiting the ETEC Rns regulon, providing a basis for development of therapeutics against this deadly human pathogen.

99 GENERAL AND MISCELLANEOUS↗
DOE OSTI2025

Radiative forcing from the 2020 shipping fuel regulation is large but hard to detect

Reduction in aerosol cooling unmasks greenhouse gas warming, exacerbating the rate of future warming. The strict sulfur regulation on shipping fuel implemented in 2020 (IMO2020) presents an opportunity to assess the potential impacts of such emission regulations and the detectability of deliberate aerosol perturbations for climate intervention. Here we employ machine learning to capture cloud natural variability and estimate a radiative forcing of +0.074 ±0.005 W m -2 related to IMO2020 associated with changes in shortwave cloud radiative effect over three low-cloud regions where shipping routes prevail. We find low detectability of the cloud radiative effect of this event, attributed to strong natural variability in cloud albedo and cloud cover. Regionally, detectability is higher for the southeastern Atlantic stratocumulus deck. These results raise concerns that future reductions in aerosol emissions will accelerate warming and that proposed deliberate aerosol perturbations such as marine cloud brightening will need to be substantial in order to overcome the low detectability.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Chromatin binding by HORMAD proteins regulates meiotic recombination initiation

The meiotic chromosome axis coordinates chromosome organization and interhomolog recombination in meiotic prophase and is essential for fertility. In S. cerevisiae , the HORMAD protein Hop1 mediates the enrichment of axis proteins at nucleosome-rich islands through a central chromatin-binding region (CBR). Here, we use cryoelectron microscopy to show that the Hop1 CBR directly recognizes bent nucleosomal DNA through a composite interface in its PHD and winged helix–turn–helix domains. Targeted disruption of the Hop1 CBR-nucleosome interface causes a localized reduction of axis protein binding and meiotic DNA double-strand breaks (DSBs) in axis islands and leads to defects in chromosome synapsis. Synthetic effects with mutants of the Hop1 regulator Pch2 suggest that nucleosome binding delays a conformational switch in Hop1 from a DSB-promoting, Pch2-inaccessible state to a DSB-inactive, Pch2-accessible state to regulate the extent of meiotic DSB formation. Phylogenetic analyses of meiotic HORMADs reveal an ancient origin of the CBR, suggesting that the mechanisms we uncover are broadly conserved.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Regulating electrodeposition morphology of lithium: towards commercially relevant secondary Li metal batteries

Lithium, the lightest and most electronegative metallic element, has long been considered the ultimate choice as a battery anode for mobile, as well as in some stationary applications. The high electronegativity of Li is, however, a double-edged sword—it facilitates a large operating voltage when paired with essentially any cathode, promising a high cell-level energy density. It is also synonymous with a high chemical reactivity and low reduction potential. The interfaces a Li metal anode forms with any other material (liquid or solid) in an electrochemical cell are therefore always mediated by one or more products of its chemical or electrochemical reactions with that material. The physical, crystallographic, mechanical, electrochemical, and transport properties of the resultant new material phases (interphases) regulate all interfacial processes at a Li metal anode, including electrodeposition during battery recharge. This Review takes recent efforts aimed at manipulating the structure, composition, and physical properties of the solid electrolyte interphase (SEI) formed on an Li anode as a point of departure to discuss the structural, electrokinetic, and electrochemical requirements for achieving high anode reversibility. An important conclusion is that while recent reports showing significant advances in the achievement of highly reversible Li anodes, e.g. as measured by the coulombic efficiency (CE), raise prospects for as significant progress towards commercially relevant Li metal batteries, the plateauing of achievable CE values to around 99 ± 0.5% apparent from a comprehensive analysis of the literature is problematic because CE values of at least 99.7%, and preferably >99.9% are required for Li metal cells to live up to the potential for higher energy density batteries offered by the Li metal anode. On this basis, we discuss promising approaches for creating purpose-built interphases on Li, as well as for fabricating advanced Li electrode architectures for regulating Li electrodeposition morphology and crystallinity. Considering the large number of physical and chemical factors involved in achieving fine control of Li electrodeposition, we believe that achievement of the remaining ~0.5% in anode reversibility will require fresh approaches, perhaps borrowed from other fields. We offer perspectives on both current and new strategies for achieving such Li anodes with the specific aim of engaging established contributors and newcomers to the field in the search for scalable solutions.

25 ENERGY STORAGE↗
DOE OSTI2022

Electrochemical pH regulation in droplet microfluidics

Here we report a method for electrochemical pH regulation in microdroplets generated in a microfluidic device. The key finding is that controlled quantities of reagents can be generated electrochemically in moving microdroplets confined within a microfluidic channel. Additionally, products generated at the anode and cathode can be isolated within descendant microdroplets. Specifically, ~5 nL water-in-oil microdroplets are produced at a T-junction and then later split into two descendant droplets. During splitting, floor-patterned microelectrodes drive water electrolysis within the aqueous microdroplets to produce H + and OH - . This results in a change in the pHs of the descendant droplets. The droplet pH can be regulated over a range of 5.9 to 7.7 by injecting controlled amounts of charge into the droplets. When the injected charge is between -6.3 and 54.5 nC nL -1 , the measured pH of the resulting droplets is within ±0.1 pH units of that predicted based on the magnitude of the injected charge. This technique can likely be adapted to electrogeneration of other reagents within microdroplets.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗