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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 1,153 records · Page 64
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Robust measurement of microbial reduction of graphene oxide nanoparticles using image analysis

ABSTRACT Shewanella oneidensis ( S. oneidensis ) has the capacity to reduce electron acceptors within a medium and is thus used frequently in microbial fuel generation, pollutant breakdown, and nanoparticle fabrication. Microbial fuel setups, however, often require costly or labor-intensive components, thus making optimization of their performance onerous. For rapid optimization of setup conditions, a model reduction assay can be employed to allow simultaneous, large-scale experiments at lower cost and effort. Since S. oneidensis uses different extracellular electron transfer pathways depending on the electron acceptor, it is essential to use a reduction assay that mirrors the pathways employed in the microbial fuel system. For microbial fuel setups that use nanoparticles to stimulate electron transfer, reduction of graphene oxide provides a more accurate model than other commonly used assays as it is a bulk material that forms flocculates in solutions with a large ionic component. However, graphene oxide flocculates can interfere with traditional absorbance-based measurement techniques. This study introduces a novel image analysis method for quantifying graphene oxide reduction, showing improved performance and statistical accuracy over traditional methods. A comparative analysis shows that the image analysis method produces smaller errors between replicates and reveals more statistically significant differences between samples than traditional plate reader measurements under conditions causing graphene oxide flocculation. Image analysis can also detect reduction activity at earlier time points due to its use of larger solution volumes, enhancing color detection. These improvements in accuracy make image analysis a promising method for optimizing microbial fuel cells that use nanoparticles or bulk substrates. IMPORTANCE Shewanella oneidensis ( S. oneidensis ) is widely used in reduction processes such as microbial fuel generation due to its capacity to reduce electron acceptors. Often, these setups are labor-intensive to operate and require days to produce results, so use of a model assay would reduce the time and expenses needed for optimization. Our research developed a novel digital analysis method for analysis of graphene oxide flocculates that may be utilized as a model assay for reduction platforms featuring nanoparticles. Use of this model reduction assay will enable rapid optimization and drive improvements in the microbial fuel generation sector.

Bennett, Danielle T. (ORCID:0009000188748827)↗
DOE OSTI2022

Development of a Markerless Deletion Mutagenesis System in Nitrate-Reducing Bacterium Rhodanobacter denitrificans

Rhodanobacter has been found as the dominant genus in aquifers contaminated with high concentrations of nitrate and uranium in Oak Ridge, TN, USA. The in situ stimulation of denitrification has been proposed as a potential method to remediate nitrate and uranium contamination. Among the Rhodanobacter species, Rhodanobacter denitrificans strains have been reported to be capable of denitrification and contain abundant metal resistance genes. However, due to the lack of a mutagenesis system in these strains, our understanding of the mechanisms underlying low-pH resistance and the ability to dominate in the contaminated environment remains limited. Here, we developed an in-frame markerless deletion system in two R. denitrificans strains. First, we optimized the growth conditions, tested antibiotic resistance, and determined appropriate transformation parameters in 10 Rhodanobacter strains. We then deleted the upp gene, which encodes uracil phosphoribosyltransferase, in R. denitrificans strains FW104-R3 and FW104-R5. The resulting strains were designated R3_Δupp and R5_Δupp and used as host strains for mutagenesis with 5-fluorouracil (5-FU) resistance as the counterselection marker to generate markerless deletion mutants. Further, to test the developed protocol, the narG gene encoding nitrate reductase was knocked out in the R3_Δupp and R5_Δupp host strains. As expected, the narG mutants could not grow in anoxic medium with nitrate as the electron acceptor. Overall, these results show that the in-frame markerless deletion system is effective in two R. denitrificans strains, which will allow for future functional genomic studies in these strains furthering our understanding of the metabolic and resistance mechanisms present in Rhodanobacter species.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Nitrous oxide reduction by two partial denitrifying bacteria requires denitrification intermediates that cannot be respired

ABSTRACT Denitrification is a form of anaerobic respiration wherein nitrate (NO 3 − ) is sequentially reduced via nitrite (NO 2 − ), nitric oxide, and nitrous oxide (N 2 O) to dinitrogen gas (N 2 ) by four reductase enzymes. Partial denitrifying bacteria possess only one or some of these four reductases and use them as independent respiratory modules. However, it is unclear if partial denitrifiers sense and respond to denitrification intermediates outside of their reductase repertoire. Here, we tested the denitrifying capabilities of two purple nonsulfur bacteria,Rhodopseudomonas palustrisCGA0092 andRhodobacter capsulatusSB1003. Each had denitrifying capabilities that matched their genome annotation; CGA0092 reduced NO 2 − to N 2 , and SB1003 reduced N 2 O to N 2 . For each bacterium, N 2 O reduction could be used both for electron balance during growth on electron-rich organic compounds in light and for energy transformation via respiration in darkness. However, N 2 O reduction required supplementation with a denitrification intermediate, including those for which there was no associated denitrification enzyme. For CGA0092, NO 3 − served as a stable, non-catalyzable molecule that was sufficient to activate N 2 O reduction. Using a β-galactosidase reporter, we found that NO 3 − acted, at least in part, by stimulating N 2 O reductase gene expression. In SB1003, NO 2 − but not NO 3 − activated N 2 O reduction, but NO 2 − was slowly removed, likely by a promiscuous enzyme activity. Our findings reveal that partial denitrifiers can still be subject to regulation by denitrification intermediates that they cannot use. IMPORTANCE Denitrification is a form of microbial respiration wherein nitrate is converted via several nitrogen oxide intermediates into harmless dinitrogen gas. Partial denitrifying bacteria, which individually have some but not all denitrifying enzymes, can achieve complete denitrification as a community by cross-feeding nitrogen oxide intermediates. However, the last intermediate, nitrous oxide (N2O), is a potent greenhouse gas that often escapes, motivating efforts to understand and improve the efficiency of denitrification. Here, we found that at least some partial denitrifying N2O reducers can sense and respond to nitrogen oxide intermediates that they cannot otherwise use. The regulatory effects of nitrogen oxides on partial denitrifiers are thus an important consideration in understanding and applying denitrifying bacterial communities to combat greenhouse gas emissions.

Biotechnology & Applied Microbiology↗
DOE OSTI2020

The Nucleoid-Associated Protein GapR Uses Conserved Structural Elements To Oligomerize and Bind DNA

Nucleoid-associated proteins (NAPs) are DNA binding proteins critical for the organization and function of the bacterial chromosome. A newly discovered NAP in Caulobacter crescentus, GapR, is thought to facilitate the movement of the replication and transcription machines along the chromosome by stimulating type II topoisomerases to remove positive supercoiling. Here, utilizing genetic, biochemical, and biophysical studies of GapR in light of a recently published DNA-bound crystal structure of GapR, we identified the structural elements involved in oligomerization and DNA binding. Moreover, we show that GapR is maintained as a tetramer upon its dissociation from DNA and that tetrameric GapR is capable of binding DNA molecules in vitro. Analysis of protein chimeras revealed that two helices of GapR are functionally conserved in H-NS, demonstrating that two evolutionarily distant NAPs with distinct mechanisms of action utilize conserved structural elements to oligomerize and bind DNA.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Role of glucuronoxylomannan and steryl glucosides in protecting against cryptococcosis

The development of vaccines for fungal diseases, including cryptococcosis, is an emergent line of research and development. In previous studies, we showed that a Cryptococcus mutant lacking the SGL1 gene (∆sgl1) accumulates certain glycolipids called steryl glucosides (SGs) on the fungal capsule, promoting an effective immunostimulation that totally protects the host from a secondary cryptococcal infection. However, this protection is lost when the cryptococcal capsule is absent in the ∆sgl1 background. The cryptococcal capsule is mainly composed of glucuronoxylomannan (GXM), a polysaccharide microfiber consisting of glucuronic acid, xylose, and mannose linked by glycosidic bonds forming specific triads. In this study, we engineered cells to lack each of the GXM components and tested the effect of these deletions on protection under the condition of SG accumulation. We found that glucuronic acid and xylose are required for protection, and their absence abrogates the production of IFNγ and IL-17A by γδ T cells, which are necessary stimulants for the protective phenotype of the ∆sgl1. We analyzed the structure of the GXM microfibers and found that although the deletion of SGL1 only slightly affects the size and distribution of these microfibers, it significantly changes the ratio of mannose to other components. In conclusion, this study identifies the structural modifications that the deletion of SGL1 and the consequent accumulation of SGs impart to the GXM structure of C. neoformans. This provides significant insights into the protective mechanisms mediated by SG accumulation on the capsule, with important implications for the future development of an efficacious cryptococcal vaccine.

Cryptococcus neoformans↗
DOE OSTI2022

Anaerobic Biohydrogenation of Isoprene by Acetobacterium wieringae Strain Y

Isoprene is a ubiquitously distributed, biogenic, and climate-active organic compound. Microbial isoprene degradation in oxic environments is fairly well understood; however, studies exploring anaerobic isoprene metabolism remain scarce, with no isolates for study available. Here, we obtained an acetogenic isolate, designated Acetobacterium wieringae strain Y, which hydrogenated isoprene to a mixture of methyl-1-butenes at an overall rate of 288.8 ± 20.9 μM day -1 with concomitant acetate production at a rate of 478.4 ± 5.6 μM day -1 . Physiological characterization demonstrated that isoprene was not utilized in a respiratory process; rather, isoprene promoted acetogenesis kinetically. Bioinformatic analysis and proteomics experiments revealed the expression of candidate ene-reductases responsible for isoprene biohydrogenation. Notably, the addition of isoprene to strain Y cultures stimulated the expression of proteins associated with the Wood-Ljungdahl pathway, indicating unresolved impacts of isoprene on carbon cycling and microbial ecology in anoxic environments (e.g., promoting CO 2 plus H 2 reductive acetogenesis while inhibiting methanogenesis). Our new findings advance understanding of microbial transformation of isoprene under anoxic conditions and suggest that anoxic environments are isoprene sinks.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Lactiplantibacillus plantarum uses ecologically relevant, exogenous quinones for extracellular electron transfer

Extracellular electron transfer (EET) is a metabolic process that frequently uses quinones to couple intracellular redox reactions with extracellular electron acceptors. The physiological relevance of this metabolism for microorganisms capable of EET but unable to synthesize their own quinones remains to be determined. To address this question, we investigated quinone utilization by Lactiplantibacillus plantarum, a microorganism required for food fermentations, that performs EET and is also a quinone auxotroph. L. plantarum selectively used 1,4-dihydroxy-2-naphthoic acid (DHNA) and more hydrophilic naphthoquinones for EET reduction of insoluble iron (ferrihydrite). However, quinones used for EET also inhibited L. plantarum growth in non-aerated conditions. Transcriptomic analysis showed that DHNA-induced oxidative stress in L. plantarum, but this was alleviated when the electron acceptor, ferric ammonium citrate (FeAC), was included in the growth medium. Although DHNA and FeAC induced L. plantarum EET, this metabolism was still dependent on direct access to environmental electron shuttles. To determine whether quinone-producing food fermentation bacteria could be sources of those electron shuttles, L. plantarum EET was measured after incubation with Lactococcus lactis and Leuconostoc mesenteroides. Quinone-producing L. lactis, but not a quinone-deficient L. lactis ΔmenC mutant, increased L. plantarum ferrihydrite reduction and medium acidification through an EET-dependent mechanism. L. plantarum EET was also stimulated by L. mesenteroides, resulting in greater environmental acidification and transient increases in L. plantarum cell numbers. Our findings show that L. plantarum overcomes the toxic effects of exogenous quinones to use those compounds for EET-conferred, ecological advantages during the early stages of food fermentations.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Metatranscriptomes of California grassland soil microbial communities in response to rewetting

When very dry soil is rewet, rapid stimulation of microbial activity has important implications for ecosystem biogeochemistry, yet associated changes in microbial transcription are poorly known. Here, we present metatranscriptomes of California annual grassland soil microbial communities, collected over 1 week from soils rewet after a summer drought—providing a time series of short-term transcriptional response during rewetting.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Exploring the Meta-regulon of the CRP/FNR Family of Global Transcriptional Regulators in a Partial-Nitritation Anammox Microbiome

Microbiomes are important contributors to many ecosystems, including ones where nutrient cycling is stimulated by aeration control. Optimizing cyclic aeration helps reduce energy needs and maximize microbiome performance during wastewater treatment; however, little is known about how most microbial community members respond to these alternating conditions.

transcription factors↗
DOE OSTI2024

Soil microbiome interventions for carbon sequestration and climate mitigation

Mitigating climate change in soil ecosystems involves complex plant and microbial processes regulating carbon pools and flows. Here, we advocate for the use of soil microbiome interventions to help increase soil carbon stocks and curb greenhouse gas emissions from managed soils. Direct interventions include the introduction of microbial strains, consortia, phage, and soil transplants, whereas indirect interventions include managing soil conditions or additives to modulate community composition or its activities. Approaches to increase soil carbon stocks using microbially catalyzed processes include increasing carbon inputs from plants, promoting soil organic matter (SOM) formation, and reducing SOM turnover and production of diverse greenhouse gases. Marginal or degraded soils may provide the greatest opportunities for enhancing global soil carbon stocks. Among the many knowledge gaps in this field, crucial gaps include the processes influencing the transformation of plant-derived soil carbon inputs into SOM and the identity of the microbes and microbial activities impacting this transformation. As a critical step forward, we encourage broadening the current widespread screening of potentially beneficial soil microorganisms to encompass functions relevant to stimulating soil carbon stocks. Moreover, in developing these interventions, we must consider the potential ecological ramifications and uncertainties, such as incurred by the widespread introduction of homogenous inoculants and consortia, and the need for site-specificity given the extreme variation among soil habitats. Incentivization and implementation at large spatial scales could effectively harness increases in soil carbon stocks, helping to mitigate the impacts of climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Multifactorial genetic control and magnesium levels govern the production of a Streptomyces antibiotic with unusual cell density dependence

Streptomyces bacteria are renowned both for their antibiotic production capabilities and for their cryptic metabolic potential. Their metabolic repertoire is subject to stringent genetic control, with many of the associated biosynthetic gene clusters being repressed by the conserved nucleoid-associated protein Lsr2. In an effort to stimulate new antibiotic production in wild Streptomyces isolates, we leveraged the activity of an Lsr2 knockdown construct and successfully enhanced antibiotic production in the wild Streptomyces isolate WAC07094. We determined that this new activity stemmed from increased levels of the angucycline-like family member saquayamycin. Saquayamycin has both antibiotic and anti-cancer activities, and intriguingly, beyond Lsr2-mediated repression, we found saquayamycin production was also suppressed at high density on solid or in liquid growth media; its levels were greatest in low-density cultures. This density-dependent control was exerted at the level of the cluster-situated regulatory gene sqnR and was mediated in part through the activity of the PhoRP two-component regulatory system, where deleting phoRP led to both constitutive antibiotic production and sqnR expression. This suggests that PhoP functions to repress the expression of sqnR at high cell density. We further discovered that magnesium supplementation could alleviate this density dependence, although its action was independent of PhoP. Finally, we revealed that the nitrogen-responsive regulators GlnR and AfsQ1 could relieve the repression exerted by Lsr2 and PhoP. Intriguingly, we found that this low density-dependent production of saquayamycin was not unique to WAC07094; saquayamycin production by another wild isolate also exhibited low-density activation, suggesting that this spatial control may serve an important ecological function in their native environments.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2026

Dates and rates of loess deposition and soil formation on the Snake River Plain, Idaho, USA

Loess-paleosol sequences in eolian deposits on the Snake River Plain, Idaho, western United States, preserve records of late Pleistocene to Holocene glacial-interglacial cycles. Here, we examine climate-driven changes in the timing and rate of loess accretion, soil formation, and pedogenic carbonate accumulation in the eastern and central Snake River Plain. High rates of loess deposition often correspond with dry, cold, and windy conditions and/or high sediment supply, while soil formation indicates landscape stability. Optically stimulated luminescence dating of four loess-soil sequences provides a record of the timing of loess deposition, and radiocarbon dating ( 14 C) of soil inorganic carbon provides ages for soil formation and pedogenic carbonate precipitation. On the central Snake River Plain, marine isotope stage (MIS) 3 is marked by loess deposition between ca. 50 ka and 33 ka, and pedogenic carbonate accumulation between ca. 42 ka calibrated years before present (cal. B.P.) and 31 ka cal. B.P. During MIS 2, loess deposition between ca. 21 ka and 15 ka is contemporaneous with pedogenic carbonate precipitation. MIS 2 is characterized by diffuse pedogenic carbonate formation and rapid loess accumulation. Both the eastern and central Snake River Plain study sites experienced high rates of loess deposition during MIS 2; however, the eastern Snake River Plain had almost three times faster rates of loess accumulation (0.56−0.63 m/k.y. from ca. 25 ka to 17 ka) as compared to the central Snake River Plain (0.18−0.26 m/k.y. from ca. 21 ka to 15 ka). During MIS 1, loess deposition on the central Snake River Plain ca. 11 ka was coincident with pedogenic carbonate formation ca. 10 ka cal. B.P. MIS 3 and MIS 1 are characterized by A horizons and well-developed Bk horizons, indicating soil stability and lower rates of loess accumulation during these intervals. Finally, this study highlights the role of late Quaternary−scale climatic variability on rates and amounts of soil inorganic carbon storage.

Geosciences↗
DOE OSTI2021

Polarization control in spin-transparent hadron colliders by weak-field navigators involving lattice enhancement effect

Hadron polarization control schemes for Spin Transparent (ST) synchrotrons are analyzed. The spin dynamics and beam polarization in such synchrotrons are controlled by spin navigators (SN) which are special small insertions of weak magnetic fields. An SN stabilizes the beam polarization and allows for setting any desirable spin orientation at an interaction point in the operational regime, including a frequent spin flip. We present a general approach to design of SNs. We distinguish different types of SNs, namely, those not causing closed orbit perturbation as well as those producing local and global orbit distortions. In the second case, the concept of the spin response function in an ST synchrotron is applied and expanded to reveal the effect of the SN strength enhancement by magnetic lattice of the synchrotron. We provide conceptual schemes for SN designs using longitudinal and transverse magnetic fields allowing for polarization control at low as well as high energies. We also develop the ST concept for ultra-high energies. This development may enable and stimulate interest in polarized beam experiments in possible polarized collider projects such as Large Hadron Collider (LHC), Future Circular Collider (FCC) and Super Proton Proton Collider (SPPC).

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2024

QCD challenges from pp to AA collisions: 4th edition

Abstract This paper is a write-up of the ideas that were presented, developed and discussed at the fourth International Workshop on QCD Challenges from pp to AA, which took place in February 2023 in Padua, Italy. The goal of the workshop was to focus on some of the open questions in the field of high-energy heavy-ion physics and to stimulate the formulation of concrete suggestions for making progresses on both the experimental and theoretical sides. The paper gives a brief introduction to each topic and then summarizes the primary results.

Physics↗
DOE OSTI2024

Physical insights into biological memory using phospholipid membranes

Electrical signals may propagate along neuronal membranes in the brain, thus enabling communication between nerve cells. In doing so, lipid bilayers, fundamental scaffolds of all cell membranes, deform and restructure in response to such electrical activity. These changes impact the electromechanical properties of the membrane, which then physically store biological memory. This memory can exist either over a short or long period of time. Traditionally, biological memory is defined by the strengthening or weakening of transmissions between individual neurons. In this report we show that electrical stimulation may also alter the properties of the lipid membrane, thus pointing toward a novel mechanism for memory storage. Furthermore, based on the analysis of existing electrophysiological data, we study molecular mechanisms underlying the long-term potentiation in phospholipid membranes. Finally, we examine possible relationships between the memory capacitive properties of lipid membranes, neuronal learning, and memory.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Phloem Loading and Unloading of Sucrose: What a Long, Strange Trip from Source to Sink

Sucrose is transported from sources (mature leaves) to sinks (importing tissues such as roots, stems, fruits, and seeds) through the phloem tissues in veins. In many herbaceous crop species, sucrose must first be effluxed to the cell wall by a sugar transporter of the SWEET family prior to being taken up into phloem companion cells or sieve elements by a different sugar transporter, called SUT or SUC. The import of sucrose into these cells is termed apoplasmic phloem loading. In sinks, sucrose can similarly exit the phloem apoplasmically or, alternatively, symplasmically through plasmodesmata into connecting parenchyma storage cells. Recent advances describing the regulation and manipulation of sugar transporter expression and activities provide stimulating new insights into sucrose phloem loading in sources and unloading processes in sink tissues. Additionally, new breakthroughs have revealed distinct subpopulations of cells in leaves with different functions pertaining to phloem loading. These and other discoveries in sucrose transport are discussed.

Plant Sciences↗
DOE OSTI2020

Unconventional Catalytic Approaches to Ammonia Synthesis

Ammonia is a critically important industrial chemical and is largely responsible for sustaining the growing global population. To provide ammonia to underdeveloped regions and/or regions far from industrial production hubs, modular systems have been targeted and often involve unconventional production methodologies. These novel approaches for ammonia production can tap renewable resources at smaller scales located at the point of use, while decreasing the CO 2 footprint. Plasma-assisted catalysis and electrochemical ammonia synthesis have promise owing to their atmospheric pressure and low-temperature operation conditions and the ability to construct units at scales desired for modularization. Fundamental and applied studies are underway to assess these processes, although many unknowns remain. In this review, we discuss recent developments and opportunities for unconventional ammonia synthesis with a focus on plasma-stimulated systems.

42 ENGINEERING↗
DOE OSTI2019

Review—Electrolytic Metal Atoms Enabled Manufacturing of Nanostructured Sensor Electrodes

Sensing materials play a key role in the successful implementation of electrochemical sensors, and nanotechnology has emerged as an important and rapidly growing field for stimulating the innovation of high-performance sensors. The fabrication, characterization, and evaluation of the nanostructured electrodes are therefore a focus of this field. Compared to a variety of dry and wet technologies which have been extensively developed for this purpose, electrochemical methods are typically convenient, highly effective, and potentially low-cost for the production of different nanostructures. This minireview is designed to introduce a unique electrochemical method - electrolytic metal-atom enabled manufacturing (EM 2 ) and its application in electrochemical sensors. The EM 2 technique employs electrolytic metal atoms generated from their corresponding salt precursor as a tool to nanostructure a wide range of substrate electrodes used in electrochemical sensors, based on a one-pot electrochemical deposition and dissolution of the metal atoms in the same electrolyte bath. Briefly, the metal atoms are electrodeposited on a substrate electrode during the cathode reduction, and they are selectively removed from the substrate during the subsequent anode oxidation. Because of the interactions between the electrolytic metal atoms and the substrate atoms, the repetitive electrodeposition and dissolution of the former on the substrate enable the nanostructuration of the substrate, particularly within its surface layers. The nanostructured electrodes have demonstrated very attractive performance for the determination of numerous analytes, such as high sensitivity and selectivity, high interference tolerance, and low detection limits. However, the EM 2 technique and the application of the resulting nanostructured electrodes in electrochemical sensors and beyond have still been very limitedly investigated. In order to bring the community from academic, industries, agencies, and customers together to develop the EM 2 technique and advance electrochemical sensor systems, this minireview will introduce the thermodynamic and kinetic fundamentals of this technique, the characterization of resulting nanostructures, the analysis of their electrochemical behavior, and the implementation of this technique for the development of advanced sensor electrodes. Finally, an outlook with a focus on further research areas is provided.

Jiang, Junhua (ORCID:0000000324379812)↗