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At least 307 records · Page 17
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Characterizing and Engineering Trehalose Biosynthesis Pathways to Improve Acetate Tolerance in Pseudomonas putida KT2440

Alkaline pretreatment can depolymerize lignin into a diverse mixture of monomers and smaller compounds, enabling bioconversion of these compounds to value-added chemicals in engineered bacterial hosts such as Pseudomonas putida KT2440. Acetate and salts comprise approximately 8% and 32% of the lignin stream, respectively. High concentrations of these components can cause cell death in P. putida, so lignin-derived streams must be fed in lower amounts to decrease stress. Investigation of the mechanisms of bacterial tolerance to chemicals in lignin-rich substrates is therefore required to overcome this obstacle in lignin bioconversion. Previous work has shown that trehalose, an endogenously produced disaccharide, is involved in tolerance to heat, cold, and osmotic stress, as well as implicated in acid stress in other bacteria. As such, trehalose biosynthesis presents a useful target to increase acetate and osmotic tolerance in P. putida. This work investigates the native TreSA, TreSB, and TreY/TreZ trehalose biosynthesis pathways in this bacterial strain as well as the OtsAB pathway of Sphingobium sp. SYK-6. Overexpression of the OtsAB pathway in P. putida increased tolerance to acetate relative to wild-type. Additionally, functional knockouts of treSA, treSB, treY, and treZ in P. putida showed that interruption of any trehalose biosynthesis pathway, and, in the case of TreY/TreZ, interruption of the pathway at any point, significantly hindered growth in acetate as well as on glucose and LB broth. Each trehalose biosynthesis pathway was then engineered for overexpression in P. putida to determine whether overexpression of these genes conferred additional tolerance to acetate. The TreSA, TreSB, OtsA, and OtsB enzymes were also expressed and purified to determine the reaction rates and kinetics of these pathways. The hypothetical glycoside hydrolase family 15 protein, encoded in the gene located in between otsB and otsA in the Sphingobium operon, was purified as well to investigate its potential involvement in the OtsAB pathway. The findings of this work illuminated the mechanisms of trehalose biosynthesis in P. putida and identified genetic targets to improve strain tolerance to common components of alkaline-pretreated lignin streams. These findings could ultimately improve yields of desired products from lignin in engineered strains of P. putida.

alkaline pretreatment↗
DOE OSTI2024

Probing the Isospin Composition of Short-Range Correlated Pairs at Jefferson Lab Hall B

Nucleons in short-range correlated (SRC) pairs, due to their close proximity and high relative momentum, can provide insight into the short-range part of the strong nuclear interaction. In particular, the prevalence of np pairs is due to the dominance of a tensor term for correlated nucleons with momenta of approximately 400?600 MeV/c. This dissertation comprises two studies advancing the community?s understanding of the isospin composition of SRC pairs. First, I performed a study of proton and neutron knockout from initially low-momentum and high-momentum states in 3He. Previous work has shown that protons are disproportionately represented in high-momentum states in neutron-rich nuclei. I demonstrate that spectral functions for the proton-rich nucleus 3He predict, in agreement with data, that neutrons are disproportionately represented in high-momentum states, but that 3He does not display the same strong prevalence of np pairs that is observed in larger nuclei. Second, Generalized Contact Formalism (GCF), a well-supported theory for predicting SRC behavior, predicts the transition from an isospin-dependent, tensor-dominant interaction at intermediate distances to a scalar-dominant, isospin-independent interaction at very short distances. This dissertation uses data from the CLAS12 Nuclear Targets Experiments in Hall B at Jefferson Lab to measure the relative abundances of pp and pn pairs for increasing relative momentum and decreasing separation. I provide an independent confirmation of the previously-observed increase in pp pairs at increasing momentum of the struck nucleon. I also contribute to the application of the new CLAS12 Central Neutron Detector by precisely measuring the neutron detection efficiency and developing a machine learning model for rejecting charged particle background.

Seroka, Erin↗
DOE OSTI2025

Analyzing the Effects of the Interference between One- and Two-Body Currents on Neutrino-Nucleus Scattering in ACHILLES

Modeling improvements of neutrino–nucleus scattering are an essential aspect of reducing systematic uncertainties for current and future neutrino oscillation experiments. In particular, retaining quantum mechanical effects such as the interference between one-body (1p1h) and two-body (2p2h) currents in our cross-section models is an essential consideration. This work investigates the impact of this interference term on neutrino–argon scattering using the ACHILLES event generator, which directly implements the interference model developed by Lovato, Rocco, and Steinberg. Using fluxes relevant to SBND, the DUNE near detector, and MiniBooNE, charged- and neutral-current event samples are generated and predicted event rates are plotted against a variety of kinematic variables. For events simulated using the SBND flux, it is found that interference contributes approximately 10 \% to the total charged-current event rate, and serves to enhance the quasi-elastic peak. When considering events generated using the DUNE flux, resonance interactions contribute more to the predicted event rate, as the neutrino flux extends out to higher energies. The relative interference contribution subsequently decreases to roughly 7 \%. Neutral-current simulations show a higher rate of neutron knockout. Finally, a comparison of argon-to-carbon cross-section ratios is performed utilizing fluxes from SBND and MiniBooNE.

Pando, Nathan [Fermilab]↗
DOE OSTI2026

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗
DOE OSTI2026

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗
DOE OSTI2026

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗
DOE OSTI2026

Impact of Two-Body Currents on Semi-Exclusive Lepton-Nucleus Reactions

We generalize the spectral-function formalism to describe two-nucleon knockout processes in exclusive kinematics. Significant improvements are introduced both in the treatment of the current operators entering the $Δ$-current contribution and in the modeling of correlations between the two struck nucleons, including a consistent treatment of isospin dependence and the explicit incorporation of angular correlations. The framework is validated through comparisons with relativistic Fermi-gas calculations and with semi-exclusive electron-nucleus scattering data. Our results demonstrate that an accurate description of nuclear dynamics plays a crucial role in modeling this reaction mechanism. We further present a study of selected electroweak observables relevant to neutrino-scattering experiments.

Rocco, N. [Fermilab; Valencia U., IFIC] (ORCID:000↗
DOE OSTI2026

Comparisons of triple-differential cross sections for quasielastic-like $ν_μ$-hydrocarbon interactions using $\langle E_ν\rangle \sim$ 3~GeV versus $\sim$ 6~GeV beams in MINERvA

Neutrino charged-current quasielastic-like scattering, a reaction category extensively used in neutrino oscillation measurements, receives contributions from single nucleon knockout processes, multinucleon processes, and inelastic scattering with subsequent rescattering or absorption in the nucleus to produce only nucleons in the final state. In this article, comparisons are presented of the same measurement in two different wideband neutrino beams: one beam peaks near 3 GeV with few neutrinos above 6 GeV; the other peaks near 6 GeV with few neutrinos above 10 GeV. Comparisons of differential cross sections in muon and proton kinematics for these two exposures probe deviations from free-neutron scattering that arise from the processes involving the nuclear medium, and provide a test of neutrino interaction models used to infer neutrino energies in oscillation experiments. Discrepancies are observed between the data and predictions that point to overestimates of the final state interactions of both protons and charged pions in quasielastic-like events.

Ruterbories, D. [Rochester U.]↗
DOE OSTI2026

Measuring the neutrino-oxygen neutral current quasielastic cross section using the accelerator neutrino neutron interaction experiment

The Accelerator Neutrino Neutron Interaction Experiment (ANNIE) is a 26-ton gadolinium-doped water Cherenkov detector located on-axis to Fermilab’s Booster Neutrino Beam (BNB). ANNIE is uniquely positioned to perform high-statistics measurements of neutrino-nucleus interactions in water, benefiting from a large neutrino flux due to a short (100-meter) baseline. A central focus of ANNIE’s physics program is the measurement of both charged current (CC) and neutral current (NC) cross sections on water, including neutral current quasielastic (NCQE) and CC-inclusive channels. The NCQE measurement is particularly critical for constraining uncertainties in rare-event searches such as the Diffuse Supernova Neutrino Background (DSNB), where atmospheric $\nu$NCQE interactions constitute a significant and poorly constrained background. This dissertation presents a measurement of the flux-averaged neutrino-oxygen neutral current quasielastic ($\nu$NCQE) cross section using $2.573 \times 10^{20}$~POT of BNB exposure from the 2022 and 2023 beam years. The $\nu$NCQE interaction is identified through the primary $\gamma$-rays produced by nuclear de-excitation of the residual $^{15}$N$^*$ or $^{15}$O$^*$ nucleus following nucleon knockout from $^{16}$O. A dedicated Monte Carlo (MC) re-tuning campaign was conducted using an americium-beryllium (AmBe) calibration source, Michel electrons from stopped muons, and throughgoing dirt muons originating upstream of the detector. This multi-sample approach provided a wide-ranging $\mathcal{O}(\text{MeV})$--$\mathcal{O}(\text{GeV})$ dataset for tuning the simulated detector response, which was subsequently validated against AmBe neutron and Michel electron data for use in the $\nu$NCQE analysis. A dedicated laser calibration campaign was carried out to reduce timing uncertainties across the PMT system, enabling reconstruction of the BNB bunch substructure with sufficient resolution to serve as a background rejection tool. By selecting events in-time with individual neutrino bunches, beam-correlated $\nu$NCQE events are separated from diffuse and accelerator-induced backgrounds, notably skyshine neutrons and externally-originating events, that would otherwise dominate traditional charge-based selections within a small-scale, surface-level, short-baseline detector. A data-driven estimation of the skyshine neutron and external background rates was performed and incorporated into the systematic uncertainty budget. The flux-averaged $\nu$NCQE cross section on oxygen is measured to be $1.57 \pm 0.06\,(\text{stat.})$ $^{+0.91}_{-0.67}\,(\text{syst.})$ $\times 10^{-38}\ \text{cm}^{2}$. A full systematic budget is constructed by propagating uncertainties in the secondary hadronic interaction modeling, background cross section normalizations, detector response, neutrino flux, and the primary $\gamma$-ray emission probabilities from oxygen nuclear de-excitation. An idealized de-excitation model, constructed from existing measurements in the literature is developed to benchmark the predictions of the \textsc{GENIE} event generator. A comparison reveals that \textsc{GENIE} systematically overpredicts the primary $\gamma$-ray emission probability from oxygen de-excitation by a factor of $1.49\times$ for $E_\gamma > 6$~MeV and $3.07\times$ in the $3$--$6$~MeV band. This comparison motivates the dominant systematic uncertainty in this analysis, where a conservative uncertainty of $^{+39.9\%}_{-0\%}$ on the primary $\gamma$-ray signal prediction is assigned. The ANNIE result is consistent with and complementary to existing flux-averaged $\nu$NCQE cross section measurements from T2K and Super-Kamiokande, providing an independent measurement with a different detector, neutrino beam, and analysis methodology. Looking ahead, an upgrade to the ANNIE DAQ infrastructure enabling continuous extended readout will allow a complementary $\nu$NCQE neutron multiplicity measurement, directly relevant to constraining the NCQE background in DSNB searches, competitive with the recent T2K measurement at SK-Gd. The planned Super-SANDI upgrade, deploying a large Water-based Liquid Scintillator (WbLS) volume, will further extend ANNIE's reach to hadronic final states and exclusive NC channels, and enable joint measurements with liquid argon detectors sharing the BNB beamline ahead of DUNE and Hyper-Kamiokande.

Doran, Steven [Iowa State U.]↗
DOE OSTI2025

Proton emission in ultraperipheral Pb-Pb collisions at $\sqrt{𝑠_{𝑁⁢𝑁}}$ = 5.02 TeV

The first measurements of proton emission accompanied by neutron emission in the electromagnetic dissociation (EMD) of 208 Pb nuclei in the ALICE experiment at the Large Hadron Collider are presented. The EMD protons and neutrons emitted at very forward rapidities are detected by the proton and neutron zero degree calorimeters of the ALICE experiment. The emission cross sections of zero, one, two, and three protons accompanied by at least one neutron were measured in ultraperipheral 208 Pb − 208 Pb collisions at a center-of-mass energy per nucleon pair $\sqrt{𝑠_{𝑁⁢𝑁}}$ = 5.02TeV. The 0p and 3p cross sections are described by the RELDIS model within their measurement uncertainties, while the 1p and 2p cross sections are underestimated by the model by 17–25%. According to this model, these 0p, 1p, 2p, and 3p cross sections are associated, respectively, with the production of various isotopes of Pb, Tl, Hg, and Au in the EMD of 208 Pb . The cross sections of the emission of a single proton accompanied by the emission of one, two, or three neutrons in EMD were also measured. The data are significantly overestimated by the RELDIS model, which predicts that the (1p,1n), (1p,2n), and (1p,3n) cross sections are very similar to the cross sections for the production of the thallium isotopes 206,205,204 Tl.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
DOE OSTI2020

Self-assembling Shell Proteins PduA and PduJ have Essential and Redundant Roles in Bacterial Microcompartment Assembly

Protein self-assembly is a common and essential biological phenomenon, and bacterial microcompartments present a promising model system to study this process. Bacterial microcompartments are large, protein-based organelles which natively carry out processes important for carbon fixation in cyanobacteria and the survival of enteric bacteria. These structures are increasingly popular with biological engineers due to their potential utility as nanobioreactors or drug delivery vehicles. However, the limited understanding of the assembly mechanism of these bacterial microcompartments hinders efforts to repurpose them for non-native functions. Here, we comprehensively investigate proteins involved in the assembly of the 1,2-propanediol utilization bacterial microcompartment from Salmonella enterica serovar Typhimurium LT2, one of the most widely studied microcompartment systems. We first demonstrate that two shell proteins, PduA and PduJ, have a high propensity for self-assembly upon overexpression, and we provide a novel method for self-assembly quantification. Using genomic knock-outs and knock-ins, we systematically show that these two proteins play an essential and redundant role in bacterial microcompartment assembly that cannot be compensated by other shell proteins. At least one of the two proteins PduA and PduJ must be present for the bacterial microcompartment shell to assemble. We also demonstrate that assembly-deficient variants of these proteins are unable to rescue microcompartment formation, highlighting the importance of this assembly property. Our work provides insight into the assembly mechanism of these bacterial organelles and will aid downstream engineering efforts.

1,2-propanediol utilization MCP↗
DOE OSTI2024

Differential cross sections of the 16 O (𝑛,𝛼) reaction at neutron energies from 3.8 to 15 MeV

The importance of studying the 16 O (𝑛,𝛼) reaction is motivated by multiple nuclear applications which rely on an accurate nuclear reaction data library for oxygen. Discrepancies between past experimental data on the 16 O (𝑛,𝛼) 13 C reaction and its time-reverse 13 C ⁡(𝛼,𝑛) 16 O reaction have led to various different nuclear data evaluations. Here, we have measured 16 O (𝑛,𝛼) reaction cross sections using the LENZ instrument with the unmoderated white neutron source at LANSCE. Results from 2016/2017 data are discussed and used to benchmark the mcnp and geant simulations of the LENZ experimental setup. We report partial differential cross sections of 16 O (𝑛,𝛼 0 ) at 𝐸 𝑛 = 3.8–15 MeV and 16 O ⁡(𝑛,𝛼 1 +𝛼 2 +𝛼 3 ) at 𝐸 𝑛 =9–15 MeV, based on the new measurement in 2021. The resonances that we observed are in good agreement with the levels in 17 O that were previously measured. The LENZ cross sections are in better agreement with the ENDF/B-VIII.0 evaluation than the with reduced cross section found in ENDF/B-VII.1 up to 6 MeV. However, the current results for 16 O ⁡(𝑛,𝛼 0 ) 13 C g.s. appear to be in the best agreement over the entire energy range with that of JENDL/AN-2005 (ENDF/B-VI.0).

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
NASA NTRS2003

Oscillatory shear stress stimulates endothelial production of O2- from p47phox-dependent NAD(P)H oxidases, leading to monocyte adhesion

Arterial regions exposed to oscillatory shear (OS) in branched arteries are lesion-prone sites of atherosclerosis, whereas those of laminar shear (LS) are relatively well protected. Here, we examined the hypothesis that OS and LS differentially regulate production of O2- from the endothelial NAD(P)H oxidase, which, in turn, is responsible for their opposite effects on a critical atherogenic event, monocyte adhesion. We used aortic endothelial cells obtained from C57BL/6 (MAE-C57) and p47phox-/- (MAE-p47-/-) mice, which lack a component of NAD(P)H oxidase. O2- production was determined by dihydroethidium staining and an electron spin resonance using an electron spin trap methoxycarbonyl-2,2,5,5-tetramethyl-pyrrolidine. Chronic exposure (18 h) to an arterial level of OS (+/- 5 dynes/cm2) increased O2- (2-fold) and monocyte adhesion (3-fold) in MAE-C57 cells, whereas chronic LS (15 dynes/cm2, 18 h) significantly decreased both monocyte adhesion and O2- compared with static conditions. In contrast, neither LS nor OS were able to induce O2- production and monocyte adhesion to MAE-p47-/-. Treating MAE-C57 with a cell-permeable superoxide dismutase compound, polyethylene glycol-superoxide dismutase, also inhibited OS-induced monocyte adhesion. In addition, over-expressing p47phox in MAE-p47-/- restored OS-induced O2- production and monocyte adhesion. These results suggest that chronic exposure of endothelial cells to OS stimulates O2- and/or its derivatives produced from p47phox-dependent NAD(P)H oxidase, which, in turn, leads to monocyte adhesion, an early and critical atherogenic event.

NASA Program Fundamental Space Biology↗
NASA NTRS2003

Reversible skeletal abnormalities in gamma-glutamyl transpeptidase-deficient mice

Gamma-glutamyl transpeptidase (GGT) is a widely distributed ectopeptidase responsible for the degradation of glutathione in the gamma-glutamyl cycle. This cycle is implicated in the metabolism of cysteine, and absence of GGT causes a severe intracellular decrease in this amino acid. GGT-deficient (GGT-/-) mice have multiple metabolic abnormalities and are dwarf. We show here that this latter phenotype is due to a decreased of the growth plate cartilage total height resulting from a proliferative defect of chondrocytes. In addition, analysis of vertebrae and tibiae of GGT-/- mice revealed a severe osteopenia. Histomorphometric studies showed that this low bone mass phenotype results from an increased osteoclast number and activity as well as from a marked decrease in osteoblast activity. Interestingly, neither osteoblasts, osteoclasts, nor chondrocytes express GGT, suggesting that the observed defects are secondary to other abnormalities. N-acetylcysteine supplementation has been shown to reverse the metabolic abnormalities of the GGT-/- mice and in particular to restore the level of IGF-1 and sex steroids in these mice. Consistent with these previous observations, N-acetylcysteine treatment of GGT-/- mice ameliorates their skeletal abnormalities by normalizing chondrocytes proliferation and osteoblastic function. In contrast, resorbtion parameters are only partially normalized in GGT-/- N-acetylcysteine-treated mice, suggesting that GGT regulates osteoclast biology at least partly independently of these hormones. These results establish the importance of cysteine metabolism for the regulation of bone remodeling and longitudinal growth.

NASA Discipline Regulatory Physiology↗
NASA NTRS2003

Cell output, cell cycle duration and neuronal specification: a model of integrated mechanisms of the neocortical proliferative process

The neurons of the neocortex are generated over a 6 day neuronogenetic interval that comprises 11 cell cycles. During these 11 cell cycles, the length of cell cycle increases and the proportion of cells that exits (Q) versus re-enters (P) the cell cycle changes systematically. At the same time, the fate of the neurons produced at each of the 11 cell cycles appears to be specified at least in terms of their laminar destination. As a first step towards determining the causal interrelationships of the proliferative process with the process of laminar specification, we present a two-pronged approach. This consists of (i) a mathematical model that integrates the output of the proliferative process with the laminar fate of the output and predicts the effects of induced changes in Q and P during the neuronogenetic interval on the developing and mature cortex and (ii) an experimental system that allows the manipulation of Q and P in vivo. Here we show that the predictions of the model and the results of the experiments agree. The results indicate that events affecting the output of the proliferative population affect both the number of neurons produced and their specification with regard to their laminar fate.

Evaluation Studies↗
NASA NTRS2003

Ubiquitin-protein ligases in muscle wasting: multiple parallel pathways?

PURPOSE OF REVIEW: Studies in a wide variety of animal models of muscle wasting have led to the concept that increased protein breakdown via the ubiquitin-proteasome pathway is responsible for the loss of muscle mass seen as muscle atrophy. The complexity of the ubiquitination apparatus has hampered our understanding of how this pathway is activated in atrophying muscles and which ubiquitin-conjugating enzymes in muscle are responsible. RECENT FINDINGS: Recent experiments have shown that two newly identified ubiquitin-protein ligases (E3s), atrogin-1/MAFbx and MURF-1, are critical in the development of muscle atrophy. Other in-vitro studies also implicated E2(14k) and E3alpha, of the N-end rule pathway, as playing an important role in the process. SUMMARY: It seems likely that multiple pathways of ubiquitin conjugation are activated in parallel in atrophying muscle, perhaps to target for degradation specific classes of muscle proteins. The emerging challenge will be to define the protein targets for, as well as inhibitors of, these E3s.

Review↗