Search NASA⌕ Search

SEARCH · Search NASA

Results for “sample complexity analysis”

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 1,027 records · Page 57
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Circuit-level design principles for transmission-mode microwave impedance microscopy

A recently developed technique of transmission-mode microwave impedance microscopy (T-MIM) has greatly extended the capabilities of standard reflection-mode MIM to novel applications, such as the in operando study of nanoscale electro-acoustic devices. As is common for new techniques, systematic design principles for boosting sensitivity and balancing bandwidth are lacking. Here, we show numerically and analytically that the T-MIM signal is proportional to the reflection-mode voltage enhancement factor η of the circuit, as long as the output impedance of the local voltage source is properly treated. We show that this proportionality holds in the currently achievable “weak sampling” regime and beyond, for which we demonstrate a realistic path with commercially available superconducting components and critically coupled impedance matching networks. Furthermore, we demonstrate that for these next-generation designs, the sensitivity is generally maximized at a slightly different frequency from the unloaded S 11 resonance, which can be explained by the maximum power transfer theorem.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2023

Uncertainty quantification of bank vegetation impacts on the flood flow field in the American River, California, using large‐eddy simulations

Bank vegetation plays a key role in both hydrodynamics and morphodynamics of natural rivers; however, these effects are often unaccounted for in the computational flow dynamics of natural waterways. Recent studies using the large‐eddy simulation (LES), however, have attempted to gain insights into the impacts of bank vegetation on the mean flow field of the natural rivers using a vegetation model, which applies a sink term to the momentum equations of motion. This approach accounts for the effects of the vegetation and provides a practical approach to account for the complex patches of bank vegetation in large‐scale rivers. To implement the vegetation model, a drag coefficient reflecting the overall resistance of vegetal structures to the flow is needed, but due to the lack of calibrated data and range of size, density and type of vegetation, this parameter can be a significant source of uncertainty in the model results. Here, in this study, we use uncertainty quantification (UQ) to investigate the hydrodynamics and bed shear results when a bank vegetation is incorporated in an LES model. To this end, we used the polynomial chaos expansion and Monte Carlo sampling techniques to determine the uncertainties associated with the drag coefficient in the vegetation model and from uncertainties in the bed roughness and inflow discharge. The UQ analysis provided spatially varying confidence levels for the spanwise and vertical distribution of velocity magnitude and for the bed shear stress distributions. In addition, Sobol indices were computed to indicate the relative influence that each parameter had on the overall uncertainty. In general, it was found that uncertainty in flow discharge was the dominant source of uncertainty; however, the drag coefficient in the vegetation model and the bed roughness parameter also made significant contribution to the uncertainty near the banks and bed, respectively.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Incorporating geological structure into sensitivity analysis of subsurface contaminant transport

Simulating subsurface contaminant transport at the kilometer-scale often entails modeling reactive flow and transport within and through complex geologic structures. These structures are typically meshed by hand and as a result geologic structure is usually represented by one or a few deterministically generated geological models for uncertainty studies of flow and transport in the subsurface. Uncertainty in geologic structure can have a significant impact on contaminant transport. In this study, the impact of geologic structure on contaminant tracer transport in a shale formation is investigated for a simplified generic deep geologic repository for permanent disposal of spent nuclear fuel. An open-source modeling framework is used to perform a sensitivity analysis study on transport of two tracers from a generic spent nuclear fuel repository with uncertain location of the interfaces between the stratum of the geologic structure. The automated workflow uses sampled realizations of the geological structural model in addition to uncertain flow parameters in a nested sensitivity analysis. Concentration of the tracers at observation points within, in line with, and downstream of the repository are used as the quantities of interest for determining model sensitivity to input parameters and geological realization. Finally, the results of the study indicate that the location of strata interfaces in the geological structure has a first-order impact on tracer transport in the example shale formation, and that this impact may be greater than that of the uncertain flow parameters.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2022

Application of Linear Additive Conditions for Near-Infrared Diffuse Reflectance Absorption Spectroscopy

Determining the homogeneity of material mixing in real time during product processing is critical for quality control. According to the Kubelka–Munk (K-M) function of diffuse reflectance absorption spectrum, absorbance (A) is approximately linear with the content of the components when the sample scattering coefficient (S) is in a certain range. The S is determined by the particle size of powder samples. Therefore, this study determined particle size ranges that satisfy linear additivity in near-infrared diffuse reflectance spectroscopy (NIRDRS). Thus, the proposed NIRDRS analysis technique can be used to determine the homogeneity of material mixes or analyze the percentages of the components in the mixture. In this study, vitamin B3 and vitamin C were used for preparing mixed samples with varying percentages. The experimental results revealed that linear additivity is satisfied when the powder particle size is in the range of less than 280, 280–450, and 450–900 μm. When the confidence level is 0.01, the actual mixed spectra are not significantly different from the “simulated mixed spectra” constructed by linear addition, with their relative deviations less than 1.08%. The absolute errors of the actual and analytic percentages were within 2.98% for each component in the mixtures. The above conclusions also hold for sorghum, which has a complex material composition. Statistical models cannot analyze the percentages of components in the mixture. In contrast, linear addition and direct calibration approach avoids the use of a large number of samples for statistical modeling and analyze the percentages of mixed samples. Meanwhile, it can be used to discriminate and analyze the material mixing uniformity by building a mechanistic model.

Feng, Zhiyue↗
DOE OSTI2020

Crewmember microbiome may influence microbial composition of ISS habitable surfaces

The International Space Station (ISS) is a complex built environment physically isolated from Earth. Assessing the interplay between the microbial community of the ISS and its crew is important for preventing biomedical and structural complications for long term human spaceflight missions. In this study, we describe one crewmember’s microbial profile from body swabs of mouth, nose, ear, skin and saliva that were collected at eight different time points pre-, during and post-flight. Additionally, environmental surface samples from eight different habitable locations in the ISS were collected from two flights. Environmental samples from one flight were collected by the crewmember and samples from the next flight were collected after the crewmember departed. The microbial composition in both environment and crewmember samples was measured using shotgun metagenomic sequencing and processed using the Livermore Metagenomics Analysis Toolkit. Ordination of sample to sample distances showed that of the eight crew body sites analyzed, skin, nostril, and ear samples are more similar in microbial composition to the ISS surfaces than mouth and saliva samples; and that the microbial composition of the crewmember’s skin samples are more closely related to the ISS surface samples collected by the crewmember on the same flight than ISS surface samples collected by other crewmembers on different flights. In these collections, species alpha diversity in saliva samples appears to decrease during flight and rebound after returning to Earth. This is the first study to compare the ISS microbiome to a crewmember’s microbiome via shotgun metagenomic sequencing. We observed that the microbiome of the surfaces inside the ISS resemble those of the crew’s skin. These data support future crew and ISS microbial surveillance efforts and the design of preventive measures to maintain crew habitat onboard spacecraft destined for long term space travel.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Establishing Isotopic Measurement Capabilities using Laser-Induced Breakdown Spectroscopy for the Molten Salt Reactor Campaign

Proof-of-principle H isotope ratios of aqueous aerosol systems and liquid droplets on filter paper have been measured using laser-induced breakdown spectroscopy (LIBS) with root mean square error of prediction values down to 1.9%. Molten salt reactors (MSRs) will consist of a complex chemical and radiological system consistently producing new fission products as the reactor operates. Some of these fission products and/or their daughter species will leave the salt in the reactor off-gas. Monitoring the composition of the off-gas, as well as the salt itself, is important for monitoring reactor performance, including burnup, corrosion, and the concentration of impurities. Tritium is of concern for MSRs because it will be produced from the irradiation of key salt constituents, including Li and Be. LIBS offers an avenue for in situ salt and off-gas monitoring by firing a laser onto or into the sample stream to generate a plasma. The plasma light can be monitored to measure an elemental fingerprint of the sample. Extending this analysis to include isotopic ratios offers a critical expansion of the in situ monitoring capabilities being developed. This study demonstrates the expansion of Oak Ridge National Laboratory’s LIBS capabilities to monitor isotopes and shows how simple calibrations may provide rapid semiquantitative models.

07 ISOTOPE AND RADIATION SOURCES↗
NASA NTRS1985

DLTS analysis of radiation-induced defects in one-MeV electron irradiated germanium and Alsub0.17Gasub0.83As solar cells

The radiation-induced deep-level defects in one-MeV electron-irradiated germanium and AlxGal-xAs solar cell materials using the deep-level transient spectroscopy (DLTS) and C-V techniques were investigated. Defect and recombination parameters such as defect density and energy levels, capture cross sections and lifetimes for both electron and hole traps were determined. The germanium and AlGaAs p/n junction cells were irradiated by one-MeV electrons. The DLTS, I-V, and C-V measurements were performed on these cells. The results are summarized as follows: (1) for the irradiated germanium samples, the dominant electron trap was due to the E sub - 0.24 eV level with density around 4x10 to the 14th power 1/cu cm, independent of electron fluence, its origin is attributed to the vacancy-donor complex defect formed during the electron irradiation; (2) in the one-MeV electron irradiated Al0.17Ga0.83 as sample, two dominant electron traps with energies of Ec-0.19 and -0.29 eV were observed, the density for both electron traps remained nearly constant, independent of electron fluence. It is shown that one-MeV electron irradiation creates very few or no new deep-level traps in both the germanium and AlxGa1-xAs cells, and are suitable for fabricating the radiation-hard high efficiency multijunction solar cells for space applications.

Li, S. B.↗
NASA NTRS1986

Size-density relations in dark clouds: Non-LTE effects

One of the major goals of molecular astronomy has been to understand the physics and dynamics of dense interstellar clouds. Because the interpretation of observations of giant molecular clouds is complicated by their very complex structure and the dynamical effects of star formation, a number of studies have concentrated on dark clouds. Leung, Kutner and Mead (1982) (hereafter LKM) and Myers (1983), in studies of CO and NH3 emission, concluded that dark clouds exhibit significant correlations between linewidth and cloud radius of the form delta v varies as R(0.5) and between mean density and radius of the form n varies as R(-1), as originally suggested by Larson (1981). This result suggests that these objects are in virial equilibrium. However, the mean densities inferred from the CO data of LKM are based on an local thermodynamic equilibrium (LTE) analysis of their 13CO data. At the very low mean densities inferred by LKM for the larger clouds in their samples, the assumption of LTE becomes very questionable. As most of the range in R in the density-size correlation comes from the clouds observed in CO, it seems worthwhile to examine how non-LTE effects will influence the derived densities. One way to assess the validity of LTE-derived densities is to construct cloud models and then to interpret them in the same way as the observed data. Microturbulent models of inhomogeneous clouds of varying central concentration with the linewidth-size and mean density-size relations found by Myers show sub-thermal excitation of the 13CO line in the larger clouds, with the result that LTE analysis considerbly underestimates the actual column density. A more general approach which doesn't require detailed modeling of the clouds is to consider whether the observed T sub R*(13CO)/T sub R*(12CO) ratios in the clouds studied by LKM are in the range where the LTE-derived optical depths (and hence column densities) can be seriously in error due to sub-thermal excitation of the 13CO molecule.

Maloney, P.↗
NASA NTRS2004

The Gas Chromatograph Mass Spectrometer for the Huygens Probe

Titan is unique in the solar system, the only moon that has a dense atmosphere. The major constituents of the atmosphere, nitrogen and methane, are continuously broken apart by a combination of solar UV, impinging electrons from Saturn s magnetosphere, and a steady flux of cosmic rays. The resulting molecular fragments recombine and form a variety of new species, many of which were detected for the first time by Voyager1 . The ubiquitous, surface- hiding aerosol blanket manifests the existence of still more complex compounds. In addition to hydrocarbons and nitriles, the atmosphere is known to contain CO, CO2 and externally delivered H2O. The Gas Chromatograph Mass Spectrometer (GCMS) on the Huygens Probe will measure the chemical composition of the atmosphere of Titan from 170 Km altitude (approximately 1hPa) to the surface (approximately 1500hPa) and determine the isotope ratios of the major constituents. The GCMS will also analyze gas samples from the Aerosol Collector Pyrolyser (ACP) and may be able to obtain compositional information of several surface materials. The GCMS consists of a quadrupole mass spectrometer (QP) with a secondary electron multiplier ion detector, a three-column gas chromatograph (GC) and an elaborate gas sampling system. The gas sampling system will provide atmospheric samples to the QP for nearly continuous analysis during the Probe descent and batch samples at several altitudes for GC analysis. It also contains a chemical scrubber for noble gas analysis and an enrichment cell for trace constituent enhancement. In addition to the sampling of the atmosphere periodic gas samples, derived from the pyrolysis of aerosols, will be transferred from the ACP to the GCMS for direct QP and full GCMS analysis. The QP can analyze molecular masses from 2 to 141Dalton. The nominal detection threshold is at a mixing ratio of 10E-8. Data rate is 885 bits/sec. The mass of the instrument is 17.3 kg and the energy required for operation during the descent is 110 Watt-hours.

Niemann, H. B.↗
NASA NTRS2004

The Gas Chromatograph Mass Spectrometer for the Huygens Probe

Titan is unique in the solar system, the only moon that has a dense atmosphere. The major constituents of the atmosphere, nitrogen and methane, are continuously broken apart by a combination of solar UV, impinging electrons from Saturn's magnetosphere, and a steady flow of cosmic rays. The resulting molecular fragments recombine and form a variety of new species, many of which were detected for the first time by Voyager 1. The ubiquitous, surface-hiding aerosol blanket manifests the existence of still more complex compounds. In addition to hydrocarbons and nitriles, the atmosphere is known to contain CO, CO2 and externally delivered H2O. The Gas Chromatograph Mass Spectrometer (GCMS) on the Huygens Probe will measure the chemical composition of the atmosphere of Titan from 170 km altitude (approximately lhPa) to the surface (approximately 1500hPa) and determine the isotope ratios of the major constituents. The GCMS will also analyze gas samples from the Aerosol Collector Pyrolyser (ACP) and may be able to obtain compositional information of several surface materials. The GCMS consists of a quadrupole mass spectrometer (QP) with a secondary electron multiplier ion detector, a three-column gas chromatograph (GC) and an elaborate gas sampling system. The gas sampling system will provide atmospheric samples to the QP for nearly continuous analysis during the Probe descent and batch samples at several altitudes for GC analysis. It also contains a chemical scrubber for noble gas analysis and an enrichment cell for trace constituent enhancement. In addition to the sampling of the atmosphere periodic gas samples, derived from the pyrolysis of aerosols, will be transferred from the ACP to the GCMS for direct QP and full GCMS analysis. The QP can analyze molecular masses from 2 to 14lDalton. The nominal detection threshold is at a mixing ratio of 10E-8. Data rate is 885 bits/sec. The mass of the instrument is 17.3 kg and the energy required for operation during the descent is 110 Watt-hours.

Niemann, H. B.↗
NASA NTRS2019

Measured Interfacial Residual Strains Produced by In-Flight Ice

The formation of ice on aircraft is a highly dynamic process during which ice will expand and contract upon freezing and undergoing changes in temperature. Finite Element Analysis (FEA) simulations were performed investigating the stress build up in a simplified case with uniform temperature changes between an idealized ice sample and acrylic substrate. These results were used to place strain gages on custom-built acrylic and aluminum specimens; these specimens were then placed in icing conditions such that ice was grown on top of the specimen. Tee rosettes were placed in two configurations adjacent to thermocouple sensors. It was hypothesized that the ice would expand on freezing and contract as the temperature of the interface returned to the equilibrium conditions. While results from the aluminum specimens matched this hypothesis, results from the acrylic specimens show a short period of contraction followed by a much larger expansion at the interface, indicating more complex ice growth thermodynamics than anticipated. Samples were observed to delaminate, and the data suggests that the residual strain is significant to the shedding of ice for in-flight applications.

residual strain↗
NASA NTRS1997

An Efficient Multiblock Method for Aerodynamic Analysis and Design on Distributed Memory Systems

The work presented in this paper describes the application of a multiblock gridding strategy to the solution of aerodynamic design optimization problems involving complex configurations. The design process is parallelized using the MPI (Message Passing Interface) Standard such that it can be efficiently run on a variety of distributed memory systems ranging from traditional parallel computers to networks of workstations. Substantial improvements to the parallel performance of the baseline method are presented, with particular attention to their impact on the scalability of the program as a function of the mesh size. Drag minimization calculations at a fixed coefficient of lift are presented for a business jet configuration that includes the wing, body, pylon, aft-mounted nacelle, and vertical and horizontal tails. An aerodynamic design optimization is performed with both the Euler and Reynolds Averaged Navier-Stokes (RANS) equations governing the flow solution and the results are compared. These sample calculations establish the feasibility of efficient aerodynamic optimization of complete aircraft configurations using the RANS equations as the flow model. There still exists, however, the need for detailed studies of the importance of a true viscous adjoint method which holds the promise of tackling the minimization of not only the wave and induced components of drag, but also the viscous drag.

Reuther, James↗
DOE OSTI2026

Understanding polaronic transport in complex oxides by combining precise synthesis and first-principles many-body theory

In complex oxides, charge carriers often couple strongly with lattice vibrations to form polarons–entangled electron–phonon quasiparticles whose transport properties remain difficult to characterize. Experimental access to intrinsic polaronic transport requires ultraclean samples, while theoretical description demands methods beyond low-order perturbation theory. Here, we show a predictive theory–experiment workflow to study polaron transport in complex oxides. Focusing on a prototypical polaronic oxide, anatase TiO 2 , we combine growth of high-quality oxygen-vacancy-doped films using hybrid molecular beam epitaxy with a first-principles electron–phonon diagrammatic Monte-Carlo (FEP-DMC) framework recently developed for accurate polaron predictions. Our films exhibit record-high electron mobility for anatase TiO 2 , in excellent agreement with FEP-DMC calculations conducted prior to experiment, which predict a room-temperature mobility of 45 ± 15 cm −2 V −1 s −1 and a mobility-temperature scaling of μ ∝ T −1.9 ± 0.077 . Microscopic analysis using scanning transmission electron microscopy and x-ray photoelectron spectroscopy reveals the role of oxygen vacancies in modulating transport at lower temperatures. FEP-DMC further provides quantitative insight into polaron formation energy, phonon cloud distribution, lattice distortion around the polaron, and the polaronic contribution to mobility. Together, these results provide a deeper microscopic understanding of large-polaron transport in a complex oxide and provide the blueprint to characterize other polaronic materials.

anatase TiO2↗
DOE OSTI2025

Studying Aerosol, Clouds, and Air Quality in the Coastal Urban Environment of Southeastern Texas

A multi-agency succession of field campaigns was conducted in southeastern Texas during July 2021 through October 2022 to study the complex interactions of aerosols, clouds and air pollution in the coastal urban environment. As part of the Tracking Aerosol Convection interactions Experiment (TRACER), the TRACER- Air Quality (TAQ) campaign the Experiment of Sea Breeze Convection, Aerosols, Precipitation and Environment (ESCAPE) and the Convective Cloud Urban Boundary Layer Experiment (CUBE), a combination of ground-based supersites and mobile laboratories, shipborne measurements and aircraft-based instrumentation were deployed. These diverse platforms collected high-resolution data to characterize the aerosol microphysics and chemistry, cloud and precipitation micro- and macro-physical properties, environmental thermodynamics and air quality-relevant constituents that are being used in follow-on analysis and modeling activities. We present the overall deployment setups, a summary of the campaign conditions and a sampling of early research results related to: (a) aerosol precursors in the urban environment, (b) influences of local meteorology on air pollution, (c) detailed observations of the sea breeze circulation, (d) retrieved supersaturation in convective updrafts, (e) characterizing the convective updraft lifecycle, (f) variability in lightning characteristics of convective storms and (g) urban influences on surface energy fluxes. The work concludes with discussion of future research activities highlighted by the TRACER model-intercomparison project to explore the representation of aerosol-convective interactions in high-resolution simulations.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Standard Analytical Methods for Pyrolysis Bio-Oils

There has been significant recent interest in the production of renewable fuels and chemicals from biomass and waste feedstocks. Pyrolysis pathways produce a liquid bio-oil product, which must be processed further, or upgraded, to yield fuel or chemical products. Bio-oils are very complex and often unstable samples, and research and development on upgrading processes needs reliable analytical information. In particular, chemical characterization techniques are needed to quantify both functional groups and individual compounds present in bio-oils. Reliable analytics are also needed to enable the bioenergy industry, as industrial facilities often have different analytical needs and capabilities than research facilities. In this presentation, we will discuss the development of a suite of standard analytical methods for pyrolysis bio-oils. Analytical methods to be discussed include: Determination of Carbon, Hydrogen, Nitrogen, and Oxygen in bio-oils; Accelerated Aging of Fast Pyrolysis Bio-oil using Carbonyl Titration; Determination of Water Content in Bio-oils by Volumetric Karl Fischer Titration; Determination of Carbon Functional Groups; Elemental Analysis of Bio-oils by Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES) - Na, K, Mg, Ca, S, P, and Fe; Determination of Phenolic Groups in Bio-oils using Revised Folin-Ciocalteu Methods: Single Cuvette and Plate Reader; Corrosivity of Bio-oils: Screening Test using Metal Leaching; Determination of Biogenic Content by 14C Measurement using Liquid Scintillation Counter. These new analytical methods are publicly available as Laboratory Analytical Procedures (https://www.nrel.gov/bioenergy/bio-oil-analysis.html), along with previously developed standard methods: GC-MS, Acid Titration, Carbonyl Titration, and 31P NMR. Additionally, the development of diffusion ordered NMR for characterization of bio-oil molecular weight will be discussed. Collectively, this suite of analytical methods represents the most comprehensive set of standard methods available for pyrolysis bio-oils. These standard methods are commonly used by the bioenergy community, and provide reliable information that enables research, scaleup, and industrial processing of biomass to produce renewable fuels and chemicals.

analytical↗
DOE OSTI2019

A CFD Study Assisted with Experimental Confirmation for Liquid Shape Control of Electromagnetically Levitated Bulk Materials

Two types of optimized electromagnetic levitators were designed to achieve the free surface shape control of metallic melts as the combined results of the Lorentz force, sample gravity, and surface tension. The levitation behavior of bulk melts was investigated using computational fluid dynamics (CFD) modeling coupled with high-frequency electromagnetic field analysis and the arbitrary Lagrangian–Eulerian (ALE) method. The difference in the oscillation behavior between the solid and molten samples was explained by the damping of the electromagnetic induction and liquid viscosity. The motion of the mass center, melt shape, flow pattern, and Lorentz force in the levitated melt were determined within a wide excitation current range. With the increase in the applied current, the melt’s centroid position rose sharply in the area with low current but displayed a slow increase in the area with high current. Meanwhile, the stable shape of the bulk melt showed the typical transition from a long taper through a short taper and then into a rhombus. The internal flow pattern transformed from a simple double-loop structure to a complex configuration with three or four loops. The dependence of the deformation on the Bond number was analyzed in the two types of levitators. In addition, the stable shape and swing process of the bulk Al melt within the two types of electromagnetic levitation (EML) systems were quantitatively studied under protective inert gas conditions. The melt contour could be well described by the 10th Legendre polynomial function with a deviation of less than 0.5 pct.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Selection and characterization of ssDNA aptamers specifically recognizing pathogenic Vibrio alginolyticus

Abstract Vibrio alginolyticus ( V. alginolyticus ) is a major opportunistic pathogen to both marine animals and humans, which has also caused heavy economic losses to mariculture. The aim of this study was to develop highly specific aptamers for V. alginolyticus . Single‐stranded DNA (ssDNA) aptamers with high binding affinity to viable V. alginolyticus were generated by Systematic Evolution of Ligands by Exponential Enrichment (SELEX) and identified by flow cytometric analysis in this study. The selected aptamers showed high specificity for V. alginolyticus and low apparent binding for other bacteria. The aptamers formed distinct stem‐loop structures, which could form the basis of aptamers’ specific binding to the target V. alginolyticus . Aptamer VA2 and VA8 showed particularly high binding affinity constant (K d ) of 14.31 ± 4.26 and 90.00 ± 13.51 nM, respectively. The aptamers produced no cytotoxic effects in vitro and in vivo. ssDNA aptamers were successfully selected against the viable bacteria pathogen V. alginolyticus by SELEX. The aptamers selected in this study could be not only applied as specific chemical molecular probes for studying V. alginolyticus pathogenesis to Trachinotus ovatus , but also developing rapid convenient diagnosis assay for V. alginolyticus infection, even when applied to the complex sample matrix, such as food and environment samples.

Yu, Qing↗
DOE OSTI2024

Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism

Abstract Background Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling. Results Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa , dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L 2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix . Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems. Conclusions Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix , and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling.

59 BASIC BIOLOGICAL SCIENCES↗