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At least 757 records · Page 42
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Structural evolution of a DNA repair self-resistance mechanism targeting genotoxic secondary metabolites

Abstract Microbes produce a broad spectrum of antibiotic natural products, including many DNA-damaging genotoxins. Among the most potent of these are DNA alkylating agents in the spirocyclopropylcyclohexadienone (SCPCHD) family, which includes the duocarmycins, CC-1065, gilvusmycin, and yatakemycin. The yatakemycin biosynthesis cluster in Streptomyces sp. TP-A0356 contains an AlkD-related DNA glycosylase, YtkR2, that serves as a self-resistance mechanism against yatakemycin toxicity. We previously reported that AlkD, which is not present in an SCPCHD producer, provides only limited resistance against yatakemycin. We now show that YtkR2 and C10R5, a previously uncharacterized homolog found in the CC-1065 biosynthetic gene cluster of Streptomyces zelensis , confer far greater resistance against their respective SCPCHD natural products. We identify a structural basis for substrate specificity across gene clusters and show a correlation between in vivo resistance and in vitro enzymatic activity indicating that reduced product affinity—not enhanced substrate recognition—is the evolutionary outcome of selective pressure to provide self-resistance against yatakemycin and CC-1065.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Inhibiting ACK1-mediated phosphorylation of C-terminal Src kinase counteracts prostate cancer immune checkpoint blockade resistance

Solid tumours are highly refractory to immune checkpoint blockade (ICB) therapies due to the functional impairment of effector T cells and their inefficient trafficking to tumours. T-cell activation is negatively regulated by C-terminal Src kinase (CSK); however, the exact mechanism remains unknown. Here we show that the conserved oncogenic tyrosine kinase Activated CDC42 kinase 1 (ACK1) is able to phosphorylate CSK at Tyrosine 18 (pY18), which enhances CSK function, constraining T-cell activation. Mice deficient in the Tnk2 gene encoding Ack1, are characterized by diminished CSK Y18-phosphorylation and spontaneous activation of CD 8+ and CD 4+ T cells, resulting in inhibited growth of transplanted ICB-resistant tumours. Furthermore, ICB treatment of castration-resistant prostate cancer (CRPC) patients results in re-activation of ACK1/pY18-CSK signalling, confirming the involvement of this pathway in ICB insensitivity. An ACK1 small-molecule inhibitor, (R)-9b, recapitulates inhibition of ICB-resistant tumours, which provides evidence for ACK1 enzymatic activity playing a pivotal role in generating ICB resistance. Overall, our study identifies an important mechanism of ICB resistance and holds potential for expanding the scope of ICB therapy to tumours that are currently unresponsive.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2025

A pronounced decline in northern vegetation resistance to flash droughts from 2001 to 2022

Climate change has led to the transition of droughts into rapid and intensified phenomena known as flash droughts, presenting considerable challenges for risk management, particularly concerning their impact on ecosystem productivity. Quantifying the ecosystem’s capacity to maintain productivity during flash droughts, referred to as ecosystem resistance, is crucial to assess drought impacts. However, it remains uncertain how the resistance of ecosystem productivity to flash drought changes over time. Here we show that vegetation resistance to flash droughts declines by up to 27% (±5%) over the Northern Hemisphere hotspots during 2001-2022, including eastern Asia, western North America, and northern Europe. The notable decline in vegetation resistance is mainly attributed to increased vapour pressure deficit and temperature, and enhanced vegetation structural sensitivity to water availability. Flash droughts pose higher ecological risks than slowly-developing droughts during the growing seasons, where ecosystem productivity experiences faster decline rates with a shorter response time. Our results underscore the limited ecosystem capacity to resist flash droughts under climate change.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2017

Evaluating the Sources of Graphene’s Resistivity Using Differential Conductance

We explore the contributions to the electrical resistance of monolayer and bilayer graphene, revealing transitions between different regimes of charge carrier scattering. In monolayer graphene at low densities, a nonmonotonic variation of the resistance is observed as a function of temperature. Such behaviour is consistent with the influence of scattering from screened Coulomb impurities. At higher densities, the resistance instead varies in a manner consistent with the influence of scattering from acoustic and optical phonons. The crossover from phonon-, to charged-impurity, limited conduction occurs once the concentration of gate-induced carriers is reduced below that of the residual carriers. In bilayer graphene, the resistance exhibits a monotonic decrease with increasing temperature for all densities, with the importance of short-range impurity scattering resulting in a “universal” density-independent (scaled) conductivity at high densities. At lower densities, the conductivity deviates from this universal curve, pointing to the importance of thermal activation of carriers out of charge puddles. These various assignments, in both systems, are made possible by an approach of “differential-conductance mapping”, which allows us to suppress quantum corrections to reveal the underlying mechanisms governing the resistivity.

36 MATERIALS SCIENCE↗
DOE OSTI2019

Modeling and Cost Benefit Analysis to Guide Deployment of POC Diagnostics for Non-typhoidal Salmonella Infections with Antimicrobial Resistance

Invasive non-typhoidal Salmonella (NTS) is among the leading causes of blood stream infections in sub-Saharan Africa and other developing regions, especially among pediatric populations. Invasive NTS can be difficult to treat and have high case-fatality rates, in part due to emergence of strains resistant to broad-spectrum antibiotics. Furthermore, improper treatment contributes to increased antibiotic resistance and death. Point of care (POC) diagnostic tests that rapidly identify invasive NTS infection, and differentiate between resistant and non-resistant strains, may greatly improve patient outcomes and decrease resistance at the community level. Here we present for the first time a model for NTS dynamics in high risk populations that can analyze the potential advantages and disadvantages of four strategies involving POC diagnostic deployment, and the resulting impact on antimicrobial treatment for patients. Our analysis strongly supports the use of POC diagnostics coupled with targeted antibiotic use for patients upon arrival in the clinic for optimal patient and public health outcomes. We show that even the use of imperfect POC diagnostics can significantly reduce total costs and number of deaths, provided that the diagnostic gives results quickly enough that patients are likely to return or stay to receive targeted treatment.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A theoretical investigation of the effect of Ga alloying on thermodynamic stability, electronic-structure, and oxidation resistance of Ti 2 AlC MAX phase

We present a systematic investigation of thermodynamic stability, phase-reaction, and chemical activity of Al containing disordered Ti 2 (Al-Ga)C MAX phases using machine-learning driven high-throughput framework to understand the oxidation resistance behavior with increasing temperature and exposure to static oxygen. The A-site (at Al) disordering of Ti 2 AlC with Ga shows significant change in the chemical activity of Al with increasing temperature and exposure to static oxygen, which is expected to enable surface segregation of Al, thereby, the formation of Al 2 O 3 and improved oxidation resistance. We performed in-depth convex hull analysis of ternary Ti-Al-C, Ti-Ga-C, and Ti-Al-Ga-C based MAX phase, and provide detailed contribution arising from electronic, chemical and vibrational entropies. The thermodynamic analysis shows change in the Gibbs formation enthalpy (ΔG form ) at higher temperatures, which implies an interplay of temperature-dependent enthalpy and entropic contributions in oxidation resistance Ga doped Ti 2 AlC MAX phases. A detailed electronic structure and chemical bonding analysis using crystal orbital Hamilton population method reveal the origin of change in phases stability and in oxidation resistance in disorder Ti2(Al 1-x Ga x )C MAX phases. Our electronic structure analysis correlate well with the change in oxidation resistance of Ga doped MAX phases. We believe our study provides a useful guideline to understand to role of alloying on electronic, thermodynamic, and oxidation related mechanisms of bulk MAX phases, which can work as a precursor to understand oxidation behavior of twodimensional MAX phases, i.e., MXenes (transition metal carbides, carbonitrides and nitrides).

36 MATERIALS SCIENCE↗
DOE OSTI2024

Cacao pod transcriptome profiling of seven genotypes identifies features associated with post-penetration resistance to Phytophthora palmivora

Abstract The oomycete Phytophthora palmivora infects the fruit of cacao trees ( Theobroma cacao ) causing black pod rot and reducing yields. Cacao genotypes vary in their resistance levels to P. palmivora , yet our understanding of how cacao fruit respond to the pathogen at the molecular level during disease establishment is limited. To address this issue, disease development and RNA-Seq studies were conducted on pods of seven cacao genotypes (ICS1, WFT, Gu133, Spa9, CCN51, Sca6 and Pound7) to better understand their reactions to the post-penetration stage of P. palmivora infection. The pod tissue- P. palmivora pathogen assay resulted in the genotypes being classified as susceptible (ICS1, WFT, Gu133 and Spa9) or resistant (CCN51, Sca6 and Pound7). The number of differentially expressed genes (DEGs) ranged from 1625 to 6957 depending on genotype. A custom gene correlation approach identified 34 correlation groups. De novo motif analysis was conducted on upstream promoter sequences of differentially expressed genes, identifying 76 novel motifs, 31 of which were over-represented in the upstream sequences of correlation groups and associated with gene ontology terms related to oxidative stress response, defense against fungal pathogens, general metabolism and cell function. Genes in one correlation group (Group 6) were strongly induced in all genotypes and enriched in genes annotated with defense-responsive terms. Expression pattern profiling revealed that genes in Group 6 were induced to higher levels in the resistant genotypes. An additional analysis allowed the identification of 17 candidate cis -regulatory modules likely to be involved in cacao defense against P. palmivora . This study is a comprehensive exploration of the cacao pod transcriptional response to P. palmivora spread after infection. We identified cacao genes, promoter motifs, and promoter motif combinations associated with post-penetration resistance to P. palmivora in cacao pods and provide this information as a resource to support future and ongoing efforts to breed P. palmivora -resistant cacao.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2020

Carbapenems drive the collateral resistance to ceftaroline in cystic fibrosis patients with MRSA

Chronic airways infection with methicillin-resistant Staphylococcus aureus (MRSA) is associated with worse respiratory disease cystic fibrosis (CF) patients. Ceftaroline is a cephalosporin that inhibits the penicillin-binding protein (PBP2a) uniquely produced by MRSA. We analyzed 335 S. aureus isolates from CF sputum samples collected at three US centers between 2015–2018. Molecular relationships demonstrated that high-level resistance of preceding isolates to carbapenems were associated with subsequent isolation of ceftaroline resistant CF MRSA. In vitro evolution experiments showed that pre-exposure of CF MRSA to meropenem with further selection with ceftaroline implied mutations in mecA and additional mutations in pbp1 and pbp2 , targets of carbapenems; no effects were achieved by other β-lactams. An in vivo pneumonia mouse model showed the potential therapeutic efficacy of ceftaroline/meropenem combination against ceftaroline-resistant CF MRSA infections. Thus, the present findings highlight risk factors and potential therapeutic strategies offering an opportunity to both prevent and address antibiotic resistance in this patient population.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2017

Localised nanoscale resistive switching in GaP thin films with low power consumption

Nanoscale localisation of the electroforming-free resistive switching (RS) behaviour in polycrystalline GaP thin films has been observed for the first time. A combination of conductive atomic force microscopy and first-order reversal curve current–voltage measurements indicated that the grain boundaries are the preferred sites for the formation of the conductive switching filaments. It is proposed, based on TEM and XPS results, that local electrochemical migration of Ga ions along the grain boundaries plays a critical role in the switching mechanism. In the low-resistance (ON) state, the conduction mechanism was found to be the space-charge-limited current mechanism, while the high-resistance (OFF) state was governed by the Frenkel–Poole mechanism. Here, a high OFF/ON resistance ratio (~10 4 ) and lower power consumption than current RS devices, in addition to the easy integration of GaP with silicon substrates, make these GaP films promising for future applications in future non-volatile resistive random access memory (RRAM).

36 MATERIALS SCIENCE↗
DOE OSTI2010

Growth kinetics and electronic properties of unintentionally doped semi-insulating GaN on SiC and high-resistivity GaN on sapphire grown by ammonia molecular-beam epitaxy

Growth of unintentionally doped (UID) semi-insulating GaN on SiC and highly resistive GaN on sapphire using the ammonia molecular-beam epitaxy technique is reported. The semi-insulating UID GaN on SiC shows room temperature (RT) resistivity of 10{sup 11} {Omega} cm and well defined activation energy of 1.0 eV. The balance of compensation of unintentional donors and acceptors is such that the Fermi level is lowered to midgap, and controlled by a 1.0 eV deep level defect, which is thought to be related to the nitrogen antisite N{sub Ga}, similar to the ''EL2'' center (arsenic antisite) in unintentionally doped semi-insulating GaAs. The highly resistive GaN on sapphire shows RT resistivity in range of 10{sup 6}-10{sup 9} {Omega} cm and activation energy varying from 0.25 to 0.9 eV. In this case, the compensation of shallow donors is incomplete, and the Fermi level is controlled by levels shallower than the 1.0 eV deep centers. The growth mechanisms for the resistive UID GaN materials were investigated by experimental studies of the surface kinetics during growth. The required growth regime involves a moderate growth temperature range of 740-780 deg. C, and a high ammonia flux (beam equivalent pressure of 1x10{sup -4} Torr), which ensures supersaturated coverage of surface adsorption sites with NH{sub x} radicals. Such highly nitrogen rich growth conditions lead to two-dimensional layer by layer growth and reduced oxygen incorporation.

36 MATERIALS SCIENCE↗
DOE OSTI2011

In situ transmission electron microscopy analysis of conductive filament during solid electrolyte resistance switching

An in situ transmission electron microscopy (TEM) analysis of a solid electrolyte, Cu-GeS, during resistance switching is reported. Real-time observations of the filament formation and disappearance process were performed in the TEM instrument and the conductive-filament-formation model was confirmed experimentally. Narrow conductive filaments were formed corresponding to resistance switching from high- to low-resistance states. When the resistance changed to high-resistance state, the filament disappeared. It was also confirmed by use of selected area diffractometry and energy-dispersive x-ray spectroscopy that the conductive filament was made of nanocrystals composed mainly of Cu.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Electrical resistivity of Au-ZnO nanocomposite films

The electrical resistivity of electron beam codeposited gold and zinc oxide (Au-ZnO) films was investigated over the full composition range. The electrical resistivity was shown to increase monotonically with increasing ZnO content, with three characteristic regimes of behavior associated primarily with (1) grain boundary electron scattering due to grain refinement at ZnO volume fractions below 0.3, (2) percolation theory for ZnO volume fractions at and above the percolation threshold (f{sub c} = 0.85), and (3) a transition region between these where it was proposed that resistivity was influenced by the formation of Au-Zn complexes due to an oxygen deficiency in the deposited ZnO. The electrical resistivity of the composite films remained below 100 {mu}{Omega} cm for ZnO volume fractions below 0.5. A model combining the general effective media equation and Mayadas-Shatzkes grain boundary electron scattering model was shown to generally describe the composition dependence of electrical resistivity for the investigated oxide dispersion hardened metal-matrix composite thin films.

36 MATERIALS SCIENCE↗
DOE OSTI2013

Resistive magnetohydrodynamic reconnection: Resolving long-term, chaotic dynamics

In this paper, we address the long-term evolution of an idealised double current system entering reconnection regimes where chaotic behavior plays a prominent role. Our aim is to quantify the energetics in high magnetic Reynolds number evolutions, enriched by secondary tearing events, multiple magnetic island coalescence, and compressive versus resistive heating scenarios. Our study will pay particular attention to the required numerical resolutions achievable by modern (grid-adaptive) computations, and comment on the challenge associated with resolving chaotic island formation and interaction. We will use shock-capturing, conservative, grid-adaptive simulations for investigating trends dominated by both physical (resistivity) and numerical (resolution) parameters, and confront them with (visco-)resistive magnetohydrodynamic simulations performed with very different, but equally widely used discretization schemes. This will allow us to comment on the obtained evolutions in a manner irrespective of the adopted discretization strategy. Our findings demonstrate that all schemes used (finite volume based shock-capturing, high order finite differences, and particle in cell-like methods) qualitatively agree on the various evolutionary stages, and that resistivity values of order 0.001 already can lead to chaotic island appearance. However, none of the methods exploited demonstrates convergence in the strong sense in these chaotic regimes. At the same time, nonperturbed tests for showing convergence over long time scales in ideal to resistive regimes are provided as well, where all methods are shown to agree. Both the advantages and disadvantages of specific discretizations as applied to this challenging problem are discussed.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2013

The coherent interlayer resistance of a single, rotated interface between two stacks of AB graphite

The coherent, interlayer resistance of a misoriented, rotated interface between two stacks of AB graphite is determined for a variety of misorientation angles. The quantum-resistance of the ideal AB stack is on the order of 1 to 10 mΩ μm{sup 2}. For small rotation angles, the coherent interlayer resistance exponentially approaches the ideal quantum resistance at energies away from the charge neutrality point. Over a range of intermediate angles, the resistance increases exponentially with cell size for minimum size unit cells. Larger cell sizes, of similar angles, may not follow this trend. The energy dependence of the interlayer transmission is described.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Resistive wall tearing mode generated finite net electromagnetic torque in a static plasma

The MARS-F code [Y. Q. Liu et al., Phys. Plasmas 7, 3681 (2000)] is applied to numerically investigate the effect of the plasma pressure on the tearing mode stability as well as the tearing mode-induced electromagnetic torque, in the presence of a resistive wall. The tearing mode with a complex eigenvalue, resulted from the favorable averaged curvature effect [A. H. Glasser et al., Phys. Fluids 18, 875 (1975)], leads to a re-distribution of the electromagnetic torque with multiple peaking in the immediate vicinity of the resistive layer. The multiple peaking is often caused by the sound wave resonances. In the presence of a resistive wall surrounding the plasma, a rotating tearing mode can generate a finite net electromagnetic torque acting on the static plasma column. Meanwhile, an equal but opposite torque is generated in the resistive wall, thus conserving the total momentum of the whole plasma-wall system. The direction of the net torque on the plasma is always opposite to the real frequency of the mode, agreeing with the analytic result by Pustovitov [Nucl. Fusion 47, 1583 (2007)]. When the wall time is close to the oscillating time of the tearing mode, the finite net torque reaches its maximum. Without wall or with an ideal wall, no net torque on the static plasma is generated by the tearing mode. However, re-distribution of the torque density in the resistive layer still occurs.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗
DOE OSTI2014

Dual operation characteristics of resistance random access memory in indium-gallium-zinc-oxide thin film transistors

In this study, indium-gallium-zinc-oxide thin film transistors can be operated either as transistors or resistance random access memory devices. Before the forming process, current-voltage curve transfer characteristics are observed, and resistance switching characteristics are measured after a forming process. These resistance switching characteristics exhibit two behaviors, and are dominated by different mechanisms. The mode 1 resistance switching behavior is due to oxygen vacancies, while mode 2 is dominated by the formation of an oxygen-rich layer. Furthermore, an easy approach is proposed to reduce power consumption when using these resistance random access memory devices with the amorphous indium-gallium-zinc-oxide thin film transistor.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Room temperature resistive state switching with hysteresis in GdMnO{sub 3} thin film with low threshold voltage

In this paper, we report a room temperature resistive state switching with hysteresis, in a thin film of GdMnO{sub 3} grown on NdGaO{sub 3} substrate. The switched states have a resistance ratio ≈10{sup 3}. The switching is unipolar in nature, with a low set voltage <3 V, while the reset voltage <0.3 V. The switching occurs between a high resistance polaronic insulating state and a low resistance metallic state. The resistance state transition has been ascribed to an electronic mechanism that originates from co-existing phases (created by charge disproportionation) that can undergo a percolative transition enabled by the applied bias.

36 MATERIALS SCIENCE↗
DOE OSTI2014

Anomalous effect due to oxygen vacancy accumulation below the electrode in bipolar resistance switching Pt/Nb:SrTiO{sub 3} cells

In conventional semiconductor theory, greater doping decreases the electronic resistance of a semiconductor. For the bipolar resistance switching (BRS) phenomena in oxides, the same doping principle has been used commonly to explain the relationship between the density variation of oxygen vacancies (V{sub o}¨) and the electronic resistance. We find that the V{sub o}¨ density can change at a depth of ∼10 nm below the Pt electrodes in Pt/Nb:SrTiO{sub 3} cells, depending on the resistance state. Using electron energy loss spectroscopy and secondary ion mass spectrometry, we found that greater V{sub o}¨ density underneath the electrode resulted in higher resistance, contrary to the conventional doping principle of semiconductors. To explain this seemingly anomalous experimental behavior, we provide quantitative explanations on the anomalous BRS behavior by simulating the mobile V{sub o}¨ [J. S. Lee et al., Appl. Phys. Lett. 102, 253503 (2013)] near the Schottky barrier interface.

36 MATERIALS SCIENCE↗