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At least 667 records · Page 37
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Biofilm Interaction Mapping and Analysis (BIMA) of Interspecific Interactions in Pseudomonas Co-culture Biofilms

Pseudomonas species are ubiquitous in nature and include numerous medically, agriculturally and technologically beneficial strains of which the interspecific interactions are of great interest for biotechnologies. Specifically, co-cultures containing Pseudomonas stutzeri have been used for bioremediation, biocontrol, aquaculture management and wastewater denitrification. Furthermore, the use of P. stutzeri biofilms, in combination with consortia-based approaches, may offer advantages for these processes. Understanding the interspecific interaction within biofilm co-cultures or consortia provides a means for improvement of current technologies. However, the investigation of biofilm-based consortia has been limited. We present an adaptable and scalable method for the analysis of macroscopic interactions (colony morphology, inhibition, and invasion) between colony-forming bacterial strains using an automated printing method followed by analysis of the genes and metabolites involved in the interactions. Using Biofilm Interaction Mapping and Analysis (BIMA), these interactions were investigated between P. stutzeri strain RCH2, a denitrifier isolated from chromium (VI) contaminated soil, and 13 other species of pseudomonas isolated from non-contaminated soil. One interaction partner, Pseudomonas fluorescens N1B4 was selected for mutant fitness profiling of a DNA-barcoded mutant library; with this approach four genes of importance were identified and the effects on interactions were evaluated with deletion mutants and mass spectrometry based metabolomics.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Editorial: Structure and mechanism of microbial membrane active transporters

Membrane active transporters play essential roles in microbial physiology. They couple energy transduction to conformational changes that drive translocation of nutrients, substrates and ions, as well as molecular communication. The structure and function of microbial membrane active transporters are highly diverse. Typical examples include the primary active transporters in the ATP-binding cassette (ABC) superfamily (Thomas and Tampé, 2020; Davidson et al., 2008; Locher et al., 2002), the secondary active transporters in the Major Facilitator Superfamily (MFS) (Drew et al., 2021; Kaback and Guan, 2019), and the ligand-gated porins in the TonB-dependent transporter (TBDT) family (Klebba et al., 2021). As structural, proteogenomic, and computational methods advance, active transporters are increasingly recognized as dynamic molecular machines whose mechanisms can now be visualized and modeled with remarkable precision, building on decades of biochemical and biophysical discovery that established the foundations of this field. The transporter studies recruited in this Research Topic provide us with new insights into the field including structure-function of sugar transporters in yeast, structural prediction and classification of ABC complexes in Bacillus subtilis, Type VI Secretion System (T6SS) in Bacteroides fragilis, amino acids uptake in Escherichia coli and bacterial spore germination.

mechanism↗
DOE OSTI2022

Unexpected features in the optical vibrational spectra of δ-UO 3

Uranium trioxide displays a complex chemical phase space, with at least six structurally distinct polymorphs accessible via different synthetic routes. Remarkably, despite its technological importance, full structural and electronic characterization of these polymorphs remains an open area of study. δ-UO 3 in particular has attracted significant theoretical attention due to its high point group and space group symmetries, having U (VI) in octahedral coordination with polyhedra interconnected through corner-sharing to build a 3-D cubic lattice with space group symmetry Pm-3m and Z = 1. Critical experimental information, such as its optical vibrational spectra, are not known. Here, we study the Raman and infrared (IR) spectra of δ-UO 3 together with the support of density functional theory (DFT) calculations for spectral interpretation. A symmetry analysis of the DFT-predicted phonon eigenmodes indicates that δ-UO 3 should have two IR active modes and no Raman active modes. Experimental results, however, indicate significant Raman scattering from δ-UO 3 . We therefore propose four potential explanations for this apparent contradiction: a possible tetragonal distortion to the cubic cell, the existence of a surface impurity layer, vacancy scattering, and structural activation of Raman signal. We use powder X-ray diffraction and confocal Raman spectroscopy with depth profiling to investigate these possibilities and suggest future experiments to explore this phenomenon in more detail. Understanding the lattice dynamics of δ-UO 3 is important for identification of technogenic U phases via Raman and infrared spectroscopy and our results indicate that the simple understanding of δ-UO 3 as a high-symmetry cubic structure should be reconsidered.

98 NUCLEAR DISARMAMENT, SAFEGUARDS, AND PHYSICAL P↗
DOE OSTI2023

Quantifying neptunium oxidation states in nitric acid through spectroelectrochemistry and chemometrics

Controlled-potential in situ thin-layer spectropotentiometry was leveraged to generate visible/near-infrared (VIS/NIR) absorption spectral data sets for the development of chemometric models to quantify Np(III/IV/V/VI) oxidation states in HNO 3 . This technology would be valuable in laboratory studies and when monitoring process solutions to guide feed adjustments for radiochemical separations—the performance of which depends on oxidation state. This approach successfully isolated and stabilized Np species in pure (~99%) oxidation states without compromising solution optical properties. Multivariate curve resolution–alternating least squares models were evaluated to resolve spectral and component concentrations from a scan that sequentially produced Np(VI), Np(V), Np(IV), and Np(III) spectra with mixtures of two valences at a time. Although it provided a useful approximation, the method was not able to quantitively resolve each component likely because of rotational ambiguity. Additionally, partial least squares regression models were built from artificial and electrochemically generated VIS/NIR spectral training sets to study the effect of interionic interactions on spectral characteristics. Models built with true Bi-chemical mixtures of coexisting Np oxidation states and spectra generated from additive combinations of pure end points had similar prediction performance. This methodology can be used to directly quantify Np concentration and the ratio of Np oxidation states and other actinides in remote settings such as hot cells.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
DOE OSTI2023

Genome-wide characterization of the soybean DOMAIN OF UNKNOWN FUNCTION 679 membrane protein gene family highlights their potential involvement in growth and stress response

The DMP (DUF679 membrane proteins) family is a plant-specific gene family that encodes membrane proteins. The DMP family genes are suggested to be involved in various programmed cell death processes and gamete fusion during double fertilization in Arabidopsis. However, their functional relevance in other crops remains unknown. This study identified 14 genes from the DMP family in soybean (Glycine max) and characterized their physiochemical properties, subcellular location, gene structure, and promoter regions using bioinformatics tools. Additionally, their tissue-specific and stress-responsive expressions were analyzed using publicly available transcriptome data. Phylogenetic analysis of 198 DMPs from monocots and dicots revealed six clades, with clade-I encoding senescence-related AtDMP1/2 orthologues and clade-II including pollen-specific AtDMP8/9 orthologues. The largest clade, clade-III, predominantly included monocot DMPs, while monocot- and dicot-specific DMPs were assembled in clade-IV and clade-VI, respectively. Evolutionary analysis suggests that soybean GmDMPs underwent purifying selection during evolution. Using 68 transcriptome datasets, expression profiling revealed expression in diverse tissues and distinct responses to abiotic and biotic stresses. The genes Glyma.09G237500 and Glyma.18G098300 showed pistil-abundant expression by qPCR, suggesting they could be potential targets for female organ-mediated haploid induction. Furthermore, cis-acting regulatory elements primarily related to stress-, hormone-, and light-induced pathways regulate GmDMPs, which is consistent with their divergent expression and suggests involvement in growth and stress responses. Overall, our study provides a comprehensive report on the soybean GmDMP family and a framework for further biological functional analysis of DMP genes in soybean or other crops.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Assessment of a reconfiguration of the InterSpread Plus US national FMD model as a potential tool to analyze a foot-and-mouth disease outbreak on a single large cattle feedlot in the United States

An incursion of foot-and-mouth disease (FMD) into the United States remains a concern of high importance and would have devastating socioeconomic impacts to the livestock and associated industries. This highly transmissible and infectious disease poses continual risk for introduction into the United States (US), due to the legal and illegal global movement of people, animals, and animal products. While stamping out has been shown to effectively control FMD, depopulation of large cattle feedlots (>50,000 head) presents a number of challenges for responders due to the resources required to depopulate and dispose of large numbers of animals in a timely and effective manner. However, evaluating alternative strategies for FMD control on large feedlots requires a detailed within-farm modeling approach, which can account for the unique structure of these operations. To address this, we developed a single feedlot, within-farm spread model using a novel configuration within the InterSpread Plus (ISP) framework. As proof of concept we designed six scenarios: (i) depopulation - the complete depopulation of the feedlot, (ii) burn-through – a managed “burn-through” where the virus is allowed to spread through the feedlot and only movement restriction and biosecurity are implemented, (iii) firebreak-NV – targeted depopulation of infected pens and adjacent pens without vaccination; (iv) firebreak - targeted depopulation of infected pens and adjacent pens with vaccination of remaining pens; (v) harvest-NV - selective harvest of pens where a 100% movement restriction is applied for 28-30 days, then pens are set for selection to be sent to slaughter, while allowing a controlled “burn-through” without vaccination; and (vi) harvest - selective harvest of pens with vaccination. Overall, the burn-through scenario (ii) had the shortest epidemic duration (31d (30, 33)) median (25th, 75th percentiles), while the firebreak scenario (iv) had the longest (47d (38,55)). Additionally, we found that scenarios implementing depopulation delayed the peak day of infection and reduced the total number of pens infected compared to non-depopulation scenarios.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Evaluation of Deep Learning Model Architectures for Point-of-Care Ultrasound Diagnostics

Point-of-care ultrasound imaging is a critical tool for patient triage during trauma for diagnosing injuries and prioritizing limited medical evacuation resources. Specifically, an eFAST exam evaluates if there are free fluids in the chest or abdomen but this is only possible if ultrasound scans can be accurately interpreted, a challenge in the pre-hospital setting. In this effort, we evaluated the use of artificial intelligent eFAST image interpretation models. Widely used deep learning model architectures were evaluated as well as Bayesian models optimized for six different diagnostic models: pneumothorax (i) B- or (ii) M-mode, hemothorax (iii) B- or (iv) M-mode, (v) pelvic or bladder abdominal hemorrhage and (vi) right upper quadrant abdominal hemorrhage. Models were trained using images captured in 27 swine. Using a leave-one-subject-out training approach, the MobileNetV2 and DarkNet53 models surpassed 85% accuracy for each M-mode scan site. The different B-mode models performed worse with accuracies between 68% and 74% except for the pelvic hemorrhage model, which only reached 62% accuracy for all model architectures. These results highlight which eFAST scan sites can be easily automated with image interpretation models, while other scan sites, such as the bladder hemorrhage model, will require more robust model development or data augmentation to improve performance. With these additional improvements, the skill threshold for ultrasound-based triage can be reduced, thus expanding its utility in the pre-hospital setting.

47 OTHER INSTRUMENTATION↗
DOE OSTI2024

Mechanistic Insights Revealed by YbtPQ in the Occluded State

Recently, several ATP-binding cassette (ABC) importers have been found to adopt the typical fold of type IV ABC exporters. Presumably, these importers would function under the transport scheme of “alternating access” like those exporters, cycling through inward-open, occluded, and outward-open conformations. Understanding how the exporter-like importers move substrates in the opposite direction requires structural studies on all the major conformations. To shed light on this, here we report the structure of yersiniabactin importer YbtPQ from uropathogenic Escherichia coli in the occluded conformation trapped by ADP-vanadate (ADP-Vi) at a 3.1 Å resolution determined by cryo-electron microscopy. The structure shows unusual local rearrangements in multiple helices and loops in its transmembrane domains (TMDs). In addition, the dimerization of the nucleotide-binding domains (NBDs) promoted by the vanadate trapping is highlighted by the “screwdriver” action at one of the two hinge points. These structural observations are rare and thus provide valuable information to understand the structural plasticity of the exporter-like ABC importers.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Eight Up-Coming Biotech Tools to Combat Climate Crisis

Biotechnology has a high potential to substantially contribute to a low-carbon society. Several green processes are already well established, utilizing the unique capacity of living cells or their instruments. Beyond that, the authors believe that there are new biotechnological procedures in the pipeline which have the momentum to add to this ongoing change in our economy. Eight promising biotechnology tools were selected by the authors as potentially impactful game changers: (i) the Wood–Ljungdahl pathway, (ii) carbonic anhydrase, (iii) cutinase, (iv) methanogens, (v) electro-microbiology, (vi) hydrogenase, (vii) cellulosome and, (viii) nitrogenase. Some of them are fairly new and are explored predominantly in science labs. Others have been around for decades, however, with new scientific groundwork that may rigorously expand their roles. In the current paper, the authors summarize the latest state of research on these eight selected tools and the status of their practical implementation. We bring forward our arguments on why we consider these processes real game changers.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

On the Nature of Extra-Framework Aluminum Species and Improved Catalytic Properties in Steamed Zeolites

Steamed zeolites exhibit improved catalytic properties for hydrocarbon activation (alkane cracking and dehydrogenation). The nature of this practically important phenomenon has remained a mystery for the last six decades and was suggested to be related to the increased strength of zeolitic Bronsted acid sites after dealumination. We now utilize state-of-the-art infrared spectroscopy measurements and prove that during steaming, aluminum oxide clusters evolve (due to hydrolysis of Al out of framework positions with the following clustering) in the zeolitic micropores with properties very similar to (nano) facets of hydroxylated transition alumina surfaces. The Bronsted acidity of the zeolite does not increase and the total number of Bronsted acid sites decreases during steaming. O 5 Al(VI)-OH surface sites of alumina clusters dehydroxylate at elevated temperatures to form penta-coordinate Al 1 O 5 sites that are capable of initiating alkane cracking by breaking the first C-H bond very effectively with much lower barriers (at lower temperatures) than for protolytic C-H bond activation, with the following reaction steps catalyzed by nearby zeolitic Bronsted acid sites. This explains the underlying mechanism behind the improved alkane cracking and alkane dehydrogenation activity of steamed zeolites: heterolytic C-H bond breaking occurs on Al-O sites of aluminum oxide clusters confined in zeolitic pores. Our findings explain the origin of enhanced activity of steamed zeolites at the molecular level and provide the missing understanding of the nature of extra-framework Al species formed in steamed/dealuminated zeolites.

74 ATOMIC AND MOLECULAR PHYSICS↗
DOE OSTI2025

Remote Americium Detection Using an Optical Sensor: A D-Optimal Strategy for Efficient PLS-Based Modeling

A fiber-optic visible–near-infrared absorption spectroscopy system in a glove box was demonstrated for remote quantification of Am(III) (0–500 µM) and HNO 3 (0.1–9 M) using partial least squares regression (PLSR) models. The sensor platform, featuring a simple plug-and-play spectrophotometer, can enable noninvasive, real-time monitoring of actinide process solutions. To establish a flexible PLSR model calibration strategy, a D-optimal design developed using Nd(III) in previous studies was successfully extended to an actinide system with Am(III) to effectively minimize sample set size while maintaining robust prediction performance. The results suggest strong spectral similarities between Nd(III) and Am(III) and validate Nd(III) as an effective optical surrogate for trivalent actinide species. This work also supports the generalizability of a D-optimal training set selection approach for two-factor systems. The PLS1 models for Am(III) and HNO 3 outperformed a PLS2 model and maintained reasonable performance in the presence of interfering U(VI). The resulting sensor system and multivariate approach provides a flexible and scalable solution for process monitoring, control, and safety in diverse nuclear applications.

actinide↗
DOE OSTI2024

Uranium and Nickel Partitioning in a Contaminated Riparian Wetland

Uranium (U) and nickel (Ni) released 50 years ago have been immobilized in the Tims Branch wetlands located on the Savannah River Site in the United States. Sediments were collected from seven locations to identify the factors responsible for this attenuation. Ni and U contents in the solids were significantly correlated, suggesting that depositional as opposed to chemical processes contributed to their spatial distribution. Based on sequential extractions, 63 ± 16% of the U was partitioned into the organic fraction, whereas Ni was distributed between several sediment fractions. An inverse pH-organic matter (OM) correlation and positive correlations of OM with total U and organic-bound U/Ni suggest that increased OM preservation and binding to the mineral surfaces were likely responsible for Ni- and especially U-sediment retention (Tims Branch pH = 4.84 ± 0.68). EXAFS analysis indicated the predominance of U(VI) coordinated with clay minerals (~65%), together with ~35% coordinated to either OM (in areas with elevated OM levels) or iron oxides. The desorption-Kd coefficients of U (3972 ± 1370 L/kg) and Ni (30 ± 8 L/kg) indicate that dissolved Ni poses a greater long-term risk than dissolved U for migrating downstream. This study suggests that a delicate balance of geochemical properties controls whether wetlands behave as sinks or sources of contaminants.

63 RADIATION, THERMAL, AND OTHER ENVIRON. POLLUTAN↗
DOE OSTI2021

Intrinsic and Extrinsic Exciton Recombination Pathways in AgInS 2 Colloidal Nanocrystals

Ternary I-III-VI 2 nanocrystals (NCs), such as AgInS 2 and CuInS 2 , are garnering interest as heavy-metal-free materials for photovoltaics, luminescent solar concentrators, LEDs, and bioimaging. The origin of the emission and absorption properties in this class of NCs is still a subject of debate. Recent theoretical and experimental studies revealed that the characteristic Stokes-shifted and long-lived luminescence of stoichiometric CuInS 2 NCs arises from the detailed structure of the valence band featuring two sublevels with different parity. The same valence band substructure is predicted to occur in AgInS 2 NCs, yet no experimental confirmation is available to date. Here, we use complementary spectroscopic, spectro-electrochemical, and magneto-optical investigations as a function of temperature to investigate the band structure and the excitonic recombination mechanisms in stoichiometric AgInS 2 NCs. Transient transmission measurements reveal the signatures of two subbands with opposite parity, and photoluminescence studies at cryogenic temperatures evidence a dark state emission due to enhanced exchange interaction, consistent with the behavior of stoichiometric CuInS 2 NCs. Lowering the temperature as well as applying reducing electrochemical potentials further suppress electron trapping, which represents the main nonradiative channel for exciton decay, leading to nearly 100% emission efficiency.

36 MATERIALS SCIENCE↗
DOE OSTI2020

A Random Forest Approach to Identifying Young Stellar Object Candidates in the Lupus Star-forming Region

The identification and characterization of stellar members within a star-forming region are critical to many aspects of star formation, including formalization of the initial mass function, circumstellar disk evolution, and star formation history. Previous surveys of the Lupus star-forming region have identified members through infrared excess and accretion signatures. We use machine learning to identify new candidate members of Lupus based on surveys from two space-based observatories: ESA’s Gaia and NASA’s Spitzer. Astrometric measurements from Gaia's Data Release 2 and astrometric and photometric data from the Infrared Array Camera on the Spitzer Space Telescope, as well as from other surveys, are compiled into a catalog for the random forest (RF) classifier. The RF classifiers are tested to find the best features, membership list, non-membership identification scheme, imputation method, training set class weighting, and method of dealing with class imbalance within the data. We list 27 candidate members of the Lupus star-forming region for spectroscopic follow-up. Most of the candidates lie in Clouds V and VI, where only one confirmed member of Lupus was previously known. These clouds likely represent a slightly older population of star formation.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2020

Mathematical Underpinnings of the Multiwavelength Structure of the Tip of the Red Giant Branch

We consider the application of the tip of the red giant branch (TRGB) in the optical and in the near-infrared for the determination of distances to nearby galaxies. We analyze ACS VI (F555W and F814W) data and self-consistently cross-calibrate WFC3-IR JH (F110W and F120W) data using an absolute magnitude calibration of M {sub I} = −4.05 mag as determined in the Large Magellanic Cloud using detached eclipsing binary star geometric parallaxes. We demonstrate how the optical and near-infrared calibrations of the TRGB method are mathematically self-consistent, and illustrate the mathematical basis and relations among these multiwavelength calibrations. We go on to present a method for determining the reddening, extinction, and the true modulus to the host galaxy using multiwavelength data. The power of the method is that with high-precision data, the reddening can be determined using the TRGB stars themselves, and decreases the systematic (albeit generally small) uncertainty in distance due to reddening for these halo stars.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2021

The Coronal Line Spectrum of the Iron Nova V3666 Ophiuchi

Optical and infrared spectroscopy are presented for the classical nova V3666 Ophiuchi (Nova Ophiuchi 2018 No.3) from 11 months after its outburst. At that epoch, V3666 Oph displayed an [Fe x] λ0.6375 emission line stronger than Hα and nearly a factor of 3 larger, relative to Hα, than in any nova observed previously. The [Fe x] feature, with an equivalent width exceeding 1300 Å, was enormously strong relative to the continuum emission as well. V3666 Oph also reached a state of high excitation for an Fe ii type nova, displaying coronal lines of [Fe xi], [S ix], and [Ar x], and permitted features that can be identified with the C vi (8–7), (9–8), and (10–9) transitions. In addition to [Fe x] and [Fe xi], V3666 Oph also displayed bright lines of [Fe vii], indicating that the prominent iron features were not confined to a single or narrow range of ionization states. Modeling the emission line spectrum of V3666 Oph with the photoionization code Cloudy indicated that the bulk of the emission line gas was matter-bounded, severely reducing the amount of low ionization gas and resulting in coronal lines that were very strong in comparison to lines such as H i and He i, and the familiar low excitation forbidden lines of nitrogen and oxygen. Such matter-bounded regions are observationally rare in novae since they are both faint and short-lived, offering a plausible explanation for why [Fe x] λ0.6375 had not be seen at this strength previously.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2021

Synthetic Absorption Lines from Simulations of Multiphase Gas in Galactic Winds

Supernova-driven galactic winds are multiphase streams of gas that are often observed flowing at a range of velocities out of star-forming regions in galaxies. In this study, we use high-resolution 3D simulations of multiphase galactic winds modeled with the hydrodynamics code Cholla to investigate the connection between numerical studies and observations. Using a simulated interaction between a hot $T$ ~ 10 4 K supernova-driven wind and a cool $T$ ~ 10 7 K cloud of interstellar material, we create mock observables, including the optical depth ($\tau$) and covering fraction ($C$ $f$ ) of six commonly observed ions (Si II , C II , Si IV , C IV , N V , and O VI ) as a function of gas velocity. We compare our mock observables to surveys of galactic winds in the literature, finding good agreement with velocities and profiles of the low ions. We then compute "empirical" values for the optical depth and covering fraction following observational techniques and compare them to the values calculated directly from the simulation data. We find that the empirically computed values tend to underestimate the "true" value of $\tau$ for ions with high optical depth and overestimate the "true" value of $\tau$ for ions with low optical depth relative to the simulated data. In conclusion, the empirically estimated covering fractions match our direct calculations very well for the low-ionization ions; for the high-ionization ions, the empirical covering fractions underestimate the directly computed values by up to ~40%.

79 ASTRONOMY AND ASTROPHYSICS↗
DOE OSTI2022

A Near-infrared Look at AGN Feedback in Bulgeless Galaxies

While it is generally believed that supermassive black holes (SMBHs) lie in most galaxies with bulges, few SMBHs have been confirmed in bulgeless galaxies. Identifying such a population could provide important insights to the BH seed population and secular BH growth. To this end, we obtained near-infrared (NIR) spectroscopic observations of a sample of low-redshift bulgeless galaxies with mid-infrared colors suggestive of active galactic nuclei (AGNs). We find additional evidence of AGN activity (such as coronal lines and broad permitted lines) in 69% (9/13) of the sample, demonstrating that mid-infrared selection is a powerful tool to detect AGNs. More than half of the galaxies with confirmed AGN activity show fast outflows in [O III ] in the optical and/or [Si vi] in the NIR, with the latter generally having much faster velocities that are also correlated to their spatial extent. We are also able to obtain virial BH masses for some targets and find they fall within the scatter of other late-type galaxies in the M BH –M stellar relation. The fact that they lack a significant bulge component indicates that secular processes, likely independent of major mergers, grew these BHs to supermassive sizes. Finally, we analyze the rotational gas kinematics and find two notable exceptions: two AGN hosts with outflows that appear to be rotating faster than expected. There is an indication that these two galaxies have stellar masses significantly lower than expected from their dark matter halo masses. This, combined with the observed AGN activity and strong gas outflows, may be evidence of the effects of AGN feedback.

79 ASTRONOMY AND ASTROPHYSICS↗