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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 829 records · Page 46
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Sugar loading is not required for phloem sap flow in maize plants

We report phloem transport of photoassimilates from leaves to non-photosynthetic organs, such as the root and shoot apices and reproductive organs, is crucial to plant growth and yield. For nearly 90 years, evidence has been generally consistent with the theory of a pressure-flow mechanism of phloem transport. Central to this hypothesis is the loading of osmolytes, principally sugars, into the phloem to generate the osmotic pressure that propels bulk flow. Here we used genetic and light manipulations to test whether sugar import into the phloem is required as the driving force for phloem sap flow. Using carbon-11 radiotracer, we show that a maize sucrose transporter1 (sut1) loss-of-function mutant has severely reduced export of carbon from photosynthetic leaves (only ~4% of the wild type level). Yet, the mutant remarkably maintains phloem pressure at ~100% and sap flow speeds at ~50–75% of those of wild type. Potassium (K+) abundance in the phloem was elevated in sut1 mutant leaves. Fluid dynamic modelling supports the conclusion that increased K+ loading compensated for decreased sucrose loading to maintain phloem pressure, and thereby maintained phloem transport via the pressure-flow mechanism. Furthermore, these results suggest that sap flow and transport of other phloem-mobile nutrients and signalling molecules could be regulated independently of sugar loading into the phloem, potentially influencing carbon–nutrient homoeostasis and the distribution of signalling molecules in plants encountering different environmental conditions.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Direct observation of permafrost degradation and rapid soil carbon loss in tundra

Evidence indicates that 5–15% of the vast pool of soil carbon stored in northern permafrost ecosystems could be emitted as greenhouse gases by 2100 under the current path of global warming. Yet, direct measurements of changes in soil carbon remain scarce, largely because ground subsidence that occurs as the permafrost soils begin to thaw confounds the traditional quantification of carbon pools based on fixed depths or soil horizons. This issue is overcome when carbon is quantified in relation to a fixed ash content, which uses the relatively stable mineral component of soil as a metric for pool comparisons through time. We applied this approach to directly measure soil carbon pool changes over five years in experimentally warmed and ambient tundra ecosystems at a site in Alaska where permafrost is degrading due to climate change. We show a loss of soil carbon of 5.4% per year (95% confidence interval: 1.0, 9.5) across the site. Our findings point to lateral hydrological export as a potential pathway for these surprisingly large losses. This research highlights the potential to make repeat soil carbon pool measurements at sentinel sites across the permafrost region, as this feedback to climate change may be occurring faster than previously thought.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2026

Iron as a driver of organic carbon fate in permafrost regions

Iron (Fe) and its biogeochemical interactions with organic carbon (OC) exert critical controls over carbon storage and water quality across Arctic and sub-Arctic landscapes. Permafrost thaw affects Fe–organic carbon interactions by exposing thawed material and driving shifts in hydrologic regimes. Here we propose a conceptual framework describing how Fe–OC interactions respond to permafrost thaw and the implications for global carbon cycling. The framework builds on current understanding of hydrologically driven processes that are altered by permafrost thaw, including microbial Fe reduction that influences OC decomposition and carbon emissions; Fe cycling through redox transformations and sulfide oxidation; dissolution and reprecipitation of Fe–OC assemblages; and Fe export to river networks. We put forward four testable hypotheses—on topics from Fe supply to its role in soil OC storage and transfer to rivers—to advance understanding of the coupled environmental controls on pore-scale reactions (that is, microscale reactions at mineral–water–microorganism interfaces) that are central to global Fe–OC cycling. Our framework highlights how soil-profile- and landscape-scale processes, such as hydrologic connectivity and redox dynamics, regulate pore-scale Fe–OC reactions.

Herndon, Elizabeth [ORNL] (ORCID:0000000291945493)↗
DOE OSTI2020

Genetic circuit design automation for yeast

Cells can be programmed to monitor and react to their environment using genetic circuits. Design automation software maps a desired circuit function to a DNA sequence, a process that requires units of gene regulation (gates) that are simple to connect and behave predictably. This poses a challenge for eukaryotes due to their complex mechanisms of transcription and translation. To this end, we have developed gates for yeast (Saccharomyces cerevisiae) that are connected using RNA polymerase flux as the signal carrier and are insulated from each other and host regulation. They are based on minimal constitutive promoters (~120 base pairs), for which rules are developed to insert operators for DNA-binding proteins. Using this approach, in this work we constructed nine NOT/NOR gates with nearly identical response functions and 400-fold dynamic range. In circuits, they are transcriptionally insulated from each other by placing ribozymes downstream of terminators to block nuclear export of messenger RNAs resulting from RNA polymerase readthrough. Based on these gates, Cello 2.0 was used to build circuits with up to 11 regulatory proteins. A simple dynamic model predicts the circuit response over days. Genetic circuit design automation for eukaryotes simplifies the construction of regulatory networks as part of cellular engineering projects, whether it be to stage processes during bioproduction, serve as environmental sentinels or guide living therapeutics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Multi-omics reveals nitrogen dynamics associated with soil microbial blooms during snowmelt

Snowmelt triggers a soil microbial bloom and crash that affects nitrogen (N) export in high-elevation watersheds. The mechanisms underlying these microbial dynamics are uncertain, making soil nitrogen processes difficult to predict as snowpack declines globally. Here, integration of genome-resolved metagenomics, metatranscriptomics and metabolomics in a high-elevation watershed revealed ecologically distinct soil microorganisms linked across the snowmelt time-period by their unique nitrogen cycling capacities. The molecular properties and transformations of dissolved organic N suggested that degradation or recycling of microbial biomass provided N for biosynthesis during the microbial bloom. Winter-adapted Bradyrhizobia spp. oxidized amino acids anaerobically and had the highest gene expression for denitrification during the microbial bloom. A pulse of nitrate was driven by spring-adapted Nitrososphaerales after snowmelt, but dissimilatory nitrate reduction to ammonia (DNRA) gene expression indicated significant nitrate retention potential. These findings inform our understanding of nitrogen cycling in environments sensitive to snowpack decline due to global change.

Sorensen, Patrick O↗
DOE OSTI2022

Structural basis of colibactin activation by the ClbP peptidase

Abstract Colibactin, a DNA cross-linking agent produced by gut bacteria, is implicated in colorectal cancer. Its biosynthesis uses a prodrug resistance mechanism: a non-toxic precursor assembled in the cytoplasm is activated after export to the periplasm. This activation is mediated by ClbP, an inner-membrane peptidase with an N-terminal periplasmic catalytic domain and a C-terminal three-helix transmembrane domain. Although the transmembrane domain is required for colibactin activation, its role in catalysis is unclear. Our structure of full-length ClbP bound to a product analog reveals an interdomain interface important for substrate binding and enzyme stability and interactions that explain the selectivity of ClbP for the N -acyl- d -asparagine prodrug motif. Based on structural and biochemical evidence, we propose that ClbP dimerizes to form an extended substrate-binding site that can accommodate a pseudodimeric precolibactin with its two terminal prodrug motifs in the two ClbP active sites, thus enabling the coordinated activation of both electrophilic warheads.

Biochemistry & Molecular Biology↗
DOE OSTI2023

Multicopy suppressor screens reveal convergent evolution of single-gene lysis proteins

Single-strand RNA (ssRNA) Fiersviridae phages cause host lysis with a product of single gene (sgl for single-gene lysis; product Sgl) that induces autolysis. Many different Sgls have been discovered, but the molecular targets of only a few have been identified. In this study, we used a high-throughput genetic screen to uncover genome-wide host suppressors of diverse Sgls. In addition to validating known molecular mechanisms, we discovered that the Sgl of PP7, an ssRNA phage of Pseudomonas aeruginosa, targets MurJ, the flippase responsible for lipid II export, previously shown to be the target of the Sgl of coliphage M. These two Sgls, which are unrelated and predicted to have opposite membrane topology, thus represent a case of convergent evolution. We extended the genetic screens to other uncharacterized Sgls and uncovered a common set of multicopy suppressors, suggesting that these Sgls act by the same or similar mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2019

Linking in silico MS/MS spectra with chemistry data to improve identification of unknowns

Confident identification of unknown chemicals in high resolution mass spectrometry (HRMS) screening studies requires cohesive workflows and complementary data, tools, and software. Chemistry databases, screening libraries, and chemical metadata have become fixtures in identification workflows. To increase confidence in compound identifications, the use of structural fragmentation data collected via tandem mass spectrometry (MS/MS or MS2) is vital. However, the availability of empirically collected MS/MS data for identification of unknowns is limited. Researchers have therefore turned to in silico generation of MS/MS data for use in HRMS-based screening studies. This paper describes the generation en masse of predicted MS/MS spectra for the entirety of the US EPA’s DSSTox database using competitive fragmentation modelling and a freely available open source tool, CFM-ID. The generated dataset comprises predicted MS/MS spectra for ~700,000 structures, and mappings between predicted spectra, structures, associated substances, and chemical metadata. Together, these resources facilitate improved compound identifications in HRMS screening studies. These data are accessible via an SQL database, a comma-separated export file (.csv), and EPA’s CompTox Chemicals Dashboard.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗
DOE OSTI2025

Monthly hydropower generation data for Western Canada to support Western-US interconnect power system studies

Hydroelectric power generation in Western Canada significantly contributes to power grid operations of the North American Western Interconnection through substantial generation, some of which is exported to the United States (U.S.). However, the lack of publicly available hydropower generation datasets poses challenges for future market projections and resource adequacy evaluations. We present a simulation-based monthly power system model-ready hydropower generation dataset for 110 facilities in British Columbia and Alberta from 1981 to 2019. These monthly hydropower generation estimates are developed from integrated hydrologic model simulations of runoff and reservoir-operated streamflow, followed by scaling that considers diversion inflow constraints based on hydropower water license information. To address the lack of comparable hydropower generation records, we conduct step-by-step evaluations for simulated runoff, regulated streamflow, and hydropower generation using available observations or estimates. The presented hydropower dataset aims to enhance the representation of hydropower resources in Western Canada, supporting power grid system studies for the Western Interconnection of the U.S. and Canada.

13 HYDRO ENERGY↗
DOE OSTI2019

Reconstruction of larval origins based on genetic relatedness and biophysical modeling

The assessment of the mechanisms and patterns of larval connectivity between geographically separated populations leads to a better understanding of benthic marine population dynamics, especially in commercially valuable species. This study investigated for the first time the fine-scale temporal genetic variability of new settlers and their origins in a benthic marine organism with one of the longest pelagic larval phases, the Caribbean spiny lobster (Panulirus argus). We genotyped newly settled postlarvae in the Florida Keys and adults of spiny lobster from the Florida Keys and throughout the Caribbean Sea. We identified strong larval connectivity between Dominican Republic, Belize, Nicaragua, the Florida Keys, and West-Florida. the larval dispersal modeling suggests that Florida’s lobster population could receive recruits from within and from other areas outside its state and national maritime boundaries. The genetic analyses refine the oceanographic model indicating that the connectivity patterns described could also result from unknown parental populations sourcing adults and postlarvae in different spawning seasons to the Florida Keys. We discuss the importance of small temporal scales to identify patterns in larval export. Our findings are significant on two levels. From the larval dispersal perspective, genetic results and biophysical modeling identify patterns of gene flow enhancing persistence of local populations. From an economic and fishery perspective, P. argus is the most important commercial species in the Caribbean and our results inform how considering larval source and sink dynamics across international boundaries could improve management plans at local, national, and regional levels.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2019

Predicting sedimentary bedrock subsurface weathering fronts and weathering rates

Although bedrock weathering strongly influences water quality and global carbon and nitrogen budgets, the weathering depths and rates within subsurface are not well understood nor predictable. Determination of both porewater chemistry and subsurface water flow are needed in order to develop more complete understanding and obtain weathering rates. In a long-term field study, we applied a multiphase approach along a mountainous watershed hillslope transect underlain by marine shale. Here we report three findings. First, the deepest extent of the water table determines the weathering front, and the range of annually water table oscillations determines the thickness of the weathering zone. Below the lowest water table, permanently water-saturated bedrock remains reducing, preventing deeper pyrite oxidation. Secondly, carbonate minerals and potentially rock organic matter share the same weathering front depth with pyrite, contrary to models where weathering fronts are stratified. Thirdly, the measurements-based weathering rates from subsurface shale are high, amounting to base cation exports of about 70 kmol c ha -1 y -1 , yet consistent with weathering of marine shale. Finally, by integrating geochemical and hydrological data we present a new conceptual model that can be applied in other settings to predict weathering and water quality responses to climate change.

58 GEOSCIENCES↗
DOE OSTI2022

Structure of the pre-mRNA leakage 39-kDa protein reveals a single domain of integrated zf-C3HC and Rsm1 modules

In Saccharomyces cerevisiae, the pre-mRNA leakage 39-kDa protein (ScPml39) was reported to retain unspliced pre-mRNA prior to export through nuclear pore complexes (NPCs). Pml39 homologs outside the Saccharomycetaceae family are currently unknown, and mechanistic insight into Pml39 function is lacking. Here we determined the crystal structure of ScPml39 at 2.5 Å resolution to facilitate the discovery of orthologs beyond Saccharomycetaceae, e.g. in Schizosaccharomyces pombe or human. The crystal structure revealed integrated zf-C3HC and Rsm1 modules, which are tightly associated through a hydrophobic interface to form a single domain. Both zf-C3HC and Rsm1 modules belong to the Zn-containing BIR (Baculovirus IAP repeat)-like super family, with key residues of the canonical BIR domain being conserved. Features unique to the Pml39 modules refer to the spacing between the Zn-coordinating residues, giving rise to a substantially tilted helix αC in the zf-C3HC and Rsm1 modules, and an extra helix αAB' in the Rsm1 module. Conservation of key residues responsible for its distinct features identifies S. pombe Rsm1 and Homo sapiens NIPA/ZC3HC1 as structural orthologs of ScPml39. Based on the recent functional characterization of NIPA/ZC3HC1 as a scaffold protein that stabilizes the nuclear basket of the NPC, our data suggest an analogous function of ScPml39 in S. cerevisiae.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Partners in root nodule symbiosis respond uniquely to heavy metal stresses in a host genotype-dependent manner

Abstract The mutualistic symbiosis between legume roots and soil rhizobia culminates in the formation of root nodules, where nitrogen is fixed. Root nodule symbiosis is inhibited by heavy metal stress. In this study, we investigated the relative responses of the symbiotic partners to a non-essential heavy metal cadmium (Cd) and an essential heavy metal zinc (Zn) stress and identified patterns in gene expression. We performed dual transcriptomics in nodules, using theMedicago truncatula-Sinorhizobium melilotisymbiotic system. Phenotypes were measured in the wild-typeMedicago truncatulaand a mutant in anABCtransporter gene (Mtabcg36), which showed compromised nodule formation in control conditions and further after heavy metal treatment. We observed that the rhizobia were particularly sensitive to Zn in mutant nodules. The greatest degree of differential gene expression in the host plant were observed under Cd and Zn treatments in wild-type nodules. Most Cd-regulated host genes were also differentially regulated by Zn, revealing little discernment between an essential and a non-essential ion under increased exposure. Furthermore, the host response to both the stresses affected auxin and iron homeostasis genes in a host genotype-dependent manner. Our results suggested impaired cadmium export from the mutant nodules. These results have potential implications in agricultural management systems and bioremediation strategies.

Science & Technology - Other Topics↗
DOE OSTI2021

Prokaryotic responses to a warm temperature anomaly in northeast subarctic Pacific waters

Recent studies on marine heat waves describe water temperature anomalies causing changes in food web structure, bloom dynamics, biodiversity loss, and increased plant and animal mortality. However, little information is available on how water temperature anomalies impact prokaryotes (bacteria and archaea) inhabiting ocean waters. This is a nontrivial omission given their integral roles in driving major biogeochemical fluxes that influence ocean productivity and the climate system. Here we present a time-resolved study on the impact of a large-scale warm water surface anomaly in the northeast subarctic Pacific Ocean, colloquially known as the Blob, on prokaryotic community compositions. Multivariate statistical analyses identified significant depth- and season-dependent trends that were accentuated during the Blob. Moreover, network and indicator analyses identified shifts in specific prokaryotic assemblages from typically particle-associated before the Blob to taxa considered free-living and chemoautotrophic during the Blob, with potential implications for primary production and organic carbon conversion and export.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Mangrove peat and algae leachates elicit rapid and contrasting molecular and microbial responses in coastal waters

Abstract As sea level rises, previously sequestered blue carbon can be exported offshore as particulate or dissolved organic matter where it may be re-mineralized or sequestered. The priming effect, or interactive effects of organic matter turnover with a mixed substrate, is well described in soils, but still debated in aquatic systems. Priming may contribute to enhanced blue carbon re-mineralization in coastal environments. Here we examined mangrove-derived dissolved organic matter turnover in a lab incubation, with leachates from mangrove peat, 13 C-labeled algae, and peat+algae (primed). Particulate and dissolved organic matter were assessed; microbial metatranscriptomes were evaluated; and dissolved organic matter was characterized with high resolution mass spectrometry. Stable isotopes indicated rapid allocation of algal-derived dissolved organic matter into particulate organic matter. The algal treatment had the greatest increase in carbon dioxide, but primed and peat treatments had the greatest loss of dissolved organic carbon, greater RNA concentrations, and similar changes in total carbon dioxide. This suggests that, while total carbon dioxide did not increase under priming conditions, the addition of a peat substrate may promote microbial biomass production relative to carbon dioxide production. This work highlights that more targeted studies investigating the specific mechanisms of priming are necessary to address the molecular and microbial transformations associated with priming in aquatic systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Systematic characterization of human gut microbiome-secreted molecules by integrated multi-omics

The human gut microbiome produces a complex mixture of biomolecules that interact with human physiology and play essential roles in health and disease. Crosstalk between micro-organisms and host cells is enabled by different direct contacts, but also by the export of molecules through secretion systems and extracellular vesicles. The resulting molecular network, comprised of various biomolecular moieties, has so far eluded systematic study. Here we present a methodological framework, optimized for the extraction of the microbiome-derived, extracellular biomolecular complement, including nucleic acids, (poly)peptides, and metabolites, from flash-frozen stool samples of healthy human individuals. Our method allows simultaneous isolation of individual biomolecular fractions from the same original stool sample, followed by specialized omic analyses. The resulting multi-omics data enable coherent data integration for the systematic characterization of this molecular complex. Our results demonstrate the distinctiveness of the different extracellular biomolecular fractions, both in terms of their taxonomic and functional composition. This highlights the challenge of inferring the extracellular biomolecular complement of the gut microbiome based on single-omic data. The developed methodological framework provides the foundation for systematically investigating mechanistic links between microbiome-secreted molecules, including those that are typically vesicle-associated, and their impact on host physiology in health and disease.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2015

Extracellular vesicles from Paracoccidioides pathogenic species transport polysaccharide and expose ligands for DC-SIGN receptors

Extracellular vesicles (EVs) mediate non-conventional transport of molecules across the fungal cell wall. We aimed at describing the carbohydrate composition and surface carbohydrate epitopes of EVs isolated from the pathogenic fungi Paracoccidioides brasiliensis and P. lutzii using standard procedures. Total EV carbohydrates were ethanol-precipitated from preparations depleted of lipids and proteins, then analyzed by chemical degradation, gas chromatography-mass spectrometry, nuclear magnetic resonance and size-exclusion chromatography. EV glycosyl residues of Glc, Man, and Gal comprised most probably two major components: a high molecular mass 4,6-α-glucan and a galactofuranosylmannan, possibly an oligomer, bearing a 2-α-Manp main chain linked to β-Galf (1,3) and α-Manp (1,6) end units. The results also suggested the presence of small amounts of a (1→6)- Manp polymer, (1→3)-glucan and (1→6)-glucan. Glycan microarrays allowed identification of EV surface lectin(s), while plant lectin microarray profiling revealed terminal Man and GlcNAc residues exposed at the EVs surface. Mammalian lectin microarray profiling showed that DC-SIGN receptors recognized surface carbohydrate in Paracoccidioides EVs. Our results suggest that oligosaccharides, cytoplasmic storage, and cell wall polysaccharides can be exported in fungal EVs, which also expose surface PAMPs and lectins. As a result, the role of these newly identified components in the interaction with the host remains to be unraveled.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Generation of ionic liquid tolerant Pseudomonas putida KT2440 strains via adaptive laboratory evolution

Although the use of ionic liquids (ILs) for the pretreatment of lignocellulosic biomass has been limited due to high costs, recent efforts to develop low-cost protic ILs show promise for achieving cost-effectiveness for biorefineries. However, an additional challenge remains in that ILs present in biomass hydrolysates are toxic to most microbial hosts, resulting in poor growth phenotypes. To address this issue, we applied an adaptive laboratory evolution (ALE) approach for tolerizing Pseudomonas putida KT2440, an industrially relevant bacterial host, to two low-cost ILs (triethanolammonium acetate [TEOH][OAc] and triethylammonium hydrogen sulfate [TEA][HS]). After continuous cultivations with gradually increased IL levels, we obtained evolved strains showing significant improvements in their growth performance under high concentrations of the ILs (maximum 4% [TEOH][OAc] and 8% [TEA][HS], in w/v) at which the wild-type strain cannot grow. Sequencing of evolved strains revealed multiple regions where mutations were associated with improved performance in minimal media conditions (relA, gacS, oprB/PP_1446, fleQ, tktA, and uvrY/PP_4100) and in IL-specific conditions (PP_5350, PP_4929/emrE, oprD, and PP_5324). We further validated the causality of the PP_5350 and emrE genes for improved IL tolerance via reverse engineering and transcriptomic analysis. Here, a common mutation in the PP_5350 gene, encoding a RpiR family transcriptional regulator, was shown to significantly upregulate the glyoxylate cycle for efficient acetate catabolism. In addition, it was suggested that the emrE gene encodes an efflux pump which can export [TEA][HS]. Finally, the cultivation of two of the best performing evolved strains with IL-treated biomass hydrolysates demonstrated their considerable potential to be used as platform strains. Taken as a whole, this work provides strains for utilization of IL-treated biomass and a mechanistic understanding that could be further leveraged to develop efficient microbial bioprocesses.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗