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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 OSTI2023

Energetic considerations for engineering novel biochemistries in photosynthetic organisms

Humans have been harnessing biology to make valuable compounds for generations. From beer and biofuels to pharmaceuticals, biology provides an efficient alternative to industrial processes. With the continuing advancement of molecular tools to genetically modify organisms, biotechnology is poised to solve urgent global problems related to environment, increasing population, and public health. However, the light dependent reactions of photosynthesis are constrained to produce a fixed stoichiometry of ATP and reducing equivalents that may not match the newly introduced synthetic metabolism, leading to inefficiency or damage. While photosynthetic organisms have evolved several ways to modify the ATP/NADPH output from their thylakoid electron transport chain, it is unknown if the native energy balancing mechanisms grant enough flexibility to match the demands of the synthetic metabolism. In this review we discuss the role of photosynthesis in the biotech industry, and the energetic considerations of using photosynthesis to power synthetic biology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Grape ASR Regulates Glucose Transport, Metabolism and Signaling

To decipher the mediator role of the grape Abscisic acid, Stress, Ripening (ASR) protein, VvMSA, in the pathways of glucose signaling through the regulation of its target, the promoter of hexose transporter VvHT1, we overexpressed and repressed VvMSA in embryogenic and non-embryogenic grapevine cells. The embryogenic cells with organized cell proliferation were chosen as an appropriate model for high sensitivity to the glucose signal, due to their very low intracellular glucose content and low glycolysis flux. In contrast, the non-embryogenic cells displaying anarchic cell proliferation, supported by high glycolysis flux and a partial switch to fermentation, appeared particularly sensitive to inhibitors of glucose metabolism. By using different glucose analogs to discriminate between distinct pathways of glucose signal transduction, we revealed VvMSA positioning as a transcriptional regulator of the glucose transporter gene VvHT1 in glycolysis-dependent glucose signaling. The effects of both the overexpression and repression of VvMSA on glucose transport and metabolism via glycolysis were analyzed, and the results demonstrated its role as a mediator in the interplay of glucose metabolism, transport and signaling. The overexpression of VvMSA in the Arabidopsis mutant abi8 provided evidence for its partial functional complementation by improving glucose absorption activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A 1D–0D–3D coupled model for simulating blood flow and transport processes in breast tissue

In this work, we present mixed dimensional models for simulating blood flow and transport processes in breast tissue and the vascular tree supplying it. These processes are considered, to start from the aortic inlet to the capillaries and tissue of the breast. Large variations in biophysical properties and flow conditions exist in this system necessitating the use of different flow models for different geometries and flow regimes. In total, we consider four different model types. First, a system of 1D nonlinear hyperbolic partial differential equations (PDEs) is considered to simulate blood flow in larger arteries with highly elastic vessel walls. Second, we assign 1D linearized hyperbolic PDEs to model the smaller arteries with stiffer vessel walls. The third model type consists of ODE systems (0D models). It is used to model the arterioles and peripheral circulation. Finally, homogenized 3D porous media models are considered to simulate flow and transport in capillaries and tissue within the breast volume. Sink terms are used to account for the influence of the venous and lymphatic systems. Combining the four model types, we obtain two different 1D–0D–3D coupled models for simulating blood flow and transport processes: The first model results in a fully coupled 1D–0D–3D model covering the complete path from the aorta to the breast combining a generic arterial network with a patient specific breast network and geometry. The second model is a reduced one based on the separation of the generic and patient specific parts. The information from a calibrated fully coupled model is used as inflow condition for the patient specific sub-model allowing a significant computational cost reduction. Several numerical experiments are conducted to calibrate the generic model parameters and to demonstrate realistic flow simulations compared to existing data on blood flow in the human breast and vascular system. Moreover, we use two different breast vasculature and tissue data sets to illustrate the robustness of our reduced sub-model approach.

multiscale blood flow models↗
DOE OSTI2020

Plant‐mediated methane transport in emergent and floating‐leaved species of a temperate freshwater mineral‐soil wetland

Abstract Methane flux from freshwater mineral‐soil (FWMS) wetlands and its variability among sites is largely modulated by plant‐mediated transport. However, plant‐mediated transport processes are rarely resolved in land surface models and are poorly parametrized for plants commonly found in FWMS wetlands. Here, relationships between methane flux and CO 2 uptake, as well as plant conductance of methane were evaluated for three plant species and two characteristic functional types: emergent (narrow‐leaved cattail) and floating‐leaved (American lotus and water lily). We found significant but contrasting correlations between methane flux and CO 2 uptake in cattails ( r 2 = 0.51, slope = −0.16, during morning) and water lily ( r 2 = 0.32, slope = 0.064, after midday). This relationship was not significant in American lotus, showing that stomata regulation of methane fluxes is species‐specific and not generalizable across the floating‐leaved plant functional type. Conductance of methane per leaf area showed distinct seasonal dynamics across species. Conductance was similar among the floating‐leaved species (6.2 × 10 −3 m d −1 in lotus and 7.2 × 10 −3 m d −1 in water lily) and higher than conductance in the emergent species (2.7 × 10 −3 m d −1 ). Our results provide direct observations of plant conductance rates and identify the vegetation parameters (leaf area, stomatal conductance) that modify them. Our results further suggest that models of methane emissions from FWMS should parameterize plant‐mediated transport in different plant functional types, scaled by leaf area and with variable seasonal phenological dynamics, and consider possible species‐specific mechanisms that control methane transport through plants.

Villa, Jorge A.↗
DOE OSTI2023

Structural insights into opposing actions of neurosteroids on GABA A receptors

γ-Aminobutyric acid type A (GABA A ) receptors mediate fast inhibitory signaling in the brain and are targets of numerous drugs and endogenous neurosteroids. A subset of neurosteroids are GABA A receptor positive allosteric modulators; one of these, allopregnanolone, is the only drug approved specifically for treating postpartum depression. There is a consensus emerging from structural, physiological and photolabeling studies as to where positive modulators bind, but how they potentiate GABA activation remains unclear. Other neurosteroids are negative modulators of GABA A receptors, but their binding sites remain debated. Here we present structures of a synaptic GABA A receptor bound to allopregnanolone and two inhibitory sulfated neurosteroids. Allopregnanolone binds at the receptor-bilayer interface, in the consensus potentiator site. In contrast, inhibitory neurosteroids bind in the pore. MD simulations and electrophysiology support a mechanism by which allopregnanolone potentiates channel activity and suggest the dominant mechanism for sulfated neurosteroid inhibition is through pore block.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Leakless end-to-end transport of small molecules through micron-length DNA nanochannels

Designed and engineered protein and DNA nanopores can be used to sense and characterize single molecules and control transmembrane transport of molecular species. However, designed biomolecular pores are less than 100 nm in length and are used primarily for transport across lipid membranes. Nanochannels that span longer distances could be used as conduits for molecules between nonadjacent compartments or cells. We design micrometer-long, 7-nm-diameter DNA nanochannels that small molecules can traverse according to the laws of continuum diffusion. Binding DNA origami caps to channel ends eliminates transport and demonstrates that molecules diffuse from one channel end to the other rather than permeating through channel walls. These micrometer-length nanochannels can also grow, form interconnects, and interface with living cells. This work thus shows how to construct multifunctional, dynamic agents that control molecular transport, opening ways of studying intercellular signaling and modulating molecular transport between synthetic and living cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Exploring Proteomes of Robust Yarrowia lipolytica Isolates Cultivated in Biomass Hydrolysate Reveals Key Processes Impacting Mixed Sugar Utilization, Lipid Accumulation, and Degradation

Yarrowia lipolytica is an important industrial oleaginous yeast due to its robust phenotypes for effective conversion of inhibitory lignocellulosic biomass hydrolysates into neutral lipids. While lipid accumulation has been well characterized in this organism, its interconnected lipid degradation phenotype is poorly understood during fermentation of biomass hydrolysates.

proteomic analysis↗
DOE OSTI2022

Quantifying Subsurface Biogeochemical Variability in a High Altitude Watershed During Winter Isolation

Shallow subsurface microbial and geochemical processes in watersheds are dynamic and responsive to seasonal and long-term environmental change. At high elevation or latitude, such changes may occur during winter months when normal sampling is impossible, impractical, unsafe, or may actually alter the processes being studied. Yet accurate modeling of biogeochemical parameters in these environments requires sampling that can capture events and persistent cold climate trends. Gaps in current models exist where data have not been collected during extended snow- or ice-covered periods. The goals of our exploratory study were to examine the biogeochemical processes occurring in a well-studied high altitude watershed during winter when the system is largely inaccessible. We tested the hypothesis that during snow cover in the East River (ER) watershed, episodic excursions of microbial community structure and biogeochemical processes and concentrations fluctuated from values extrapolated from pre- and post-snow time periods. Through our research we identified previously unresolved subsurface-surface transport phenomena and a heretofore under-appreciated methane cycle occurring during wintertime months, thus providing valuable insight into watershed processes. Our research showed that autonomous sampling techniques, first used in marine systems, is extremely versatile and can be adapted for use in harsh continental settings to examine temporal changes in freshwater chemistry and microbial community assemblage. Further, we found that by sampling during periods when systems are hard to access, will lend insight and better accountability for global budgets for methane, an important greenhouse gas. By strengthening our knowledge of wintertime biogeochemical relationships in high altitude watersheds our research leads to more complete descriptions of cryptic processes and ultimately will inform and improve the reactive transport models that simulate processes in these systems.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Spatiotemporal dynamics of ionic reorganization near biological membrane interfaces

Electrical signals in excitable cells involve spatially localized ionic fluxes through ion channels and pumps on cellular lipid membranes. Common approaches to understand how these fluxes spread assume that the membrane and the surrounding electrolyte comprise an equivalent circuit of capacitors and resistors, which ignores the localized nature of transmembrane ion transport, the resulting ionic gradients and electric fields, and their spatiotemporal relaxation. Here, we consider a model of localized ion pumping across a lipid membrane, and use theory and simulation to investigate how the electrochemical signal propagates spatiotemporally in and out of plane along the membrane. The localized pumping generates long-ranged electric fields with three distinct scaling regimes along the membrane: a constant potential near-field region, an intermediate monopolar region, and a far-field dipolar region. Upon sustained pumping, the monopolar region expands radially in plane with a steady speed that is enhanced by the dielectric mismatch and the finite thickness of the lipid membrane. For unmyelinated lipid membranes in physiological settings, we find remarkably fast propagation speeds of ∼ 40 m / s , allowing faster ionic reorganization compared to bare diffusion. Together, our paper shows that transmembrane ionic fluxes induce transient long-ranged electric fields in electrolyte solutions, which may play hitherto unappreciated roles in biological signaling. Published by the American Physical Society 2025

Row, Hyeongjoo (ORCID:000000033623512X)↗
DOE OSTI2020

A Rapid Sequential Separation Method for Determination of Actinides and TENORM in Fracking Wastes - 20223

With recent advances in unconventional drilling technology in the US and around the world, the risks of environmental contamination and exposure due to technologically enhanced naturally occurring radioactive materials (TENORM) from fracking wastes have also surfaced. Although the Permian Basin (southeastern New Mexico, western Texas) has long been a modest producer of oil, the advent of fracking technology a decade ago turned it into hot property for producers. A 2018 assessment of undiscovered, technically recoverable continuous oil and gas resources by the U.S. Geological Survey estimates an average 46.3 billion barrels of oil and 281 trillion cubic feet of gas. This is likely to increase the use of unconventional drilling and TENORM generation. TENORM concentrations in oil and gas exploration and production waste can be several hundred to several thousand times higher than background TENORM concentrations. Both the thorium and uranium decay chains contribute to airborne radionuclides arising from the radon gas escaping the ground and subsequently decaying as airborne particulates. Additionally, radon decay products {sup 210}Pb and {sup 210}Po can build up in scale on the internal surfaces of oil and gas handling pipes and in sludge in refineries, becoming potential inhalation and ingestion hazards for workers. Furthermore, southeastern NM is also home to world's only licensed and operating transuranic nuclear waste repository, the DoE's Waste Isolation Pilot Plant (WIPP). Plutonium isotopes ({sup 239+240}Pu) and {sup 241}Am, are expected to account for more than 99% of the total radioactivity scheduled for disposal in the WIPP repository. Thus, an improved understanding of the environmental fate and transport of TENORM, liberated by unconventional drilling, is essential to assess how best to protect individuals and the environment. In this context, accurate measurement of TENORM and actinides in environmental and biological samples is essential. In this presentation, a new sequential method for the separation and pre-concentration of actinides (Pu, Am, Np) and TENORM (Po, U and Th) derived from oil and gas exploration is proposed. The TEVA method involves a rapid co-precipitation step to remove matrix interferences from the samples, followed by plutonium oxidation state adjustment to Pu (IV) and an incubation period of ∼ 1 hour at 50-60 deg. C to allow the resultant Po (II) to oxidize into Po(IV). The polonium, neptunium, thorium and plutonium are then separated on a TEVA column, while americium and uranium are separated on a TRU column. After separation, the alpha counting source was prepared by micro-precipitation with copper sulfide (CuS) for polonium and neodymium fluoride (NdF{sub 3}) for actinides. The efficiency and reliability of the procedures were tested by analyzing filter, drinking water and frack sand samples. The method is simple, robust and can be performed quickly with excellent removal of interferences, high chemical recovery and very good alpha peak resolution. (authors)

07 ISOTOPE AND RADIATION SOURCES↗
DOE OSTI2023

Resolving dynamic mineral-organic interactions in the rhizosphere by combining in-situ microsensors with plant-soil reactive transport modeling

Associations between minerals and organic matter represent one of the most important carbon storage mechanisms in soils. Plant roots are major sources of soil carbon, and resolving the dynamics and dominance of microbial consumption versus mineral sorption of root-derived carbon is critical to understanding soil carbon storage. Here we integrate in-situ rhizosphere microsensor and plant physiological measurements with a 3-D plant-soil reactive transport model to explore the fate of dissolved organic carbon (DOC) in the rhizosphere, particularly its microbial consumption and interaction with Fe oxide minerals. Over several days, a microdialysis probe sampling pore water at the root-soil interface of growing Vicia faba roots in live soil, revealed clear diel patterns of DOC concentration. Daytime DOC spikes coincided with peaks in leaf-level photosynthesis rates and were accompanied by declining redox potential and dissolved oxygen as well as increasing pH in the rhizosphere. Incorporating microsensor data into our modeling framework showed that the measured rapid loss of DOC after each mid-day spike could not be explained by consumption via aerobic respiration, nor via anaerobic respiration dominated by Fe oxide reduction. Rather, in the model, a large fraction of rhizosphere DOC was rapidly immobilized each day by adsorption to Fe oxides. Further, modeled microbial Fe reduction (fueled by DOC) did not mobilize significant organic carbon from Fe oxides during the day. Instead, the model predicted equilibrium desorption of organic carbon from Fe oxides at night. This new mechanistic modeling framework, which couples aboveground plant physiological measurements with non-destructive high-resolution monitoring of rhizosphere processes, has great potential for exploring the dynamics and balance of the various microbial reactions and mineral interactions controlling carbon transformations and storage in soils.

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

Reveal of Uranium Bioremediation Mechanisms by Bacillus Species through Proteomics Studies

Radionuclides, such as Uranium (U) and heavy metals continue to pose threats to the ecosystem health and processes at the Department of Energy (DOE) managed, Savannah River Site (SRS), located along the Savannah River near Aiken, SC. Such co-contaminated environments are difficult to remediate using conventional excavation and disposal or pump-and-treat approaches. Globally, more than 109 tons of uranium contaminated areas pose a long term threat to human and ecological health. Even with presented low concentrations in the brain, central nervous effects are still observed. Uranium and depleted uranium (DU) have long term effects on the kidneys. Some small general health effects include severe headaches and breathing problems. Uranus ions are toxic to living cells because they inhibit metabolism of carbohydrates by blocking ATP binding sites. Bioremediation by microorganisms represents an alternative solution, which is advantageous because of the possibility of biosorbent regeneration, cost-effectiveness, increased metal removal and easy recovery of some valuable metals. Bacillus sp. bacterium was previously used in the bioremediation of heavy metals in coal mine run off waters of SRS. However, its ability to bioremediate uranium was unknown so far. Hence, in the present study, uranium bioremediation by Bacillus sp. bacterium was investigated. The mechanism of bioremediation was also revealed through proteomics studies. Heavy metals contamination poses a serious threat to water, soil and human health. Soil and water are contaminated due to excessive exploitation of uranium mines for generation of nuclear energy and weaponry. It is not degradable easily and persist in soil and water for a long period of time due to its long half- life. Savannah river site (SRS) is one of the uranium contaminated sites. The physical or chemical remediation techniques are costly and complex. Microbial system approaches with competent bacteria has received increased attention due to its adaptability in various environmental matrices and cost effectiveness. However, even though there are multiple suggested pathways (F1), the specific mechanisms that drive this behavior are still unclear, especially with popular microorganisms such as Bacillus species. In a previous research (Ibeanusi et al, 2003) Bacillus sp. was shown to detoxify and precipitate a variety of heavy metals in coal pile runoff waters of SRS site. Additionally, genomic analysis demonstrated that this microorganism posses multiple attributes for chemical transport regulation and metabolic pathways. U remediation occurs during the first 20 hours of exposure. During this time period, Bacillus sp. may work primarily under two mechanisms - sorption and accumulation. These two mechanisms simultaneously work to protect the microorganism from high concentrations. Figure 10 demonstrates that certain proteins are up regulated and down regulated under extreme stressful conditions. Membrane fraction proteins were up regulated. Cytosolic fraction proteins were down regulated. This protein information coincides with the adsorption behavior. Bacillus sp. is a good candidate for U remediation at various concentrations.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2024

Substrate binding plasticity revealed by Cryo-EM structures of SLC26A2

SLC26A2 is a vital solute carrier responsible for transporting essential nutritional ions, including sulfate, within the human body. Pathogenic mutations within SLC26A2 give rise to a spectrum of human diseases, ranging from lethal to mild symptoms. The molecular details regarding the versatile substrate-transporter interactions and the impact of pathogenic mutations on SLC26A2 transporter function remain unclear. Here, using cryo-electron microscopy, we determine three high-resolution structures of SLC26A2 in complexes with different substrates. These structures unveil valuable insights, including the distinct features of the homodimer assembly, the dynamic nature of substrate binding, and the potential ramifications of pathogenic mutations. This structural-functional information regarding SLC26A2 will advance our understanding of cellular sulfate transport mechanisms and provide foundations for future therapeutic development against various human diseases.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The WUSCHELa ( PtoWUSa ) is Involved in Developmental Plasticity of Adventitious Root in Poplar

WUSCHEL-RELATED HOMEOBOX (WOX) transcription factors play critical roles in cell fate determination during plant development. As the founding member of the WOX family, WUSCHEL (WUS) is characterized for its role in maintaining stem cell in meristem. In this study, we investigated the function of Populus tomentosa WUSCHELa (PtoWUSa) in adventitious roots (ARs) in poplar. Expression profile analysis showed that PtoWUSa was not only expressed in shoot apical meristem and stem, but also expressed in ARs. Ectopic expression of PtoWUSa in Arabidopsis resulted in shortened primary root, as well as agravitropism and multiple branches. Overexpression of PtoWUSa in poplar increased the number of ARs but decreased their length. Moreover, the AR tip and lateral root tip became larger and swollen. In addition, the expression of auxin transporter genes PIN-FORMED were downregulated in ARs of transgenic plant. Taken together, these results suggest that PtoWUSa could be involved in AR development in poplar through regulating the polar auxin transport in ARs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Molecular concentration field design using closed-form steady-state solutions

Control over spatial concentration fields represents a fundamental challenge in designing synthetic biological systems and programmable soft materials. While nature creates morphogen gradients that orchestrate complex developmental processes, synthetic approaches have largely relied on empirical optimization and computationally intensive simulations. Here, we present an analytical framework for steady-state concentration fields generated by finite-sized localized sources in diffusion–degradation systems and derive closed-form solutions for one-, two-, and three-dimensional geometries. By expressing these solutions in dimensionless form, we show that gradient steepness and spatial structure are organized by the Thiele modulus, which captures the competition between diffusion and degradation length scales. The analysis reveals distinct design regimes: in degradation-dominated systems, gradient shape is governed by exponential decay and becomes dimension-independent, whereas in diffusion-dominated systems, gradient magnitude and extent follow dimension-dependent power-law scaling. Building on these results, we introduce a quantitative design strategy that uses threshold-based criteria to program concentration ranges by tuning physically accessible parameters, most directly the production rate, while holding transport and degradation properties fixed. Comparisons with numerical solutions and reported experimental systems demonstrate consistency with the predicted scaling behavior. Together, this work provides a generalizable and physically transparent framework for designing steady-state concentration fields in synthetic biological and soft matter systems, enabling predictive control of gradient-mediated organization without reliance on extensive numerical optimization.

Kim, Dong Woo [Johns Hopkins University, Baltimore↗
DOE OSTI2021

A High-Throughput Method for Identifying Novel Genes That Influence Metabolic Pathways Reveals New Iron and Heme Regulation in Pseudomonas aeruginosa

The ability to simultaneously and more directly correlate genes with metabolite levels on a global level would provide novel information for many biological platforms yet has thus far been challenging. Here, we describe a method to help address this problem, which we dub “Met-Seq” ( met abolite-coupled Tn seq uencing).

59 BASIC BIOLOGICAL SCIENCES↗