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At least 415 records · Page 23
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Physiological and metabolic responses of Zymomonas mobilis to lignocellulosic hydrolysate

Zymomonas mobilis is a promising biocatalyst for the sustainable conversion of lignocellulosic sugars into biofuels and bioproducts, yet its response to lignocellulosic hydrolysates remains poorly understood. Here, we investigate the physiological response of Z. mobilis to ammonia fiber expansion (AFEX)-pretreated switchgrass hydrolysate using a systems-level approach integrating LC–MS/MS-based lipidomics and shotgun proteomics. Growth on hydrolysate induced substantial shifts in fatty acid and membrane phospholipid composition, alongside broad proteomic remodeling. Notably, Z. mobilis exhibited a stress response characterized by the upregulation of heat shock proteins and efflux transporters and the downregulation of cell motility proteins. Unexpectedly, hydrolysate exposure also led to a robust upregulation of the Entner–Doudoroff pathway, the ethanol fermentation pathway, and other central carbon metabolism enzymes, indicating a substantial cellular investment potentially driven by additional nutrient availability in hydrolysate. These findings provide new insights into the metabolic adaptations of Z. mobilis to lignocellulosic hydrolysates, informing strategies to enhance its biofuel production capabilities.

Zymomonas mobilis↗
DOE OSTI2023

Structural comparison of allophycocyanin variants reveals the molecular basis for their spectral differences

Abstract Allophycocyanins are phycobiliproteins that absorb red light and transfer the energy to the reaction centers of oxygenic photosynthesis in cyanobacteria and red algae. Recently, it was shown that some allophycocyanins absorb far-red light and that one subset of these allophycocyanins, comprising subunits from the ApcD4 and ApcB3 subfamilies (FRL-AP), form helical nanotubes. The lowest energy absorbance maximum of the oligomeric ApcD4-ApcB3 complexes occurs at 709 nm, which is unlike allophycocyanin (AP; ApcA-ApcB) and allophycocyanin B (AP-B; ApcD-ApcB) trimers that absorb maximally at ~ 650 nm and ~ 670 nm, respectively. The molecular bases of the different spectra of AP variants are presently unclear. To address this, we structurally compared FRL-AP with AP and AP-B, performed spectroscopic analyses on FRL-AP, and leveraged computational approaches. We show that among AP variants, the α-subunit constrains pyrrole ring A of its phycocyanobilin chromophore to different extents, and the coplanarity of ring A with rings B and C sets a baseline for the absorbance maximum of the chromophore. Upon oligomerization, the α-chromophores of all AP variants exhibit a red shift of the absorbance maximum of ~ 25 to 30 nm and band narrowing. We exclude excitonic coupling in FRL-AP as the basis for this red shift and extend the results to discuss AP and AP-B. Instead, we attribute these spectral changes to a conformational alteration of pyrrole ring D, which becomes more coplanar with rings B and C upon oligomerization. This study expands the molecular understanding of light-harvesting attributes of phycobiliproteins and will aid in designing phycobiliproteins for biotechnological applications.

Gisriel, Christopher J.↗
DOE OSTI2021

CO and H 2 adsorption on Au-Ni bimetallic surfaces: a combined experimental and DFT theoretical study

Au-Ni bimetallic thin films were grown on refractory metal substrates. CO and H 2 adsorption on Au-Ni bimetallic surfaces have been studied by a combination of in situ polarization modulation infrared reflection absorption spectroscopy (PM-IRRAS), temperature-programmed desorption (TPD), and density functional theory (DFT) calculations. It is found CO desorption peak shifts from 413 K on pure Ni surfaces to 293 K on the isolated Ni atoms formed by alloying with Au atoms. The sharp decrease of CO desorption temperature on Au-Ni surfaces with increasing Au coverage is caused by the change of the favored CO adsorption sites from bridge/hollow sites on pure Ni surfaces to Ni top sites on Au-Ni bimetallic surfaces. In situ PM-IRRAS shows two CO adsorption bands on Au sites at 2119 cm −1 and 2103 cm −1 on Au-Ni surfaces at 80 K, which are due to CO bound on under-coordinated Au atoms and electron negatively charged Au sites modified with nearby Ni atoms, respectively. Even with the Au-Ni surface temperature at as low as 100 K, CO adsorption induced Ni surface segregation has been observed by in situ PM-IRRAS. Furthermore, DFT calculation results discover the adsorption energy of CO on Ni top sites continues to decrease with increasing Au coverage due to the geometric ensemble effect and the lowered d-band center after Ni alloying with Au. H 2 desorption temperature decreases from 363 K on pure Ni thin films to 302 K with increasing Au coverage to 0.6 ML. A new H 2 peak appears at around 170 K on the Au-Ni surfaces with Au coverages between 0.6 ML and 0.9 ML. This new H 2 TPD peak is assigned to H 2 desorption from the totally isolated Ni sites. With Au coverage above 1.5 ML, there is no any H 2 desorption detected. Finally, the combined surface science studies and DFT calculations provide new insights into the surface structure-activity correlation of Ni-base bimetallic surface alloys.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Wavelength modulation laser-induced fluorescence for plasma characterization

Laser-Induced Fluorescence (LIF) spectroscopy is an essential tool for probing ion and atom velocity distribution functions (VDFs) in complex plasmas. VDFs carry information about the kinetic properties of species that is critical for plasma characterization. Accurate interpretation of these functions is challenging due to factors such as multicomponent distributions, broadening effects, and background emissions. Our research investigates the use of Wavelength Modulation (WM) LIF to enhance the sensitivity of VDF measurements. Unlike standard Amplitude Modulation (AM) methods, WM–LIF measures the derivative of the LIF signal. This approach makes variations in VDF shape more pronounced. VDF measurements with WM–LIF were investigated with both numerical modeling and experimental measurements. The developed model enables the generation of both WM and AM signals, facilitating comparative analysis of fitting outcomes. Experiments were conducted in a weakly collisional argon plasma with magnetized electrons and non-magnetized ions. Measurements of the argon ion VDFs employed a narrow-band tunable diode laser, which scanned the 4p 4 D 7/2 –3d 4 F 9/2 transition centered at 664.553 nm in vacuum. A lock-in amplifier detected the second harmonic WM signal, which was generated by modulating the laser wavelength with an externally controlled piezo-driven mirror of the diode laser. Finally, our findings indicate that the WM–LIF signal is more sensitive to fitting parameters, allowing for better identification of VDF parameters such as the number of distribution components, their temperatures, and velocities. In addition, WM–LIF can serve as an independent method to verify AM measurements and is particularly beneficial in environments with substantial light noise or background emissions, such as those involving thermionic cathodes and reflective surfaces.

47 OTHER INSTRUMENTATION↗
DOE OSTI2025

Supporting Information - How Can Crop Production Adapt to growing groundwater restrictions in the West?

Abstract This data plan outlines the structure and content of datasets generated and utilized in the research presented in the manuscript abstract. Groundwater overdraft has led to serious water supply issues in the US West. Most western states manage groundwater use through a permitting system, but California has only recently begun to restrict groundwater use statewide with the 2014 passage of groundwater restrictions which target the elimination of groundwater overdraft practices by 2042. With groundwater extraction curtailed, crop production in the US West (a $95 billion industry annually) will be affected, and appropriate response strategies will be needed to ensure minimal disruption to food production and the regional economy. In this paper, we explore the adoption of alternative adaptive responses: (a) deficit irrigation; (b) switching to less water-intensive crops; (c) changing the extent of irrigated land (including fallowing); and (d) geographically shifting crop production. Employing an integrated modeling approach, we explicitly capture the interactions and feedbacks between local hydrology, changes in crop yields, crop and land use decision-making, changes in crop prices, and regional shifts in crop production. We find that the optimal adaptive response is spatially heterogeneous and comprises a portfolio of strategies. Southwestern states and California will be the most impacted by groundwater restrictions. The optimal responses in these states are to both adopt deficit irrigation strategies and reduce a portion of their irrigated croplands, resulting in a shift in crop production to northwestern states with a larger supply of water. The datasets detailed in this repository represent the output from these integrated models, specifically designed to support the analysis and visualization presented in the manuscript and supplemental information. These datasets, used in conjunction with the scripts available at our associated GitHub repository (https://github.com/pches/Femeena_etal_How_can_crop_production_adapt), enable the reproduction of figures and facilitate a comprehensive understanding of the optimal adaptive strategies in agriculture for mitigating water stress under varying groundwater extraction scenarios, as outlined in the abstract.

DNDCe↗
DOE OSTI2025

Suppression of Chorismate Mutase 1 in Hybrid Poplar to Investigate Potential Redundancy in the Supply of Lignin Precursors

Chorismate is an important branchpoint metabolite in the biosynthesis of lignin and a wide array of metabolites in plants. Chorismate mutase (CM), the enzyme responsible for transforming chorismate into prephenate, is a key regulator of metabolic flux towards the synthesis of aromatic amino acids and onwards to lignin. We examined three CM genes in hybrid poplar (Populus alba × grandidentata; P39, abbreviated as Pa×g) and used RNA interference (RNAi) to suppress the expression of Pa×gCM1, the most highly expressed isoform found in xylem tissue. Although this strategy was successful in disrupting Pa×gCM1 transcripts, there was also an unanticipated increase in lignin content, a shift towards guaiacyl lignin units, and more xylem vessels with smaller lumen areas, at least in the most severely affected transgenic line. This was accompanied by compensatory expression of the other two CM isoforms, Pa×gCM2 and Pa×gCM3, as well as widespread changes in gene expression and metabolism. This study investigates potential redundancy within the CM gene family in the developing xylem of poplar and highlights the pivotal role of chorismate in plant metabolism, development, and physiology.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Cosmological Simulations of Stellar Halos with Gaia Sausage–Enceladus Analogs: Two Sausages, One Bun?

Observations of the Milky Way’s stellar halo find that it is predominantly comprised of a radially biased population of stars, dubbed the Gaia Sausage–Enceladus, or GSE. These stars are thought to be debris from dwarf galaxy accretion early in the Milky Way’s history. Though typically considered to be from a single merger, it is possible that the GSE debris has multiple sources. To investigate this possibility, we use the IllustrisTNG50 simulation to identify stellar accretion histories in 98 Milky Way analogs—the largest sample for which such an identification has been performed—and find GSE-like debris in 32, with two-merger GSEs accounting for a third of these cases. Distinguishing single-merger GSEs from two-merger GSEs is difficult in common kinematic spaces, but differences are more evident through chemical abundances and star formation histories. This is because single-merger GSEs are typically accreted more recently than the galaxies in two-merger GSEs: the median infall times (with 16th and 84th percentiles) are $5.{9}_{-2.0}^{+3.3}$ and $10.{7}_{-3.7}^{+1.2}$ Gyr ago for single- and two-merger scenarios, respectively. The systematic shifts in abundances and ages that occur as a result suggest that efforts in modeling these aspects of the stellar halo prove ever-important in understanding its assembly.

galactic archaeology↗
DOE OSTI2025

Regime Characterization of Offshore Wind Resource Using Unsupervised Learning

Predictability of wind resource conditions is critical for offshore wind design and operations. While many studies of extreme wind conditions focus on specific events such as low-level jets or ramps, these rely on threshold definitions that limit generality. Here we present a data-driven framework that combines principal component analysis (PCA), self-organizing maps (SOM), and k-means clustering to classify wind resource conditions as typical and anomalous from climatological data. Anomalies are defined not by fixed thresholds but by flagging samples located far from SOM node centers inside the baseline SOM structure. This reframes extremes as rare ebents and hence, likely difficult to anticipate by numerical weather prediction models. We applied this approach to 23 years (2000–2022) of hourly profiles from the NOW-23 hindcast model at the Humboldt Wind Energy Area. Classification is conducted on a feature space consisting of 10 m wind speed and direction, bulk shear and veer across 30–270 m, and a low-level jet index. Dimensionality reduction is achieved through PC. A 2 × 3 OM lattice trained on the PCA vectors identified six baseline regimes spanning weak to strong flow states. High quantization-error profiles are identified and re-clustered into four anomalous regimes. The baseline regimes exhibited clear seasonal and diurnal cycles. Meanwhile, the anomalous regimes represented <10 % of all hours but showed distinct combinations of speed, shear, and veer, when compared to the baseline regimes. Anomalous regimes are typically short-lived (~few hours), yet their transitions can lead to hub-height wind changes of −18 to +9 m s -1 . For a representative 15 MW turbine, these shifts imply rapid swings in capacity factor from near-full output to negligible generation. Validation with lidar buoy data showed 51% agreement in SOM labels across ~6,000 overlapping hours, with most mismatches confined to adjacent speed classes. HRRR comparisons further revealed that anomalous regimes were disproportionately associated with forecast biases exceeding 5 m s -1 . Together, these results reframe extremes in offshore wind from absolute maxima or minima to weather states that are difficult to anticipate from models.

17 WIND ENERGY↗
DOE OSTI2025

Defect-engineered GaN high electron mobility transistors for enhanced radiation tolerance

This study explores the radiation resilience of GaN high-electron-mobility transistors (HEMTs) under various preconditioning treatments—pristine, electro-pulsed, electrically overstressed, and 60 Co gamma-irradiated—with a focus on enhancing survivability in high-radiation environments. Key findings emphasize the gate region’s central role in radiation sensitivity, with increased defect concentrations leading to reduced sensitivity—as determined from reduced single-event transient intensities during pulsed-laser studies—and impacting charge-transport dynamics. Notably, the most sensitive region shifted as a function of bias state, with the drain side of the gate being most sensitive under negative gate bias and the source side under unbiased conditions due to two-dimensional electron gas disruptions. These insights clarify the mechanisms influencing radiation sensitivity in microelectronics and highlight the potential of defect and strain engineering to enhance the radiation hardness of GaN HEMTs across various operational states, providing valuable guidance for applications in space, defense, and other radiation-rich environments.

36 MATERIALS SCIENCE↗
DOE OSTI2024

High-resolution infrared spectroscopy of jet cooled cyclobutyl in the α-CH stretch region: large-amplitude puckering dynamics in a 4-membered ring radical

We report gas-phase cyclobutyl radical (c-C 4 H 7 ) is generated at a rotational temperature of T rot = 26(1) K in a slit-jet discharge mixture of 70% Ne/30% He and 0.5–0.6% cyclobromobutane (c-C 4 H 7 Br). A fully rovibrationally resolved absorption spectrum of the α-CH stretch fundamental band between 3062.9 cm −1 to 3075.7 cm −1 is obtained and analyzed, yielding first precision structural and dynamical information for this novel radical species. The α-CH stretch band origin is determined to be 3068.7887(4) cm −1 , which implies only a modest (≈0.8 cm −1 ) blue shift from rotationally unresolved infrared spectroscopic studies of cyclobutyl radicals in liquid He droplets [ A. R. Brown, P. R. Franke and G. E. Douberly, J. Phys. Chem. A , 2017, 121 , 7576–7587]. Of particular dynamical interest, a one-dimensional potential energy surface with respect to the ring puckering coordinate is computed at CCSD(T)/ANO2 level of theory and reveals a double minimum C s puckered geometry, separated by an exceedingly shallow planar C 2v transition state barrier (E barr ≈ 1 cm −1 ). Numerical solutions on this double minimum potential yield a zero-point energy for the ground state (E zero-point ≈ 27 cm −1 ) greatly in excess of the interconversion barrier. This is indicative of highly delocalized, large amplitude motion of the four-membered ring structure, for which proper vibrationally averaging of the moment of inertia tensor reproduces the experimentally determined inertial defect remarkably well. Finally, intensity alternation in the experimental spectrum due to nuclear spin statistics upon exchange of three indistinguishable H atom pairs (IH = ½) matches K a + K c = even : odd = 36 : 28 predictions, implying that the unpaired electron in the radical center lies in an out-of-plane p π orbital. Thus, high-resolution infrared spectroscopy provides first experimental confirmation of a shallow double minimum ring puckering potential with a highly delocalized ground state wave function peaked at a planar C 2v transition state geometry consistent with a cyclobutyl π radical.

Chemistry↗
DOE OSTI2025

Operando Characterization of Fe in Doped Ni x (Fe 1– x )O y H z Catalysts for Electrochemical Oxygen Evolution

Iron-doped nickel oxyhydroxides, Ni x (Fe 1– x )O y H z , are among the most promising oxygen evolution reaction (OER) electrocatalysts in alkaline environments. Although iron (Fe) significantly enhances the catalytic activity, there is still no clear consensus on whether Fe directly participates in the reaction or merely acts as a promoter. To elucidate the Fe’s role, we performed operando X-ray spectroscopy studies supported by DFT on Ni x (Fe 1– x )O y H z electrocatalysts. We probed the reversible changes in the structure and electronic character of Ni x (Fe 1– x )O y H z as the electrode potential is cycled between the resting (here at 1.10 V RHE ) and operational states (1.66 V RHE ). DFT calculations and XAS simulations on a library of Fe structures in various NiO y H z environments are in favor of a distorted local octahedral Fe(III)O 3 (OH) 3 configuration at the resting state with the NiO y H z scaffold going from α-Ni(OH) 2 to γ-NiOOH as the potential is increased. Under catalytic conditions, EXAFS and HERFD spectra reveal changes in p-d mixing (covalency) relative to the resting state between O/OH ligands and Fe leading to a shift from octahedral to square pyramidal coordination at the Fe site. XES measurements and theoretical simulations further support that the Fe equilibrium structure remains in a formal Fe(III) state under both resting and operational conditions. These spectral changes are attributed to potential dependent structural rearrangements around Fe. The results suggest that ligand dissociation leads to the C 4v symmetry as the most stable intermediate of the Fe during OER. This implies that Fe has a weakly coordinated or easily dissociable ligand that could serve to coordinate the O–O bond formation and, tentatively, play an active role in the Ni x (Fe 1– x )O y H z electrocatalyst.

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

Coupled Cluster Study of the Interactions of AnO 2 , AnO 2 + , and AnO 2 2+ (An = U, Np) with N 2 and CO

We report thermochemical and spectroscopic properties for actinyl complexes involving UO 2 2+/1+/0 and NpO 2 2+/1+/0 with N 2 and CO, together with the UO 2 -O 2 , UO 2 + -O 2 , and UO 2 + -NO complexes, have been studied for the first time using an accurate composite coupled cluster approach. Two general bonding motifs were investigated, end-on (η 1 ) and side-on (η 2 ) relative to the metal center of the actinyls. For end-on CO complexes, both C-coordinated (An-C) and O-coordinated (An-O) structures were examined, with the former always being lower in energy. All of the η 1 complexes were calculated to be stable, with dissociation energies ranging from 2 to 36 kcal/mol, except for that of UO 2 + -O 2 (the η 1 orientation for UO 2 + -NO was not amenable to single reference coupled cluster). In agreement with a previous study, the η 2 structure for UO 2 + -O 2 was calculated to be relatively strongly bound, by 22.3 kcal/mol in this work. The closely related NO complex, however, had a calculated dissociation energy of just 4.0 kcal/mol. The binding energy of O 2 to neutral UO 2 in a η 2 orientation was calculated to be very strong, 75.4 kcal/mol, and strongly resembled a UO 2 + (O 2 – ) complex at equilibrium. The N–N and C–O bonds were found to be somewhat activated for all the side-on (η 2 ) neutral An(IV) complexes, with stretching frequencies of N 2 or CO being red-shifted by as much as 480 cm –1 with a 0.06 Å bond length elongation. Dissociation energies for the η 1 complexes are strongly correlated with the extent of electron transfer from ligand to actinyl. The nature of bonding in the actinyl complexes is examined using natural resonance theory (NRT). The correlation between bonding motif and small molecule activation is in agreement with experiments in condensed phases.

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

A Spatially Resolved Evaluation of Accelerated Environmental Aging on Emerging Polypropylene-Based Photovoltaic Backsheets Using Raman Spectroscopy

For this work, accelerated aging was used to assess environmental degradation in emerging co-extruded polypropylene (PP)-based backsheets under three different environmental conditions (65°C/20% relative humidity (RH), 75°C/20% RH, and 75°C/50% RH). Although differential scanning calorimetry did not measure crystallinity changes with exposure, spatially resolved Raman spectroscopy identified crystallinity increases in the core layer of aged samples, indicating a heterogeneous postcrystallization process. The Raman results were in agreement with synchrotron-based microfocused wide-angle X-ray scattering measurements. Cross-sectional nanoindentation was used to correlate localized crystallinity shifts with changes in Young's modulus. A similar trend was found where increased modulus was measured in the core layer, supporting the relationship between modulus and crystallinity. Finally, dielectric characterization was used to assess the impact of these material property changes on performance. While changes in the backsheet material properties and dielectric performance were observed with accelerated aging, these shifts generally equilibrated with time, indicating overall stability in response to environmental stressors. Additionally, the identified heterogeneous material property changes indicate that spatially resolved crystallinity measurements may be a valuable early failure indicator to be used in the assessment of PV backsheet long-term durability.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Auroral and Non‐Auroral H 3 + Ion Winds at Uranus With Keck‐NIRSPEC and IRTF‐iSHELL

Abstract To date, no investigation has documented ionospheric flows at Uranus. Previous investigations of Jupiter and Saturn have demonstrated that mapping ion winds can be used to understand ionospheric currents and how these connect to magnetosphere‐ionosphere coupling. We present a study of Uranus's near infrared emissions (NIR) using data from the Keck II Telescope's Near InfraRed SPECtrograph (NIRSPEC) and the InfraRed Telescope Facility's iSHELL spectrograph. H 3 + emission lines were used to derive dawn‐to‐dusk intensity, ionospheric temperatures and ion densities to identify auroral emissions, with their Doppler shifts used to measure ion velocities. We confirm the presence of the southern NIR aurora in 2016, driven by elevated H 3 + column densities up to 6.0 × 10 16 m −2 . While no auroral emissions were detected in 2014, we find a 14%–20% super rotation across the planet's disk in 2014 and a 7%–18% super rotation in 2016.

Thomas, Emma M. [Department of Mathematics Physics↗
DOE OSTI2026

Exploration of Nirmatrelvir Derivatives as Optimized SARS‐CoV‐2 Antivirals

Nirmatrelvir (NMV) is a SARS‐CoV‐2 antiviral component of the approved COVID‐19 therapeutic Paxlovid. It is a reversible covalent inhibitor of SARS‐CoV‐2 main protease (M Pro ) that is effluxed from human cells by P‐glycoprotein (P‐gp). To identify NMV analogs with improved potency and reduced P‐gp efflux, a structure–activity relationship campaign was conducted. Warheads alternative to nitrile for engaging the active site cysteine were tested showing aldehyde and dichloroacetamide with better enzyme inhibition potency. Crystal structure of MPI‐136−M Pro shows its aldehyde warhead forming a thiohemiacetal with active Cys145 of M Pro . Several S4 binders were explored revealing that an O‐to‐S shift at the N ‐terminal amide leads to better enzyme inhibition. By exploring different combinations of S2, S3, and S4 binders, two inhibitors with better enzyme inhibition potency than NMV were found. Crystal structure of MPI‐148, with ( S )‐2‐azaspiro[4,5]decane‐3‐carboxylate as an alternative S2 binder, shows extensive hydrogen‐bond networks for locking the inhibitor in active site, explaining high affinity of NMV analogs. Further characterization of cellular M Pro engagement and antiviral potency against SARS‐CoV‐2 revealed four inhibitors with greater potency than NMV in P‐gp‐expressing cells. Studies with the P‐gp inhibitor CP‐100356 showed that these compounds were less sensitive to P‐gp inhibition than NMV, consistent with reduced P‐gp‐mediated efflux.

Alugubelli, Yugendar R. [Texas A&M Drug Discovery ↗
DOE OSTI2024

Genomic and phenotypic characterization of multidrug-resistant Salmonella enterica serovar Reading isolates involved in a turkey-associated foodborne outbreak

Salmonella is a global bacterial foodborne pathogen associated with a variety of contaminated food products. Poultry products are a common source of Salmonella -associated foodborne illness, and an estimated 7% of human illnesses in the United States are attributed to turkey products. From November 2017 to March 2019, the Centers for Disease Control and Prevention reported a turkey-associated outbreak of multidrug-resistant (MDR; resistant to ≥3 antimicrobial classes) Salmonella enterica serovar Reading ( S . Reading) linked to 358 human infections in 42 US states and Canada. Since S . Reading was seldom linked to human illness prior to this outbreak, the current study compared genomic sequences of S . Reading isolates prior to the outbreak (pre-outbreak) to isolates identified during the outbreak period, focusing on genes that were different between the two groups but common within a group. Following whole-genome sequence analysis of five pre-outbreak and five outbreak-associated turkey/turkey product isolates of S . Reading, 37 genes located within two distinct chromosomal regions were identified only in the pre-outbreak isolates: (1) an ~5 kb region containing four protein-coding genes including uidA which encodes beta-glucuronidase, pgdA encoding peptidoglycan deacetylase, and two hypothetical proteins and (2) an ~28 kb region comprised of 32 phage-like genes and the xerC gene, which encodes tyrosine recombinase (frequently associated with phage genes). The five outbreak isolates also had a deletional event within the cirA gene, introducing a translational frame shift and premature stop codon. The cirA gene encodes a protein with dual receptor functions: a siderophore receptor for transport of dihydroxybenzoylserine as well as a colicin Ia/b receptor. Significant differences for the identified genetic variations were also detected in 75 S . Reading human isolates. Of the 41 S . Reading isolates collected before or in 2017, 81 and 90% of the isolates contained the uidA and pgdA genes, respectively, but only 24% of the isolates collected after 2017 harbored the uidA and pgdA genes. The truncation event within the cirA gene was also significantly higher in isolates collected after 2017 (74%) compared to before or in 2017 (5%). Phenotypic analysis of the S . Reading isolates for colicin and cefiderocol sensitivities (CirA) and β-methyl-D-glucuronic acid utilization (UidA and accessory proteins) supported the genomic data. Overall, a similar genome reduction pattern was generally observed in both the turkey and human isolates of S . Reading during the outbreak period, and the genetic differences were present in genes that could potentially promote pathogen dissemination due to variation in Salmonella colonization, fitness, and/or virulence.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Infrared signature of the hydroperoxyalkyl intermediate (·QOOH) in cyclohexane oxidation: An isomer-resolved spectroscopic study

Infrared (IR) action spectroscopy is utilized to characterize carbon-centered hydroperoxy-cyclohexyl radicals (·QOOH) transiently formed in cyclohexane oxidation. The oxidation pathway leads to three nearly degenerate ·QOOH isomers, β-, γ-, and δ-QOOH, which are generated in the laboratory by H-atom abstraction from the corresponding ring sites of the cyclohexyl hydroperoxide (CHHP) precursor. The IR spectral features of jet-cooled and stabilized ·QOOH radicals are observed from 3590 to 7010 cm −1 (∼10–20 kcal mol −1 ) at energies in the vicinity of the transition state (TS) barrier leading to OH radicals that are detected by ultraviolet laser-induced fluorescence. The experimental approach affords selective detection of β-QOOH, arising from its significantly lower TS barrier to OH products compared to γ and δ isomers, which results in rapid unimolecular decay and near unity branching to OH products. The observed IR spectrum of β-QOOH includes fundamental and overtone OH stretch transitions, overtone CH stretch transitions, and combination bands involving OH or CH stretch with lower frequency modes. The assignment of β-QOOH spectral features is guided by anharmonic frequencies and intensities computed using second-order vibrational perturbation theory. The overtone OH stretch (2ν OH ) of β-QOOH is shifted only a few wavenumbers from that observed for the CHHP precursor, yet they are readily distinguished by their prompt vs slow dissociation rates to OH products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Genetic and metabolic drivers of membrane remodeling in Clostridium thermocellum under alcohol stress

Clostridium thermocellum is a leading candidate for consolidated bioprocessing of lignocellulosic biomass into biofuels due to its native cellulolytic capabilities. Beyond ethanol, C. thermocellum is being developed as a platform for producing higher-chain alcohols such as isobutanol and n-butanol. However, its physiological adaptations to alcohol stress remain poorly understood. Here, we investigate how C. thermocellum remodels its membrane lipid composition in response to exogenous ethanol, n-butanol, isobutanol, and butyrate. Exposure to linear alcohols such as n-butanol or to organic acids like butyrate increased the proportion of straight-chain fatty acids in the membrane at the expense of branched-chain species, whereas exposure to the branched alcohol isobutanol produced the opposite effect. Isotope tracer experiments demonstrated that C. thermocellum directly incorporates the carbon backbones of exogenous alcohols and acids into fatty acids, providing a mechanistic basis for these contrasting shifts. We show that the bifunctional aldehyde/alcohol dehydrogenase AdhE is essential for the assimilation of exogenous alcohols into fatty acids, acting through its oxidative activity by first oxidizing alcohols to aldehydes and then converting them to acyl-CoA intermediates. Deletion of the pyruvate:ferredoxin oxidoreductase isozyme pfor4 abolished branched-chain fatty acid synthesis, but supplementation with isobutanol restored production, indicating that Pfor4 substitutes for the canonical branched-chain α-keto acid dehydrogenase complex. These findings reveal two distinct routes for branched-chain fatty acid production in C. thermocellum: a Pfor4-dependent pathway from α-keto acid intermediates derived from amino acid synthesis, and an AdhE-dependent salvage pathway that assimilates exogenous branched-chain alcohols.

Acetivibrio thermocellus↗