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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 433 records · Page 24
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Online supercritical fluid extraction mass spectrometry (SFE-LC-FTMS) for sensitive characterization of soil organic matter

We report a novel technical approach for subcritical fluid extraction (SFE) for organic matter characterization in complex matrices such as soil. The custom platform combines on-line SFE with micro-solid phase extraction, nano liquid chromatography (LC), electrospray ionization and Fourier transform mass spectrometry (SFE-LC-FTMS). We demonstrated the utility of SFE-LC-FTMS, including results from both Orbitrap and FTICR MS, for analysis of complex mixtures of organic compounds in a solid matrix by characterizing soil organic matter in peat, a high-carbon soil. For example, in a single experiment, >6000 molecular formulas can be assigned based upon FTICR MS data from 1–50 μL of soil samples (roughly 1–50 mg of soil, dependent on soil density), nearly twice that typically obtained from direct infusion liquid solvent extraction (LSE) from an order of magnitude larger volume of the same soil. The detected species consisted predominately of lipid-like, lignin-like and protein-like compounds, based on their O/C and H/C ratios, with predominantly CHO and CHONP molecular compositions. These results clearly demonstrate that SFE has the potential to effectively extract a variety of molecular species and could become an important member of a suite of extraction methods for studying SOM and other natural organic matter. This is especially true when comprehensive coverage, minimal sample volumes, and high sensitivity are required, or when the presence of organic solvent residue in residual soil is problematic. Lastly, the SFE based extraction protocol could potentially enable spatially resolved characterization of organic matter in soil with a resolution of ~1 mm3 to facilitate studies probing the spatial heterogeneity of soil.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2016

scraps: An open-source Python-based analysis package for analyzing and plotting superconducting resonator data

We present "scraps" (SuperConducting Analysis and Plotting Software), a Python package designed to aid in the analysis and visualization of large amounts of superconducting resonator data, specifically complex transmission as a function of frequency, acquired at many different temperatures and driving powers. The package includes a least-squares fitting engine as well as a Monte-Carlo Markov Chain sampler for sampling the posterior distribution given priors, marginalizing over nuisance parameters, and estimating covariances. A set of plotting tools for generating publication-quality figures is also provided in the package. Lastly, we discuss the functionality of the software and provide some examples of its utility on data collected from a niobium-nitride coplanar waveguide resonator fabricated at Argonne National Laboratory.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2022

Effect of Micro-Structural Dispersity of SiMo Ductile Iron on High Temperature Performance during Static Oxidation

High silicon and molybdenum (SiMo) ductile iron is commonly used for car exhaust systems, and its micro-structural dispersity depends on intrinsic parameters, which include alloy composition and inoculation efficiency, as well as extrinsic factors, such as casting wall thickness and molding material, which define cooling rate during solidification. Micro-structural dispersity is referred to as the degree of heterogeneity of sizes of structural constituencies within the microstructure. A variation in the micro-structural dispersity could impact the high temperature performance of SiMo ductile iron during static oxidation and transient thermo-mechanical loading conditions. In this study, static high temperature tests were performed on SiMo ductile iron solidified in a casting with varying wall thicknesses from 5 mm to 100 mm. The faster solidified specimens (taken from near chilled casting surfaces) had extremely high micro-structural dispersity as compared to the thicker section samples. After thermal exposure, each of the samples were characterized using 2D sections and 3D µCT images, and the results indicated an order of magnitude difference in graphite phase dispersity. The surface degradation was quantified after static oxidation experiments were implemented at temperature intervals between 650 °C and 800 °C. Non-destructive µCT 3D analysis and SEM/EDS were performed on cross sections and used to quantify the scale topology and structure. Carbon analysis was used to decouple the scale formation and decarburization phenomena that occurred within the samples. These methods enabled the quantification of the oxidation of the SiMo cast iron with different micro-structural dispersity levels after being exposed to high temperature static oxidation. Additionally, the complex material behavior during oxidation-assisted transient thermo-mechanical loading will be presented in a separate article.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Complementary Metagenomic Approaches Improve Reconstruction of Microbial Diversity in a Forest Soil

ABSTRACT Soil ecosystems harbor diverse microorganisms and yet remain only partially characterized as neither single-cell sequencing nor whole-community sequencing offers a complete picture of these complex communities. Thus, the genetic and metabolic potential of this “uncultivated majority” remains underexplored. To address these challenges, we applied a pooled-cell-sorting-based mini-metagenomics approach and compared the results to bulk metagenomics. Informatic binning of these data produced 200 mini-metagenome assembled genomes (sorted-MAGs) and 29 bulk metagenome assembled genomes (MAGs). The sorted and bulk MAGs increased the known phylogenetic diversity of soil taxa by 7.2% with respect to the Joint Genome Institute IMG/M database and showed clade-specific sequence recruitment patterns across diverse terrestrial soil metagenomes. Additionally, sorted-MAGs expanded the rare biosphere not captured through MAGs from bulk sequences, exemplified through phylogenetic and functional analyses of members of the phylum Bacteroidetes . Analysis of 67 Bacteroidetes sorted-MAGs showed conserved patterns of carbon metabolism across four clades. These results indicate that mini-metagenomics enables genome-resolved investigation of predicted metabolism and demonstrates the utility of combining metagenomics methods to tap into the diversity of heterogeneous microbial assemblages. IMPORTANCE Microbial ecologists have historically used cultivation-based approaches as well as amplicon sequencing and shotgun metagenomics to characterize microbial diversity in soil. However, challenges persist in the study of microbial diversity, including the recalcitrance of the majority of microorganisms to laboratory cultivation and limited sequence assembly from highly complex samples. The uncultivated majority thus remains a reservoir of untapped genetic diversity. To address some of the challenges associated with bulk metagenomics as well as low throughput of single-cell genomics, we applied flow cytometry-enabled mini-metagenomics to capture expanded microbial diversity from forest soil and compare it to soil bulk metagenomics. Our resulting data from this pooled-cell sorting approach combined with bulk metagenomics revealed increased phylogenetic diversity through novel soil taxa and rare biosphere members. In-depth analysis of genomes within the highly represented Bacteroidetes phylum provided insights into conserved and clade-specific patterns of carbon metabolism.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

High expression of diffuse panbronchiolitis critical region 1 gene promotes cell proliferation, migration and invasion in pancreatic ductal adenocarcinoma

Highlights: • DPCR1 is overexpressed in PDAC and correlates with prognosis of PDAC patients. • Inhibition of DPCR1 suppresses PDAC cell proliferation in vitro and in vivo. • Inhibition of DPCR1 suppresses PDAC cell migration and invasion. • DPCR1 may promote tumor progression by regulating NF-κB pathway. Diffuse panbronchiolitis critical region 1 (DPCR1) is located in the major histocompatibility complex (MHC) class I. It was reported to be downregulated in invasive pituitary adenoma compared with that in non-invasive tumors, but upregulated in the precursor of gastric carcinogenesis. However, the direct effect of DPCR1 on cancer cells has rarely been reported, and the role DPCR1 in pancreatic ductal adenocarcinoma (PDAC) remains unclear. The clinical sample validation and public data analysis of the present study demonstrated that DPCR1 was upregulated markedly in PDAC and this high expression was negatively correlated with the patient prognosis. Functionally, knocking down DPCR1 in PDAC cell lines inhibited cell proliferation, migration and invasion in vitro. Tumor xenograft experiments further showed that suppression of DPCR1 inhibited tumor growth in vivo. In addition, the results of RNA deep sequencing and qRT-PCR assay showed that DPCR1 participated in PADC progression by regulating nuclear factor-kappa B signaling pathway, suggesting that it might be a novel oncogene in tumor progression and a potential therapeutic target in PDAC as well.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2017

Automated single-ion peak fitting as an efficient approach for analyzing complex chromatographic data

Chromatography provides important detail on the composition of environmental samples and their chemical processing. However, the complexity of these samples and their tendency to contain many structurally and chemically similar compounds frequently results in convoluted or poorly resolved data. Data reduction from raw chromatograms of complex environmental data into integrated peak areas consequently often requires substantial operator interaction. This difficulty has led to a bottleneck in analysis that increases analysis time, decreases data quality, and will worsen as advances in field-based instrumentation multiply the quantity and informational density of data produced. In this work, we develop and validate an automated approach to fitting chromatographic data within a target retention time window with a combination of multiple idealized peaks (Gaussian peaks either with or without an exponential decay component). Herein we compare this single-ion peak fitting approach to drawn baseline integration methods of more than 70,000 peaks collected by field-based chromatographs spanning across a wide range of volatilities and functionalities. Accuracy of peak fitting under real-world conditions is found to be within 10%. The quantitative parameters describing the fit (e.g. coefficients, fit residuals, etc.) are found to provide valuable information to increase the efficiency of quality control and provide constraints to accurately integrate peaks that are significantly convoluted with neighboring peaks. Implementation of the peak fitting method is shown to yield accurate integration of peaks otherwise too poorly resolved to separate into individual compounds and improved quantitative metrics to determine the fidelity of the data reduction process, while substantially decreasing the time spent by operators on data reduction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2017

Neutron time-of-flight reflectometer GRAINS with horizontal sample plane at the IBR-2 reactor: Possibilities and prospects

A new time-of-flight neutron reflectometer GRAINS with a horizontal sample plane (vertical scattering plane) has recently been put into operation at the pulsed reactor IBR-2 (JINR, Dubna). The scattering geometry applied makes it possible to carry out complex studies of nanostructured interfaces in solid and liquid states by measuring the specular reflectivity and the intensity of diffuse scattering of thermal neutrons from open surfaces and hidden interlayer boundaries, including solid-liquid interfaces, over a wide momentum transfer range. The classical analysis of specular reflectivity allows one to determine the scattering length density profile in the object under study in a direction perpendicular to the interface for a thickness of ~100 nm with a resolution of 1 nm. The analysis of off-specular (diffuse) neutron scattering makes it possible to characterize lateral correlations on surfaces and interlayer boundaries. The paper summarizes the first experience in the operation of the GRAINS reflectometer. The instrument characteristics are presented together with the possibilities for experiments with solid and liquid samples illustrated with simple systems. Further steps for the development of the reflectometer are discussed.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗
DOE OSTI2016

Validation of picogram- and femtogram-input DNA libraries for microscale metagenomics

High-throughput sequencing libraries are typically limited by the requirement for nanograms to micrograms of input DNA. This bottleneck impedes the microscale analysis of ecosystems and the exploration of low biomass samples. Current methods for amplifying environmental DNA to bypass this bottleneck introduce considerable bias into metagenomic profiles. For this study, we describe and validate a simple modification of the Illumina Nextera XT DNA library preparation kit which allows creation of shotgun libraries from sub-nanogram amounts of input DNA. Community composition was reproducible down to 100 fg of input DNA based on analysis of a mock community comprising 54 phylogenetically diverse Bacteria and Archaea. The main technical issues with the low input libraries were a greater potential for contamination, limited DNA complexity which has a direct effect on assembly and binning, and an associated higher percentage of read duplicates. We recommend a lower limit of 1 pg (~100–1,000 microbial cells) to ensure community composition fidelity, and the inclusion of negative controls to identify reagent-specific contaminants. Applying the approach to marine surface water, pronounced differences were observed between bacterial community profiles of microliter volume samples, which we attribute to biological variation. This result is consistent with expected microscale patchiness in marine communities. We thus envision that our benchmarked, slightly modified low input DNA protocol will be beneficial for microscale and low biomass metagenomics.

100 fg↗
DOE OSTI2016

Identification of mycotoxins by UHPLC–QTOF MS in airborne fungi and fungi isolated from industrial paper and antique documents from the Archive of Bogotá

Mold deterioration of historical documents in archives and libraries is a frequent and complex phenomenon that may have important economic and cultural consequences. In addition, exposure to toxic fungal metabolites might produce health problems. In this work, samples of broths of fungal species isolated from the documentary material and from indoor environmental samples of the Archive of Bogotá have been analyzed to investigate the presence of mycotoxins. High resolution mass spectrometry made possible to search for a large number of mycotoxins, even without reference standards available at the laboratory. For this purpose, a screening strategy based on ultra-high pressure liquid chromatography coupled to quadrupole-time of flight mass spectrometry (UHPLC–QTOF MS) under MS{sup E} mode was applied. A customized home-made database containing elemental composition for around 600 mycotoxins was compiled. The presence of the (de)protonated molecule measured at its accurate mass was evaluated in the samples. When a peak was detected, collision induced dissociation fragments and characteristic isotopic ions were also evaluated and used for tentative identification, based on structure compatibility and comparison with literature data (if existing). Up to 44 mycotoxins were tentatively identified by UHPLC–QTOF MS. 34 of these tentative compounds were confirmed by subsequent analysis using a targeted LC–MS/MS method, supporting the strong potential of QTOF MS for identification/elucidation purposes. The presence of mycotoxins in these samples might help to reinforce safety measures for researchers and staff who work on reception, restoration and conservation of archival material, not only at the Archive of Bogotá but worldwide. - Highlights: • Mold deterioration of historical documents is a frequent and complex phenomenon. • Samples of broths of fungal species isolated from Archive of Bogotá analyzed. • UHPLC–QTOF MS (MS{sup E}) applied for mycotoxins screening, without reference standards. • Customized home-made database for around 600 mycotoxins compiled. • 44 mycotoxins tentatively identified, 34 of which confirmed by LC–MS/MS.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2025

Dynamics and lipid membrane coupling of the RAS-RAF complex revealed via multiscale simulations

To gain molecular and mechanistic insights into initiation of the RAS-RAF signaling cascade, we developed and used a combination of multiscale simulation and experimental approaches. The influence and impact of the membrane on RAS and RAF proteins is a factor we are just beginning to understand and appreciate in more detail. Molecular simulation is an ideal methodology to further study this complicated relationship between the membrane and associated proteins. Our previous work using Multiscale Machine-learned Modeling Infrastructure investigated different lipid compositions solely around the KRAS4b protein and the interplay between protein behavior and these membrane environments. Multiscale Machine-learned Modeling Infrastructure uses machine learning to couple adjacent simulation scales and has been efficiently scaled across some of the world’s largest high-performance computers. Recently, we have expanded this multiresolution framework to include the all-atom simulation scale and to incorporate the RAF RBDCRD domains. Here, we present the overall analysis results from this new simulation campaign comprising a mixture of RAS and RAF RBDCRD proteins. Approximately 35,000 coarse-grained and 10,000 all-atom molecular dynamics simulations were completed, sampled from a variety of protein/lipid composition configurations that were generated from a micron-scale continuum simulation containing hundreds of copies of the proteins. Our studies suggest that orientations of the RAS-RBDCRD complex on the membrane occupy distinct configurational states, and the spatial patterns of lipid arrangements around these different protein states are unique to each state. The extent and size of lipid “fingerprints” imposed on the membrane by the RAS-RBDCRD protein complex are significantly larger than observed for just the RAS protein on its own. These protein complexes strongly associate, but we do not observe statistically significant preferred protein-protein orientations. These observations indicate that spatial colocalization of RAS-RBDCRD proteins in the same vicinity may be assisted by specific membrane environments, acting to increase the probability of signaling complex formation.

Carpenter, Timothy S. [Lawrence Livermore National↗
DOE OSTI2021

Characterization of shale using Helium and Argon at high pressures

In order to estimate the shale gas in place and the eventual recovery during shale gas operations, one of the key requirements is to accurately characterize the shale’s petrophysical and transport properties such as porosity, permeability, diffusivity, and storage capacity. Despite the many efforts reported in the technical literature aiming to provide an improved understanding of the complex pore structures and the associated fluid flow in gas shales, complete characterization of organic-rich shale samples still poses a big challenge. Here, we have characterized mass transfer and sorption in shale at different length scales using Helium (He) and Argon (Ar) as probe gases. Thermogravimetric analysis (TGA) with a shale cube of ~1 cm 3 in size and gas expansion experiments with a full-diameter core (3.5” in diameter) were used to measure sorption kinetics/isotherms and mass transfer, respectively. Both samples are from the same depth/location in the Marcellus shale formation. The TGA steady-state technique was initially used to generate excess sorption isotherms for Ar, while dynamic TGA experiments were used to study its sorption kinetics. The TGA experiments demonstrate that Ar, which has a similar sorption potential as Methane, but is generally assumed to be inert, adsorbs onto the surfaces of the mesoporous and microporous regions of the shale samples according to a Langmuir-type behavior. Helium expansion experiments, on the full-diameter core, were used to measure the overall porosity, on the basis that He is a non-sorbing and inert gas as compared to Ar. The He expansion experiments, furthermore, allow us to delineate the mass transfer of gas across the inherent hierarchy of pore sizes, including macropores (macro- and microcracks), mesopores and micropores. Similar expansion experiments were also performed with Ar to study the combined impact of mass transfer and sorption. A triple-porosity model (TPM) was utilized to interpret the He expansion experiments with the shale core and to extract (estimate) relevant transport parameters. We report and compare here the diffusivities and permeabilities of the whole core for both He and Ar, as calculated from the modeling and fitting of the experimental data. On the premise that the shale cube is representative of the matrix region of the core, the Ar sorption kinetics from the cube experiments were subsequently combined with the transport parameters extracted from the He experiments to predict the behavior of the Ar expansion test with the full-diameter core. An excellent agreement is observed between the model predictions and the experimental data. The experimental observations and their interpretation indicate that one must be cautious when using Ar to estimate the true porosity and permeability of shales. In addition, we demonstrate that He and Ar probe gases, when used in tandem, can be employed effectively as a tool to characterize shales in terms of mass transfer and sorption dynamics across scales.

04 OIL SHALES AND TAR SANDS↗
DOE OSTI2024

Phase retrieval for refraction-enhanced x-ray radiography using a deep neural network

X-ray refraction-enhanced radiography (RER) or phase contrast imaging is widely used to study internal discontinuities within materials. The resulting radiograph captures both the decrease in intensity caused by material absorption along the x-ray path, as well as the phase shift, which is highly sensitive to gradients in density. A significant challenge lies in effectively analyzing the radiographs to decouple the intensity and phase information and accurately ascertain the density profile. Conventional algorithms often yield ambiguous and unrealistic results due to difficulties in including physical constraints and other relevant information. We have developed an algorithm that uses a deep neural network to address these issues and applied it to extract the detailed density profile from an experimental RER. To generalize the applicability of our algorithm, we have developed a technique that quantitatively evaluates the complexity of the phase retrieval process based on the characteristics of the sample and the configuration of the experiment. Accordingly, this evaluation aids in the selection of the neural network architecture for each specific case. Beyond RER, the model has potential applications for other diagnostics where phase retrieval analysis is required.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2025

Sparse optimization of two-dimensional terahertz spectroscopy

Two-dimensional terahertz spectroscopy (2DTS) is a low-frequency analog of two-dimensional optical spectroscopy that is rapidly maturing as a probe of a wide variety of condensed matter systems. However, a persistent problem with 2DTS is the long experimental acquisition times, which prevent its broader adoption. A potential solution, requiring no increase in experimental complexity, is signal reconstruction via compressive sensing. In this work, we apply the sparse exponential mode analysis (SEMA) technique to 2DTS of a cuprate superconductor. We benchmark the performance of the algorithm in reconstructing terahertz nonlinearities and find that SEMA reproduces the asymmetric photon echo line shapes at sampling rates as low as 10%, reaching the reconstruction noise floor at sampling rates beyond 20%–30%. The success of SEMA in reproducing such subtle, asymmetric line shapes confirms compressive sensing as a general method to accelerate 2DTS and multidimensional spectroscopies more broadly.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
DOE OSTI2016

Characterization of microbial associations with methanotrophic archaea and sulfate-reducing bacteria through statistical comparison of nested Magneto-FISH enrichments

Methane seep systems along continental margins host diverse and dynamic microbial assemblages, sustained in large part through the microbially mediated process of sulfate-coupled Anaerobic Oxidation of Methane (AOM). This methanotrophic metabolism has been linked to consortia of anaerobic methane-oxidizing archaea (ANME) and sulfate-reducing bacteria (SRB). These two groups are the focus of numerous studies; however, less is known about the wide diversity of other seep associated microorganisms. We selected a hierarchical set of FISH probes targeting a range of Deltaproteobacteria diversity. Using the Magneto-FISH enrichment technique, we then magnetically captured CARD-FISH hybridized cells and their physically associated microorganisms from a methane seep sediment incubation. DNA from nested Magneto-FISH experiments was analyzed using Illumina tag 16S rRNA gene sequencing (iTag). Enrichment success and potential bias with iTag was evaluated in the context of full-length 16S rRNA gene clone libraries, CARD-FISH, functional gene clone libraries, and iTag mock communities. We determined commonly used Earth Microbiome Project (EMP) iTAG primers introduced bias in some common methane seep microbial taxa that reduced the ability to directly compare OTU relative abundances within a sample, but comparison of relative abundances between samples (in nearly all cases) and whole community-based analyses were robust. The iTag dataset was subjected to statistical co-occurrence measures of the most abundant OTUs to determine which taxa in this dataset were most correlated across all samples. In addition, many non-canonical microbial partnerships were statistically significant in our co-occurrence network analysis, most of which were not recovered with conventional clone library sequencing, demonstrating the utility of combining Magneto-FISH and iTag sequencing methods for hypothesis generation of associations within complex microbial communities. Network analysis pointed to many co-occurrences containing putatively heterotrophic, candidate phyla such as OD1, Atribacteria , MBG-B, and Hyd24-12 and the potential for complex sulfur cycling involving Epsilon -, Delta -, and Gammaproteobacteria in methane seep ecosystems.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

High‐speed 4‐dimensional scanning transmission electron microscopy using compressive sensing techniques

Abstract Here we show that compressive sensing allows 4‐dimensional (4‐D) STEM data to be obtained and accurately reconstructed with both high‐speed and reduced electron fluence. The methodology needed to achieve these results compared to conventional 4‐D approaches requires only that a random subset of probe locations is acquired from the typical regular scanning grid, which immediately generates both higher speed and the lower fluence experimentally. We also consider downsampling of the detector, showing that oversampling is inherent within convergent beam electron diffraction (CBED) patterns and that detector downsampling does not reduce precision but allows faster experimental data acquisition. Analysis of an experimental atomic resolution yttrium silicide dataset shows that it is possible to recover over 25 dB peak signal‐to‐noise ratio in the recovered phase using 0.3% of the total data. Lay abstract : Four‐dimensional scanning transmission electron microscopy (4‐D STEM) is a powerful technique for characterizing complex nanoscale structures. In this method, a convergent beam electron diffraction pattern (CBED) is acquired at each probe location during the scan of the sample. This means that a 2‐dimensional signal is acquired at each 2‐D probe location, equating to a 4‐D dataset. Despite the recent development of fast direct electron detectors, some capable of 100kHz frame rates, the limiting factor for 4‐D STEM is acquisition times in the majority of cases, where cameras will typically operate on the order of 2kHz. This means that a raster scan containing 256^2 probe locations can take on the order of 30s, approximately 100‐1000 times longer than a conventional STEM imaging technique using monolithic radial detectors. As a result, 4‐D STEM acquisitions can be subject to adverse effects such as drift, beam damage, and sample contamination. Recent advances in computational imaging techniques for STEM have allowed for faster acquisition speeds by way of acquiring only a random subset of probe locations from the field of view. By doing this, the acquisition time is significantly reduced, in some cases by a factor of 10‐100 times. The acquired data is then processed to fill‐in or inpaint the missing data, taking advantage of the inherently low‐complex signals which can be linearly combined to recover the information. In this work, similar methods are demonstrated for the acquisition of 4‐D STEM data, where only a random subset of CBED patterns are acquired over the raster scan. We simulate the compressive sensing acquisition method for 4‐D STEM and present our findings for a variety of analysis techniques such as ptychography and differential phase contrast. Our results show that acquisition times can be significantly reduced on the order of 100‐300 times, therefore improving existing frame rates, as well as further reducing the electron fluence beyond just using a faster camera.

Robinson, Alex W.↗
DOE OSTI2016

Comparative Genomics and Functional Analysis of Carbohydrate Utilization Networks in Unicyanobacterial Consortia Derived from Hypersaline Lake Microbial Mats

Hot Lake is a meromictic, hypersaline lake located in Washington state, USA. It harbors a phototrophic microbial mat community stable in dramatic seasonal environmental changes. The complexity of natural community hinders to analyze metabolic interactions between its members. To manage this obstacle, unicyanobacterial consortia (UCC) were sampled from the community and sequenced. UCC is a microbial community in which one cyanobacterium serves as the sole primary producer of carbon sources to several heterotrophic bacteria. Recently available metagenomes for two UCC revealed a shared set of 19 microbial operational taxonomic units (OTU), whose individual genomes were reconstructed by co‐assembly and abundance profile binning. We used this genomic data and a comparative genomics approach to infer carbohydrate utilization pathways and their transcription regulation. We scanned all UCC proteomes against the KEGG Orthology, Pfam, GO and SEED databases to reveal genes potentially involved in sugar utilization. Then we analyzed the genomic and functional contexts of gene loci encoding the obtained proteins and reconstructed the respective metabolic pathways and transcriptional regulons. As result, we observed catabolic pathways for 32 various carbohydrates and their derivatives. Distribution of the inferred catabolic pathways has highly mosaic structure across the UCC genomes. The largest number of pathways was observed in two representatives of the Halomonas genus (14–15 pathways) and one Rhodobacteriaceae sp. (15 pathways). In other UCC genomes, we found up to 10 carbohydrate utilization pathways per genome. However in 7 genomes we didn't observe any pathway. The most widely distributed pathways in UCC were the alpha‐glucosides and the DeLey‐Doudoroff galactose utilization pathways. Both were found in 7 genomes. Majority of pathways are distributed among 1–3 genomes. The reconstructed catabolic pathways were partially validated by phenotypic analyses of UCC community members that were isolated in a pure culture. In the Rhodobacteriaceae sp., we found a novel catabolic pathway that was proposed to be involved in mannoheptulose utilization. To our knowledge, the proposed mannoheptulose catabolic pathway is the first case of a pathway for heptose utilization and will require further experimental validation. The identified pathways are potentially regulated by local transcription factors (TFs) that are often co‐localized with the respective sugar catabolic gene loci. For 63 out of the 80 identified TFs we identified their cognate DNA binding motifs and reconstructed regulons using the bioinformatics approach. Support or Funding Information This research was supported by the Genomic Science Program (GSP), Office of Biological and Environmental Research (OBER), and U.S. Department of Energy (DOE) and is a contribution of the Pacific Northwest National Laboratory (PNNL) Foundational Scientific Focus Area.

Leyn, Semen A.↗
DOE OSTI2019

Kinetics of the Carbothermic Reduction of Manganese Oxide from Slag

Experiments were performed using a range of test conditions to elucidate the rate controlling step during the reaction of liquid iron-carbon droplets and slags containing manganese oxide. Four conditions were tested in the system: initial MnO content in the slag (5, 10, and 15 wt pct), initial carbon content of the metal (1, 2.5, 4.3 wt pct), initial droplet mass (0.5, 1.0, and 1.5 g), and reaction temperature (1823 K [1550 °C], 1873 K [1600 °C], and 1923 K [1650 °C]). Data were collected using the Constant Volume Pressure Increase (CVPI) technique which tracked the continuous pressure increase in the sealed furnace over time. Samples were quenched at the end of each experiment and chemistry was checked using LECO Carbon Analysis and ICP (Inductively Coupled Plasma) for manganese. The rate of reaction can be broken into a faster initial period related to internal CO formation, and a slower second reaction controlled by a complex mechanism involving transport of oxygen from slag to metal via CO{sub 2} and decomposition of the CO{sub 2} at the gas–metal interface.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Imaging and spatially resolved mass spectrometry applications in nephrology

The application of spatially resolved mass spectrometry (MS) and MS imaging approaches for studying biomolecular processes in the kidney is rapidly growing. These powerful methods, which enable label-free and multiplexed detection of many molecular classes across omics domains (including metabolites, drugs, proteins and protein post-translational modifications), are beginning to reveal new molecular insights related to kidney health and disease. Further, the complexity of the kidney often necessitates multiple scales of analysis for interrogating biofluids, whole organs, functional tissue units, single cells and subcellular compartments. Various MS methods can generate omics data across these spatial domains and facilitate both basic science and pathological assessment of the kidney. Optimal processes related to sample preparation and handling for different MS applications are rapidly evolving. Emerging technology and methods, improvement of spatial resolution, broader molecular characterization, multimodal and multiomics approaches and the use of machine learning and artificial intelligence approaches promise to make these applications even more valuable in the field of nephology. Overall, spatially resolved MS and MS imaging methods have the potential to fill much of the omics gap in systems biology analysis of the kidney and provide functional outputs that cannot be obtained using genomics and transcriptomic methods.

60 APPLIED LIFE SCIENCES↗