Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “assays”

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.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 613 records · Page 34
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Community Dynamics Drive Calcium Carbonate Production in an Enriched Consortium of Soil Microbes

Recently, there has been a focus on using soil microbes as a means to store carbon in the soil in the form of calcium carbonate, outcomes of which include soil stabilization and biocementation. The molecular processes involved in microbially induced calcium carbonate formation are known, but there is still a significant knowledge gap regarding how community interactions, emergent processes that are distinct from the roles of individual members, may drive the formation of carbonate. To answer these questions, we describe the development and application of a consortium of soil microbes consisting of one species each of the Rhodococcus , Microbacterium , and Curtobacterium genera and two species from the Bacillus genus. We term these five species cultivated together carbon storing consortium A (CSC-A). Growth assays show that only a subset of CSC-A members produces CaCO 3 with Rhodococcus producing the most CaCO 3 but the complete CSC-A produces significantly higher amounts of CaCO 3 compared to the sum total carbonate produced by all member species. The development of CSC-A shows that CaCO 3 production may be as much a community process as it is the contribution of individual species, requiring us to move beyond single species analysis to fully understand carbonate formation by microbial communities in nature. CSC-A will allow the scientific community to ask and answer key questions about the molecular interactions surrounding inorganic carbon formation in soil, an important knowledge gap that must be filled if we wish to stabilize soils and harness microbial processes for materials production.

calcium carbonate↗
DOE OSTI2020

High-throughput screening of environmental polysaccharide-degrading bacteria using biomass containment and complex insoluble substrates

Abstract Carbohydrate degradation by microbes plays an important role in global nutrient cycling, human nutrition, and biotechnological applications. Studies that focus on the degradation of complex recalcitrant polysaccharides are challenging because of the insolubility of these substrates as found in their natural contexts. Specifically, current methods to examine carbohydrate-based biomass degradation using bacterial strains or purified enzymes are not compatible with high-throughput screening using complex insoluble materials. In this report, we developed a small 3D printed filter device that fits inside a microplate well that allows for the free movement of bacterial cells, media, and enzymes while containing insoluble biomass. These devices do not interfere with standard microplate readers and can be used for both short- (24–48 h) and long-duration (> 100 h) experiments using complex insoluble substrates. These devices were used to quantitatively screen in a high-throughput manner environmental isolates for their ability to grow using lignocellulose or rice grains as a sole nutrient source. Additionally, we determined that the microplate-based containment devices are compatible with existing enzymatic assays to measure activity against insoluble biomass. Overall, these microplate containment devices provide a platform to study the degradation of complex insoluble materials in a high-throughput manner and have the potential to help uncover ecologically important aspects of bacterial metabolism as well as to accelerate biotechnological innovation.

3D printing↗
DOE OSTI2024

Omics-driven onboarding of the carotenoid producing red yeast Xanthophyllomyces dendrorhous CBS 6938

Transcriptomics is a powerful approach for functional genomics and systems biology, yet it can also be used for genetic part discovery. Here, we derive constitutive and light-regulated promoters directly from transcriptomics data of the basidiomycete red yeast Xanthophyllomyces dendrorhous CBS 6938 (anamorph Phaffia rhodozyma) and use these promoters with other genetic elements to create a modular synthetic biology parts collection for this organism. X. dendrorhous is currently the sole biotechnologically relevant yeast in the Tremellomycete class-it produces large amounts of astaxanthin, especially under oxidative stress and exposure to light. Thus, we performed transcriptomics on X. dendrorhous under different wavelengths of light (red, green, blue, and ultraviolet) and oxidative stress. Differential gene expression analysis (DGE) revealed that terpenoid biosynthesis was primarily upregulated by light through crtI, while oxidative stress upregulated several genes in the pathway. Further gene ontology (GO) analysis revealed a complex survival response to ultraviolet (UV) where X. dendrorhous upregulates aromatic amino acid and tetraterpenoid biosynthesis and downregulates central carbon metabolism and respiration. The DGE data was also used to identify 26 constitutive and regulated genes, and then, putative promoters for each of the 26 genes were derived from the genome. Simultaneously, a modular cloning system for X. dendrorhous was developed, including integration sites, terminators, selection markers, and reporters. Each of the 26 putative promoters were integrated into the genome and characterized by luciferase assay in the dark and under UV light. The putative constitutive promoters were constitutive in the synthetic genetic context, but so were many of the putative regulated promoters. Notably, one putative promoter, derived from a hypothetical gene, showed ninefold activation upon UV exposure. Thus, this study reveals metabolic pathway regulation and develops a genetic parts collection for X. dendrorhous from transcriptomic data. Therefore, this study demonstrates that combining systems biology and synthetic biology into an omics-to-parts workflow can simultaneously provide useful biological insight and genetic tools for nonconventional microbes, particularly those without a related model organism. This approach can enhance current efforts to engineer diverse microbes.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Effect of pH on the Activity of Ice-Binding Protein from Marinomonas primoryensis

The ability of an ice-binding protein (IBP) from Marinomonas primoryensis (MpIBP) to influence ice crystal growth and structure in nonphysiological pH environments was investigated in this work. The ability for MpIBP to retain ice interactivity under stressed environmental conditions was determined via (1) a modified splat assay to determine ice recrystallization inhibition (IRI) of polycrystalline ice and (2) nanoliter osmometry to evaluate the ability of MpIBP to dynamically shape the morphology of a single ice crystal. Circular dichroism (CD) was used to relate the IRI and DIS activity of MpIBP to secondary structure. The results illustrate that MpIBP secondary structure was stable between pH 6 and pH 10. It was found that MpIBP did not interact with ice at pH=4 or pH=13. At 6=pH=12 MpIBP exhibited a reduction in grain size of ice crystals as compared to control solutions and demonstrated dynamic ice shaping at 6=pH=10. The results substantiate that MpIBP retains some secondary structure and function in non-neutral pH environments; thereby, enabling its potential utility in nonphysiological materials science and engineering applications.

antifreeze proteins↗
DOE OSTI2024

Potential biological control agents of Geosmithia morbida restrict fungal pathogen growth via mycoparasitism and antibiosis

Abstract Thousand cankers disease of Juglans (walnut) and Pterocarya (wingnut) spp. (Fagales: Juglandaceae) is caused by the fungal pathogen Geosmithia morbida Kolarík, Freeland, Utley, and Tisserat (Hypocreales: Bionectriaceae) and bark beetle pest/vector, Pityophthorus juglandis Blackman (Coleoptera: Curculionidae). To further the development of biological management strategies for thousand cankers disease, we assessed the ability of 14 endophytic Trichoderma (Hypocreales: Hypocreaceae) isolates and the commercially available isolate T. afroharzianum strain KRL-AG2 to inhibit the in vitro growth of three different G. morbida isolates via mycoparasitism and antibiosis. To identify factors that may affect field success of candidate biological control agents, we quantified the growth responses of Trichoderma spp. and the commercially available entomopathogenic fungus, Beauveria bassiana (Bals.-Criv.) Vuill. (Hypocreales: Cordycipitaceae) strain GHA, to the plant secondary metabolite and antimicrobial compound, juglone in vitro. A total of 12 Trichoderma isolates (from six different Trichoderma species) demonstrated antagonistic activity towards G. morbida in dual-plate assays. Juglone consistently reduced the growth of B. bassiana strain GHA and 14 of the 15 screened Trichoderma isolates in vitro. Additionally, one metabolite-producing Trichoderma isolate, TN4-47, completely inhibited the growth of all three G. morbida isolates across all tested metabolite concentrations and had comparatively greater tolerance to juglone compared to other Trichoderma isolates. Future lines of research should focus on characterizing the active antagonistic compound present in the metabolite filtrates, determine the mode of action of the active component(s), and elucidate how abiotic and biotic factors may influence the growth, persistence, and antagonistic activity of candidate biological control agents in planta .

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Purification and characterization of a native lytic polysaccharide monooxygenase from Thermoascus aurantiacus

Lytic polysaccharide monooxygenases (LPMOs) have emerged as key proteins for depolymerization of cellulose. These copper-containing enzymes oxidize C-1 and/or C-4 bonds in cellulose, promoting increased hydrolysis of the oxidized cellulose chains. The LPMO from Thermoascus aurantiacus, a thermophilic ascomycete fungus, has been extensively studied and has served as a model LPMO. A method was developed to purify the LPMO from culture filtrates of T. aurantiacus along with its native cellobiohydrolase and endoglucanase. The activity of the purified LPMO was measured with a colorimetric assay that established the T opt of the native LPMO at 60 °C. Purification of the components of the T. aurantiacus cellulase mixture also enabled quantification of the amounts of cellobiohydrolase, endoglucanase and LPMO present in the T. aurantiacus culture filtrate, establishing that the LPMO was the most abundant protein in the culture supernatants. Here, the importance of the LPMO to activity of the mixture was demonstrated by saccharifications with Avicel and acid-pretreated corn stover.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

The role of cysteine in tellurate reduction and toxicity

The tellurium oxyanion tellurate is toxic to living organisms even at low concentrations; however, its mechanism of toxicity is poorly understood. Here, we show that exposure of Escherichia coli K-12 to tellurate results in reduction to elemental tellurium (Te[0]) and the formation of intracellular reactive oxygen species (ROS). Toxicity assays performed with E. coli indicated that pre-oxidation of the intracellular thiol pools increases cellular resistance to tellurate-suggesting that intracellular thiols are important in tellurate toxicity. X-ray absorption spectroscopy experiments demonstrated that cysteine reduces tellurate to elemental tellurium. This redox reaction was found to generate superoxide anions. These results indicate that tellurate reduction to Te(0) by cysteine is a source of ROS in the cytoplasm of tellurate-exposed cells.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural characterization and biological activity of an α-glucan from the mollusk Marcia hiantina (Lamarck, 1818)

Marcia hiantina (Mollusca, Bivalvia) (Lamarck, 1818), is an edible clam mainly distributed along the tropical coastal regions. Recent researches have demonstrated that clams can possess compounds, including polysaccharides, with a wide range of biological actions including antioxidant, immunomodulatory and antitumor activities. Here an α-glucan was isolated from M. hiantina by hot water, purified by anion exchange chromatography, and its structure was characterized by a combination of multiple nuclear magnetic resonance (NMR) methods (1D 1 H, 1 H- 1 H COSY, 1 H- 1 H TOCSY, 1 H- 1 H NOESY, 1 H- 13 C HSQC and 1 H- 13 C HSQC-NOESY spectra), gas chromatography-mass spectrometry, and high performance size exclusion chromatography (HPSEC). The analysis from NMR, monosaccharide composition, methylation analyses and HPSEC combined with multi angle light scattering (MALS) of M. hiantina-derived α-glycan confirmed a branched polysaccharide exclusively composed of glucose (Glc), mostly 4-linked in its backbone, branched occasionally at 6-positions, and having a molecular weight of ~ 570 kDa. The mollusk α-glucan was subjected to four cell-based assays: (i) viability of three cell lines (RAW264.7, HaCaT, and HT-29), (ii) activity on lipopolysaccharide (LPS)-induced prostaglandin production in RAW264.7 cells, (iii) inhibitory activities of in H 2 O 2 - and LPS-induced reactive oxygen species (ROS) production in HMC3 cells, and (iv) HaCaT cell proliferation. Furthermore, results have indicated no cytotoxicity, potent inhibition of both H 2 O 2 - and LPS-induced ROS, and potent cell proliferative activity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Integrated data-driven and experimental approaches to accelerate lead optimization targeting SARS-CoV- 2 main protease

Identification of potential therapeutic candidates can be expedited by integrating computational modeling with domain aware machine learning (ML) approaches followed by experimental validation. Generative deep learning models have been recently developed that can generate thousands of new candidates, but their physiochemical properties are typically not optimized. Using our deep learning models and a scaffold as a starting point, we generated tens of thousands of compounds for SARS-CoV-2 M pro that preserve the core scaffold. Here we utilized and implemented several computational tools such as structural alert and toxicity analysis, high throughput virtual screening, ML-based 3D quantitative structure–activity relationships, multi-parameter optimization, and graph neural networks on libraries of generated candidates to predict biological activity and binding affinity a priori. From these collective computational results, eight promising candidates were identified and tested experimentally using Native Mass Spectrometry (MS) and FRET-based functional assays. Two compounds, with quinazoline-2-thiol and acetylpiperidine core moiety showed IC 50 values in the low micromolar range: 2.95±0.0017 µM and 3.41±0.0015 µM, respectively. The molecular dynamics simulations further highlight that binding of these compounds results in allosteric modulations in the chain B and the interface domains of the M pro . The key fragments from these top hits can be used as input for closed loop lead optimization in the integrated pipeline.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Thermal impacts on nondestructive analysis measurements of uranium hexafluoride

A series of nondestructive assay measurements were performed before, during, and after localized heating of an industrial standard 12B cylinder of uranium hexafluoride to replicate dose variations previously observed on commercial 30B cylinders. While cylinders represent a closed system, enrichment measurements may be impacted by altered uranium and daughter product distributions due to sublimation. A series of measurements were performed to examine localized heating impacts on dose rates, ratios of uranium and daughter product distributions, and measured 235 U enrichment as calculated by two different approaches. The less complex enrichment meter approaches were found to be more robust and less prone to deviation than isotope ratio approaches such as FRAM, but the impact can be minimized by using observable dose changes to avoid impacted areas.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2022

Design and validation of a gamma-ray scanning system for measuring irradiated nuclear fuel

We report a prototype gamma-ray scanning system was designed to perform post-irradiation measurements of nuclear fuel at Idaho National Laboratory (INL). The system is composed of a coaxial high-purity germanium (HPGe) detector, a collimator, and mechanical positioning stages that translate the fuel sample across the front of the collimator. This paper documents the design process, modeling and the laboratory characterization performed to validate the system. The modeling of the system was done using the Monte Carlo N-Particle code with vendor-supplied design specifications, dimensional measurements, and x-ray radiographs of the HPGe detector. The characterization included measurements of calibrated radiation sources in different geometries, and calculations for absolute efficiency and dead time. Benchmark measurements were performed scanning an irradiated fuel rodlet containing ten pellets of 4.9% enriched UO2 in zirconium alloy. These results were compared to simulated spectra to further help characterize the detector model. One goal of the system is to determine the number of fissions per gram of UO2 in the fuel; comparison of the results from this prototype system's assay of the irradiated fuel rodlet are in agreement with previously estimated results.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2024

Effects of uranium metal carbon content on hydriding kinetics and corrosion blister number/area at sub-ambient pressures

Carbon is a common impurity in uranium metal, resulting in a number of uranium–carbon inclusion phases that contribute to an increase in metal defect density as carbon content increases. It is widely held that uranium hydride corrosion preferentially nucleates at these defect sites, and that an increase in carbon content will therefore represents an increase in uranium hydride corrosion sites on the metal surface. We hydrided six uranium sources with differing carbon contents to explore whether this assumption holds in a sub-ambient (~ 0.1 atm hydrogen), sealed environment, and report the resulting reaction kinetics and uranium hydride blister benchmarking data. We find that carbon content is not strongly correlated with reaction kinetics terms or the resulting hydride blister number and area, but that there is a tight relationship between corrosion blister number/area and kinetics as is expected. Further, we find that there is a strong trend of decreasing variance in the blister number, blister area, and induction time as carbon content increases (higher carbon content results in more reproducible blister populations). Additionally, we find a narrow band of uranium metal consumption at the end of the parabolic phase of reaction progress (beginning of linear growth phase) of 0.098 ± 0.011 w/w%, a fact that may be useful in assaying hydrogen corrosion of uranium metal within sealed environments generally.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2024

Tensioned metastable fluid detector sensing technology for multifarious-multiscale applications in the nuclear fuel cycle

The nuclear fuel cycle presents formidable 10 30+ multiscale challenges for high-efficiency spectroscopic sensing of alpha-neutron-fission radiation signatures amidst extreme gamma-beta radiation backgrounds at various stages of the cycle; it involves diverse arenas ranging from continuous/pulsed power production, security/safeguards, spent fuel, environmental remediation, and personnel health-dosimetry. This paper discusses the novel tensioned metastable fluid detector (TMFD) sensor technology. It discusses the results of studies demonstrating extreme (10 4 Sv/h) gamma-beta field blind high intrinsic efficiencies (80–100%) for neutron-alpha-fission radiation spectrometric detection. Example studies discussed in this paper include Neutron detection with spectroscopy; H*10 neutron radiation dosimetry upwards from ultra-low10 −2 µSv/h levels; Air and/or liquid-borne trace (10 –3 Bq/mL) quantity, 1 keV energy resolved alpha/fission spectroscopy for Rn/Po/U/Pu/Am environmental isotope assays at 106:1 (β:α) ratios; Directional-position enabled extended standoff tracking of neutron emitting (shielded/unshielded) special nuclear materials while stationary or moving at highway speeds; and, U.S. Department of Energy nuclear complex wide nuclear waste reprocessing, criticality safety, health physics, and environmental applications.

Alpha-fission-neutron spectrometry↗
DOE OSTI2025

230Th/234U radiochronometry for uranium materials by alpha spectrometry for nuclear forensics analysis

We have developed an alpha spectrometry method for 230Th/234U radiochronometry to determine the model separation age for uranium materials. This method offers an alternative to the more commonly used, but significantly more resource intensive multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS) while providing similar accuracy and precision. The development included radiochemical separation of uranium and thorium, calibration of the 232U tracer and the alpha spectrometry measurement. The method was validated by analyzing a certified reference material, CRM 125-A, which is a uranium oxide pellet assay, isotopic, and radiochronometric standard. The results were compared to those obtained by our routine MC-ICP-MS 230Th/234U radiochronometry analysis method to assess the performance parameters for alpha spectrometry compared to the state-of-the-art technique.

Macsik, Zsuzsanna [Los Alamos National Laboratory ↗
DOE OSTI2025

Nuclear forensic analysis on uranium ore concentrates: A multi-laboratory intercomparison study

A collaboration between the United States and Japan performed nuclear forensic analyses on a set of 7 uranium ore concentrate (UOC) samples with known origins to improve methodologies and best practices in the field. Overall, good agreement between the 4 participating laboratories was achieved for uranium assay, uranium isotope composition, strontium isotope composition, and trace element analysis. In conclusion, the combination of these four signatures is sufficient to distinguish the different origins among these studied UOCs.

and nuclear chemistry↗
DOE OSTI2026

A Coincident CdTe Detector Array for Enhanced Nuclear Process Monitoring

Nuclear fuel cycle aqueous separation processes desire improved real-time material characterization and process monitoring techniques; gamma coincidence spectroscopy has the potential to meet this need in these high throughput and high radiation environments based on its ability to reduce background noise, thereby enhancing detection limits and improving isotopic identification accuracy. A detector array composed of three CdTe detectors was designed to surround a chemical processing pipe in a reprocessing facility and evaluate the feasibility of passively assaying the nuclear materials flowing though this measurement point. This array uses commercial off the shelf components that are radiation hard and highly efficiency at low energies relevant to actinide photon signatures. Detector efficiency characterizations, coincidence detection, and potential configuration improvements are presented here.

Good, Erin C.↗
DOE OSTI2024

Five amino acid mismatches in the zinc-finger domains of Cellulose Synthase 5 and Cellulose Synthase 6 cooperatively modulate their functional properties by controlling homodimerization in Arabidopsis

Cellulose synthase 5 (CESA5) and CESA6 are known to share substantial functional overlap. In the zinc-finger domain (ZN) of CESA5, there are five amino acid (AA) mismatches when compared to CESA6. These mismatches in CESA5 were replaced with their CESA6 counterparts one by one until all were replaced, generating nine engineered CESA5s. Each N-terminal enhanced yellow fluorescent protein-tagged engineered CESA5 was introduced to prc1-1, a cesa6 null mutant, and resulting mutants were subjected to phenotypic analyses. For this work, we found that five single AA-replaced CESA5 proteins partially rescue the prc1-1 mutant phenotypes to different extents. Multi-AA replaced CESA5s further rescued the mutant phenotypes in an additive manner, culminating in full recovery by CESA5 G43R + S49T+S54P+S80A+Y88F . Investigations in cellulose content, cellulose synthase complex (CSC) motility, and cellulose microfibril organization in the same mutants support the results of the phenotypic analyses. Bimolecular fluorescence complementation assays demonstrated that the level of homodimerization in every engineered CESA5 is substantially higher than CESA5. The mean fluorescence intensity of CSCs carrying each engineered CESA5 fluctuates with the degree to which the prc1-1 mutant phenotypes are rescued by introducing a corresponding engineered CESA5. Taken together, these five AA mismatches in the ZNs of CESA5 and CESA6 cooperatively modulate the functional properties of these CESAs by controlling their homodimerization capacity, which in turn imposes proportional changes on the incorporation of these CESAs into CSCs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Empirical evidence that glucan-interacting amino acid side chains within the transmembrane channel collectively facilitate cellulose synthase function

The fundamental mechanism of cellulose synthesis is widely conserved across Kingdoms and depends on cellulose synthases, which are processive, dual-function, family 2 glycosyltransferases (GT-2). These enzymes polymerize glucose on the cytoplasmic side of the plasma membrane and export the glucan chain to the cell surface through an integral transmembrane (TM) channel. Structural studies of active plant cellulose synthases (CESAs) have revealed interactions between the nascent glucan chain and the side chains of polar, charged, and aromatic amino acid residues that line the TM channel. However, the functional consequences of modifying these side chains have not been tested in vivo in CESAs or other processive GT-2s. To test this, we used an established in vivo assay based on genetic complementation of CESA5 in the moss, Physcomitrium patens. For accurate prediction of glucan-interacting amino acid residues, we generated a complete homotrimeric molecular model of PpCESA5 using a combination of homology and de novo modeling. All-atom molecular dynamics-based analyses of contact metrics and interaction energy identified 23 amino acid residues with high propensity to interact with the nascent glucan chain within the TM channel or on the apoplastic surface of PpCESA5. Mutating any one of 18 of these amino acid residues to alanine, thereby removing their side chains, abolished or impaired CESA function, with the strongest effects observed upon the loss of charged amino acid side chains. This provides direct evidence to support the hypothesis that multiple amino acid residues collectively maintain a smooth energy landscape within the TM channel to facilitate glucan translocation.

59 BASIC BIOLOGICAL SCIENCES↗