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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 217 records · Page 12
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Mucin 4 is a cellular biomarker of necrotizing bronchiolitis in influenza A virus infection

Influenza A virus (IAV) in the human and swine host infects epithelial cells lining the respiratory tract causing a necrotizing bronchitis and bronchiolitis. These epithelial surfaces are protected by large glycoproteins called mucins. Mucin 4 (MUC4) is a transmembrane mucin that consists of an alpha subunit responsible for surface protection and intracellular beta subunit involved in signal transduction which repress apoptosis and stimulate epithelial proliferation. This study was designed to determine the expression and potential role of MUC4 during IAV infection. We used immunohistochemistry in combination with machine learning image analysis to quantify differential protein expression of MUC4 subunits in IAV-infected and uninfected lung in a porcine model. MUC4 protein basal expression in control animals varied significantly by litter. MUC4 protein expression was significantly increased in bronchioles with necrotizing bronchiolitis compared to histologically normal bronchioles, likely representing a regenerative response to restore mucosal integrity of conducting airways. Understanding the impact of differential MUC4 expression among healthy individuals and during IAV infection will facilitate control strategies by elucidating mechanisms associated with susceptibility to IAV that can be therapeutically or genetically regulated and may be extended to other respiratory diseases.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Design, execution, and interpretation of plant RNA-seq analyses

Genomics has transformed our understanding of the genetic architecture of traits and the genetic variation present in plants. Here, we present a review of how RNA-seq can be performed to tackle research challenges addressed by plant sciences. We discuss the importance of experimental design in RNA-seq, including considerations for sampling and replication, to avoid pitfalls and wasted resources. Approaches for processing RNA-seq data include quality control and counting features, and we describe common approaches and variations. Though differential gene expression analysis is the most common analysis of RNA-seq data, we review multiple methods for assessing gene expression, including detecting allele-specific gene expression and building co-expression networks. With the production of more RNA-seq data, strategies for integrating these data into genetic mapping pipelines is of increased interest. Finally, special considerations for RNA-seq analysis and interpretation in plants are needed, due to the high genome complexity common across plants. By incorporating informed decisions throughout an RNA-seq experiment, we can increase the knowledge gained.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A high-resolution single-molecule sequencing-based Arabidopsis transcriptome using novel methods of Iso-seq analysis

Accurate and comprehensive annotation of transcript sequences is essential for transcript quantification and differential gene and transcript expression analysis. Single-molecule long-read sequencing technologies provide improved integrity of transcript structures including alternative splicing, and transcription start and polyadenylation sites. However, accuracy is significantly affected by sequencing errors, mRNA degradation, or incomplete cDNA synthesis. We present a new and comprehensive Arabidopsis thaliana Reference Transcript Dataset 3 (AtRTD3). AtRTD3 contains over 169,000 transcripts—twice that of the best current Arabidopsis transcriptome and including over 1500 novel genes. Seventy-eight percent of transcripts are from Iso-seq with accurately defined splice junctions and transcription start and end sites. We develop novel methods to determine splice junctions and transcription start and end sites accurately. Mismatch profiles around splice junctions provide a powerful feature to distinguish correct splice junctions and remove false splice junctions. Stratified approaches identify high-confidence transcription start and end sites and remove fragmentary transcripts due to degradation. AtRTD3 is a major improvement over existing transcriptomes as demonstrated by analysis of an Arabidopsis cold response RNA-seq time-series. AtRTD3 provides higher resolution of transcript expression profiling and identifies cold-induced differential transcription start and polyadenylation site usage. AtRTD3 is the most comprehensive Arabidopsis transcriptome currently. It improves the precision of differential gene and transcript expression, differential alternative splicing, and transcription start/end site usage analysis from RNA-seq data. The novel methods for identifying accurate splice junctions and transcription start/end sites are widely applicable and will improve single-molecule sequencing analysis from any species.

transcription start and end sites↗
DOE OSTI2026

Identifying Differential Equations in Fourier Domain (FourierIdent)

We investigate identifying differential equations in the frequency domain. Fourier analysis is an important tool in theoretical analysis and numerical solvers of differential equations, yet there is limited work in exploring this connection in the identification of differential equations. This paper aims to identify the underlying differential equation in the frequency domain, from a given single realization of the differential equation perturbed by noise. Such setting imposes difficulties which are different from other identification methods where computation is carried out in the physical domain. We propose several ways to mitigate the challenges arising from noise in data and large differences in the magnitudes of frequency responses. The main takeaways are that identifying differential equations solely in the frequency domain is challenging, the method we propose is based on a form of domain partitions in the frequency domain, and this method shows benefits for complex data even with high level of noise. We introduce a Fourier feature denoising, and define the meaningful data region and the core regions of features to reduce the effect of noise in the frequency domain and to enhance the accuracy in coefficient identification. The proposed method is tested on various differential equations with linear, nonlinear, and high-order derivative feature terms, and shows advantages on complex data with many frequency modes, even under high level of noise.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2021

The oncogenic role of meiosis-specific Aurora kinase C in mitotic cells

Highlights: • AURKC is expressed in meiotic cells and some cancers. • AURKC expression increases cell migration and transformation of human mitotic cells. • Deletion of AURKC in U2OS cells decreases cell migration and soft agar growth. • Transcriptome analysis reveals that AURKC alters the extracellular matrix. Aberrant expression of meiosis-specific genes in cancer has recently emerged as a driver of some cancer formation. Aurora kinase C (AURKC) is a member of the Aurora kinase family of proteins known to regulate chromosome segregation during cell divisions. AURKC is normally expressed in meiotic cells; however, elevated levels of AURKC mRNA and protein are frequently measured in cancer cells. To understand the function of AURKC in cancer cells, expression was induced in noncancerous, human retina pigmented epithelial cells. While AURKC expression did not alter cell proliferation over 72 h, it did increase cell migration and anchorage independent growth in soft agar suggesting an oncogenic role in mitotically dividing cells. To evaluate AURKC as a potential therapeutic target, a frameshift mutation in the gene was introduced in U2OS osteosarcoma cells using CRISPR-Cas9 technology resulting in a premature stop codon. Cancer cells lacking AURKC displayed no change in cell proliferation over 72 h but did migrate less and formed fewer colonies in soft agar. Whole transcriptome sequencing analysis uncovered over 400 differentially expressed genes in U2OS cells with and without AURKC. GO analysis revealed alterations in proteinaceous extracellular matrix genes including COL1A1. These data indicate that therapeutics targeting AURKC could decrease cancer cell metastasis and disease progression. Because AURKC is transcriptionally silenced in normal mitotic cells, its disruption could specifically target cancer cells limiting the toxic side effects associated with current therapeutics.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Semiclassical theory and the Koopman-van Hove equation *

Abstract The phase space Koopman-van Hove (KvH) equation can be derived from the asymptotic semiclassical analysis of partial differential equations. Semiclassical theory yields the Hamilton–Jacobi equation for the complex phase factor and the transport equation for the amplitude. These two equations can be combined to form a nonlinear semiclassical version of the KvH equation in configuration space. There is a natural injection of configuration space solutions into phase space and a natural projection of phase space solutions onto configuration space. Hence, every solution of the configuration space KvH equation satisfies both the semiclassical phase space KvH equation and the Hamilton–Jacobi constraint. For configuration space solutions, this constraint resolves the paradox that there are two different conserved densities in phase space. For integrable systems, the KvH spectrum is the Cartesian product of a classical and a semiclassical spectrum. If the classical spectrum is eliminated, then, with the correct choice of Jeffreys–Wentzel–Kramers–Brillouin (JWKB) matching conditions, the semiclassical spectrum satisfies the Einstein–Brillouin–Keller quantization conditions which include the correction due to the Maslov index. However, semiclassical analysis uses different choices for boundary conditions, continuity requirements, and the domain of definition. For example, use of the complex JWKB method allows for the treatment of tunneling through the complexification of phase space. Finally, although KvH wavefunctions include the possibility of interference effects, interference is not observable when all observables are approximated as local operators on phase space. Observing interference effects requires consideration of nonlocal operations, e.g. through higher orders in the asymptotic theory.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2022

Conversion of (NH 4 ) 2 [ReF 6 ] into ReO 2 mixed phases: A thermal analysis study

We report the thermal behavior of (NH 4 ) 2 [ReF 6 ] was evaluated in an alumina crucible using simultaneous thermal gravimetric analysis (TGA) and differential scanning calorimetry (DSC) in an argon atmosphere. The TGA of (NH 4 ) 2 [ReF 6 ] is characterized by a single step decomposition while the DSC exhibits two exothermic peaks. Powder X-ray diffraction (PXRD) analyses of the decomposition products show the presence of a mixed ReO 2 phase. The formation of ReO2 is driven by the reaction of (NH 4 ) 2 [ReF 6 ] with Al 2 O 3 at the grain boundary of the alumina crucible. XRD peak broadenings due to the combined effect of crystallite size and lattice strain were evaluated using both Scherrer and Williamson-Hall methods.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Kinetics of TATB and LX-17 Decomposition by Thermal Analysis

The kinetics of TATB decomposition have been investigated by thermal analysis (thermogravimetric analysis, TGA, and differential scanning calorimetry, DSC) at both LLNL and the University of Alabama Birmingham. This report summarizes progress in understanding from those results within the context of identifying the global reaction mechanism, i.e., sequential, autocatalytic, competitive, or some mixture thereof. A particularly important issue is how pressure affects both the reaction rate and enthalpy. The effect of pressure helps identify dominant mechanisms and construct and constrain a global mechanism that will work over a wide range of conditions. This memorandum is simply a snapshot of current progress and not a definitive interpretation. I have written it to organize work of others and my interpretations in a systematic manner with the intention of stimulating further advances in understanding. SDT data comes from Jen Montgomery at LLNL, and high-pressure DSC comes from Victoria Stanford and Sergey Vyazovkin at University of Alabama at Birmingham. Major observations and conclusions, some new and some not, are (1) outgassing below 150 °C prior to decomposition releases adsorbed water vapor, (2) outgassing between 150 and 250 °C may come primarily from intercalated water (3) initial thermal decomposition above 250 °C or so involves dehydration of TATB to create furazans, (4) quickly heating to higher temperatures in open pans with flowing gas leads primarily to TATB evaporation between 270 and 390 °C, (5) using a pinhole crucible at atmospheric pressure largely eliminates TATB sublimation, (6) at typical thermal analysis heat rates, the main stage of decomposition is described by a single mass loss process, and decomposition of residual material is spread over a wide range of thermal severity, (7) at typical thermal analysis heat rates and constant temperatures above 300 °C, heat release occurs in two overlapping peaks, with the first one a little faster than mass loss and the second on a little slower than mass loss, (8) total heat release increases significantly with heating rate and substantially with increased pressure, and (9) isothermal experiments at 340 °C indicate that the first exotherm increases by more with LX-17 than TATB, which suggests a possible chemical role of Kel-F decomposition.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Kinetics of Pyrolysis and Thermal Evolution of Negev Desert Lithologies

The Negev desert in Israel is home to large quantities of organic-rich, shallow marine sedimentary lithologies that could potentially accommodate the disposal of spent nuclear fuel. Previous thermal analyses of Negev carbonates have focused on industrially relevant considerations such as natural gas and oil extraction or pyrolysis for recovering hydrocarbon fuels. Here, this study addresses thermal evolution of the Negev organic-rich carbonate, siliceous, and phosphorite rocks and associated chemical, mineralogical, and microstructural changes that may occur under prolonged thermal loading in the vicinity of spent nuclear fuel disposal systems. Our employed methods include high-temperature X-ray diffraction, high-temperature infrared spectroscopy, and thermal analysis integrating thermogravimetry, differential scanning calorimetry, and mass spectrometry. Further, we apply iterative iso-conversional model-free methods to derive kinetic parameters for thermal decomposition of the Negev organic-rich carbonate rocks from 200 to 550 °C. Our results have provided mechanistic insights into the thermal evolution encompassing water desorption, decomposition of organic matter, and decarbonation of carbonate phases.

58 GEOSCIENCES↗
DOE OSTI2020

Impact of Porcine Arterivirus, Influenza B, and Their Coinfection on Antiviral Response in the Porcine Lung

Interferon (IFN) cytokines induce an autonomous antiviral state in cells of the infected site to restrict virus spreading and critically regulate overall antiviral response. The antiviral state leads to host protection through expression of hundreds of IFN-stimulated genes that restrict viral infection through multiple mechanisms, for example, directly in viral genome degradation and indirectly through cellular metabolic inhibition. Young pigs were split into four treatment groups: control, porcine reproductive and respiratory syndrome virus (PRRSV, also known as porcine arterivirus) infected, influenza B virus (IBV) infected, and IBV/PRRSV coinfection. Lung tissue was collected at 3, 5, and 7 days post infection (dpi) for control, PRRSV and IBV/PRRSV coinfection, and at 3 and 5 dpi for IBV. Transcriptomic analysis, using usegalaxy.org tools, was performed against the S.scrofa 11.1 reference genome. Differentially expressed gene (DEG) analysis was carried out using DeSeq2 based on the model treatment + dpi + treatment:dpi + E. Downstream analysis examined the interaction of DEG at each dpi for over-enriched gene ontology (G.O.) terms and pathways. Comparisons of the infected groups vs. the controls yielded a total of (n = 1412) DEGs for the PRRSV group and (n = 1578) for the IBV/PRRSV group across all timepoints. The IBV group had (n = 64) total DEGs across 3 and 5 dpi. Expression data were considered statistically significant based on false discovery rate (FDR) ⫹ 0.1. Venn diagram comparisons of the DEGs across dpi showed that groups shared only 16 DEGs at 3 dpi, no DEGs were shared at 5 dpi, and for 7 dpi, only the PRRSV and IBV/PRRSV groups were compared and shared a total of 43 DEGs. Across the comparisons, differential expression was observed in antiviral genes such as IRF1, MX1, and OAS2. The IBV and IBV/PRRSV groups showed higher expression of antiviral genes at earlier dpi than the PRRSV group. Additionally, downregulated genes from the comparisons clustered around Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways effecting lung development and cellular integrity. Early expression of host IFN and antiviral genes may lead to viral RNA degradation, and assembly and transcription inhibition in the IBV infections. In comparison, expression of antiviral genes in the PRRSV group decreased across time. The decrease may explain why PRRSV infections persist, while IBV clears. Moreover, all infected groups showed prolonged upregulation in neutrophil degranulation pathway activity, possibly exacerbating symptomatic lung lesion pathology seen in these respiratory infections.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Thermal Dehydration of Aluminum (Oxy)hydroxides on Fuel Cladding Material - 20200

The aluminum cladding of research-reactor fuel undergoes general corrosion with resulting formation of adherent aluminum (oxy)hydroxide films during in-reactor and post-discharge exposure to water under various conditions and temperatures. These (oxy)hydroxides contain chemically-bound water that poses challenges for extended dry storage due to the risk of thermal or radiolytic decomposition releasing free water and/or hydrogen and oxygen gases. This study comprised laboratory experiments of thermal drying behavior of aluminum (oxy)hydroxides to identify approaches for reducing bound water on fuel cladding prior to sealed dry storage. Effective drying strategies for adherent (oxy)hydroxides on fuel cladding will improve the safety of dry storage by mitigating potential avenues for additional corrosion and/or generation of flammable gases inside the storage canister. This work is part of a broader investigation to address knowledge gaps and technical data needs for dry storage of aluminum-clad spent nuclear fuel (ASNF), which included investigation of (oxy)hydroxide formation on aluminum alloy substrates immersed in water, characterization of service-grown films from ASNF, and radiolytic yield of hydrogen from (oxy)hydroxide powders and films. The current work comprises experimental thermal dehydration of aluminum trihydroxides (bayerite and gibbsite) characteristic of low-temperature (<80 deg. C) corrosion in water and aluminum oxyhydroxide (boehmite) characteristic of high temperature (>80 deg. C) corrosion in water. First, commercially produced (oxy)hydroxide powders (boehmite and gibbsite) were tested via thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC). The effort aimed to identify or confirm key temperature ranges/thresholds for the thermal decomposition reactions, as well as impacts of ramp rate and hold times, for drying of isolated, high-surface-area (oxy)hydroxides. The information gleaned from powder tests was used to guide subsequent drying tests on adherent (oxy)hydroxide films grown on aluminum alloy substrates. TGA was used to analyze small samples of the aluminum coupons with adherent (oxy)hydroxide films. Specimens were characterized both pre- and post-drying using X-ray diffraction (XRD) to determine the film composition and scanning electron microscopy (SEM) to determine its morphology. Drying of adherent (oxy)hydroxide films was anticipated to pose additional complications relative to drying of (oxy)hydroxide powders. Anticipated challenges include achieving sufficient drying of the (oxy)hydroxide at low-enough temperature to avoid melting or other undesirable phase changes in the aluminum substrate and overcoming transport limitations of water through the thickness of a dense film or through a tortuous pore structure to reach the outer surface of the film. Inn addition, dehydration of (oxy)hydroxides significantly changes the film density, which may lead to substantial alterations in the morphology, including potential cracking and spalling of the film. TGA/DSC tests of gibbsite powders resulted in successful conversion to boehmite or alumina, depending on the maximum temperature reached. At low ramp rates (≤5 deg. C/min), the conversion to boehmite occurred around 300 deg. C (210-340 deg. C). XRD confirmed that boehmite was the only phase detected after tests reaching 450 deg. C. The transition to alumina occurred around 510 deg. C (470-550 deg. C), with XRD detecting only alumina after tests reaching at least 600 deg. C. Boehmite powders dehydrated to alumina at about 400 deg. C (330-460 deg. C) for coarse (77-μm particle diameter) powder and about 490 deg. C (420-520 deg. C) for fine (0.7-μm particle diameter) powder. For all powders tested, the maximum percent mass loss after drying to high temperature slightly exceeded the theoretical mass loss for complete dehydration of the stoichiometric (oxy)hydroxide to alumina, which is likely attributable to physisorbed water in the powder. Drying of a thick (∼8.6 μm), predominantly bayerite adherent film displayed a dramatic change in film morphology, with the initially continuous trihydroxide film cracking into sections on the order of 50 μm square and partially delaminating. The outermost layer of the film completely faked of in some regions. The layer exposed under the spalled oxide also displayed prominent cracking, with spacing on the order of 10 μm, but this surface layer appeared to remain completely adhered to the aluminum substrate. TGA showed mass losses per unit surface area up to ∼1.0 mg/cm{sup 2}. XRD characterization of the remaining oxide was inconclusive, with no crystalline phases detected. (authors)

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
DOE OSTI2025

Mapping Hsp104 interactions using cross‐linking mass spectrometry

Molecular machines from the AAA+ (ATPases Associated with diverse cellular Activity) superfamily of protein disaggregases play important roles in protein folding, disaggregation and DNA processing. Recent cryo-EM structures of AAA+ molecular machines have uncovered nuanced changes in their conformation that underlie their specialized functions. Structural knowledge of these molecular machines in complex with substrates begins to explain their mechanism of activity. Here, we explore how cross-linking mass spectrometry (XL-MS) can be used to interpret changes in conformation induced by ATP in Hsp104 and how a substrate may interact with Hsp104. We applied a panel of cross-linking reagents to produce cross-linking maps of Hsp104 and interpret our data on previously determined X-ray and cryo-EM structures of Hsp104 from a thermophilic yeast, Calcarisporiella thermophila. We developed an analysis pipeline to differentiate between intra-subunit and inter-subunit contacts within the hexameric homo-oligomer. We identify cross-links that break the asymmetry that is present in Hsp104 in an ATP-hydrolysis competent conformation but is absent in an ATP-hydrolysis-defective mutant. Finally, we identify contacts between Hsp104 and a selected protein (proprotein convertase subtilisin/kexin type 9 PCSK9) to reveal contacts on the central channel of Hsp104 across the length of this protein indicating that we might have trapped interactions consistent with its translocation. Our simple and robust XL-MS-based experiments and methods help interpret how these molecular machines change conformation and bind to other proteins even in the context of homo-oligomeric assemblies enabling coupling state-of-the-art modeling approaches with XL-MS.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

Understanding the Role of Hydroxyl Functionalization in Linear Poly(Ethylenimine) for Oxidation‐Resistant Direct Air Capture of CO 2

Aminopolymer-based adsorbents are a prominent class of materials being used for direct air capture of CO 2 at the industrial scale. However, improving their working lifetime, specifically by increasing their resilience to oxidative degradation, remains an ongoing challenge. Toward this end, functionalization of aminopolymers with non-amine functionalities such as hydroxyls has emerged in recent years as a promising strategy toward improving adsorbent lifetime. Although there is a growing body of work demonstrating the effectiveness of this approach and investigating the origin of this improved stability, studies to date have primarily focused on branched aminopolymer systems such as branched poly(ethylenimine). In this work, hydroxyl-functionalized linear poly(ethylenimine) is used to continue to probe the underlying protective mechanism of this strategy. A combination of thermogravimetric analysis, NMR relaxometry, differential scanning calorimetry, and computational simulations is used to better understand the relationship between the extent of chemical functionalization, physical properties, and adsorbent performance.

amine-based adsorbent↗
DOE OSTI2025

UnigeneFinder: An Automated Pipeline for Gene Calling From Transcriptome Assemblies Without a Reference Genome

ABSTRACT For most species, transcriptome data are much more readily available than genome data. Without a reference genome, gene calling is cumbersome and inaccurate because of the high degree of redundancy in de novo transcriptome assemblies. To simplify and increase the accuracy of de novo transcriptome assembly in the absence of a reference genome, we developed UnigeneFinder. Combining several clustering methods, UnigeneFinder substantially reduces the redundancy typical of raw transcriptome assemblies. This pipeline offers an effective solution to the problem of inflated transcript numbers, achieving a closer representation of the actual underlying genome. UnigeneFinder performs comparably or better, compared with existing tools, on plant species with varying genome complexities. UnigeneFinder is the only available transcriptome redundancy solution that fully automates the generation of primary transcript, coding region, and protein sequences, analogous to those available for high‐quality reference genomes. These features, coupled with the pipeline’s cross‐platform implementation, focus on automation, and an accessible, user‐friendly interface, make UnigeneFinder a useful tool for many downstream sequence‐based analyses in nonmodel organisms lacking a reference genome, including differential gene expression analysis, accurate ortholog identification, functional enrichments, and evolutionary analyses. UnigeneFinder also runs efficiently both on high‐performance computing (HPC) systems and personal computers, further reducing barriers to use.

Xue, Bo [Plant Resilience Institute Michigan State↗
DOE OSTI2022

Utilization of the Critic Subnetwork of a Generative Adversarial Network as Detector of Morphological Material Change in Image Data

The resolution of computed tomography (CT) has become high enough to monitor morphological changes due to aging in materials in long-term applications. For this work, we explored the utility of the critic of a generative adversarial network (GAN) to automatically detect such changes. The GAN was trained with images of pristine Pharmatose, which is used as a surrogate energetic material. It is important to note that images of the material with altered morphology were only used during the test phase. The GAN-generated images reproduced the microstructure of Pharmatose well, although some unrealistic particle fusion was seen. Calculated morphological metrics (volume fraction, interfacial line length, and local thickness) for the synthetic images also showed good agreement with the training data, albeit with signs of mode collapse in the interfacial line length. While the critic exposed changes in particle size, it showed limited ability to distinguish images by particle shape. The detection of shape differences was also a more challenging task for the selected morphological metrics that related to energetic material performance. We further tested the critic with images of aged Pharmatose. Subtle changes due to aging are difficult for the human analyst to detect; but both critic and morphological metrics analysis showed image differentiation.

36 MATERIALS SCIENCE↗
DOE OSTI2024

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

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

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

From phase decomposition to evaporation: A multi-modal evaluation of thermally degraded model lightweight high-entropy alloy

Lightweight high-entropy alloys (LHEAs) have the potential to replace conventional lightweight materials due to their superior mechanical properties and thermal stability. However, the thermal degradation pattern of LHEAs from phase decomposition to evaporation is not clear. We develop a new Al-based dual phase (FCC + HCP) LHEA—AlTi 0.45 CuZn, and further investigate its thermal degradation behavior for potential high-temperature structural applications. Using multimodal advanced characterization techniques such as differential scanning calorimetry/thermogravimetric analysis, scanning/transmission electron microscopy, and synchrotron X-ray diffraction/pair distribution function (XRD/PDF), a sequence of thermal degradation events beyond the thermal phase stability limit—between 250 and 360 °C—is observed. These include phase decomposition at ~360 °C, Zn evaporation at ~750 °C, and LHEA melting at 880 °C which results in ~25% cumulative weight loss. The formation of Al-Ti phase off the AlTi 0.45 CuZn matrix is due to the largest negative mixing enthalpy for Al-Ti than other binary pairs. Similarly, Zn evaporation from AlTi 0.45 CuZn LHEA is due to its faster evaporation rate than other constituent elements. The high-resolution synchrotron XRD and PDF results support the aforementioned observations; in addition, they reveal local atomic arrangements, local strain, and sluggish grain growth in the LHEA. Among other LHEAs of close density range (5.55 ≤ ρ ≤ 5.85 g/cc), the investigated LHEA exhibits outstanding nano-indentation hardness values due to the coupled grain size effect and HCP phase strengthening of the FCC matrix. As the search for LHEAs for lightweight applications grows, this study shows the potential use of AlTi 0.45 CuZn LHEA for structural applications even at elevated temperatures.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
DOE OSTI2025

Signature of 0 + excited state and shape coexistence in 94 Kr through 93 Kr(d,p) 94 Kr reaction

A measurement of the excitation spectrum of 94 Kr via one-neutron transfer to the ground state of 93 Kr using the 93 Kr(d,p) 94 Kr reaction at 8A MeV, observing the outgoing protons, performed with the IRIS facility at TRIUMF is reported. Two states in 94 Kr, at 1.50±0.14 MeV and 2.20±0.14 MeV, were observed. An adiabatic-wave approximation analysis of the differential cross sections leads us to identify the lower energy state as being populated with neutron transfer to the 3 s1/2 orbital. This leads to the first observation of the lowest 0 + excited state in 94 Kr, hence signaling shape co-existence. Theoretical calculations performed within the in-medium similarity renormalization group framework are presented that also show the existence of a low-energy 0 + state, aligning qualitatively with the observation.

74 ATOMIC AND MOLECULAR PHYSICS↗