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At least 361 records · Page 20

The mevalonate pathway of isoprenoid biosynthesis supports metabolic flexibility in Mycobacterium marinum

ABSTRACT Isoprenoids are a diverse class of natural products that are essential in all domains of life. Most bacteria synthesize isoprenoids through either the methylerythritol phosphate (MEP) pathway or the mevalonate (MEV) pathway, while a small subset encodes both pathways, including the pathogen Mycobacterium marinum (Mm). It is unclear whether the MEV pathway is functional in Mm, or why Mm encodes seemingly redundant metabolic pathways. Here, we show that the MEP pathway is essential in Mm, while the MEV pathway is dispensable in culture, with the ΔMEV mutant having no growth defect in axenic culture but a competitive growth defect compared to WT Mm. We found that the MEV pathway does not play a role in ex vivo or in vivo acute infection but does play a role in survival of peroxide stress. Metabolite profiling revealed that modulation of the MEV pathway causes compensatory changes in the concentration of MEP intermediates DOXP and CDP-ME, suggesting that the MEV pathway is functional and that the pathways interact at the metabolic level. Finally, the MEV pathway is upregulated early in the shift down to hypoxia, suggesting that it may provide metabolic flexibility to this bacterium. Interestingly, we found that our complemented strains, which vary in copy number of the polyprenyl synthetase idsB2 , responded differently to peroxide and UV stresses, suggesting a role for this gene as a determinant of downstream prenyl phosphate metabolism. Together, these findings suggest that MEV may serve as an anaplerotic pathway to make isoprenoids under stress conditions. IMPORTANCE Organisms from all domains of life utilize isoprenoids to carry out thousands of critical and auxiliary cellular processes, including signaling, maintaining membrane integrity, stress response, and host-pathogen interactions. The common precursor of all isoprenoids is synthesized via one of two biosynthetic pathways. Importantly, some bacteria encode both pathways, including M. marinum . We found that only one pathway is essential in M. marinum , while the nonessential pathway may confer metabolic flexibility to help the bacterium better adapt to various environmental conditions. We also found that the polyprenyl synthetase IdsB2 plays an important role in driving such phenotypes. Further, we demonstrate metabolic interplay between both functional pathways. These insights represent the first characterization of isoprenoid biosynthesis in dual pathway-encoding mycobacteria.

Qabar, Christine M. [Department of Plant and Micro↗

A case study on the use of carbon sticky tabs for microbeam uranium isotope measurement with an emphasis on understanding the influence of subtle variations in substrate composition

In this paper we integrate laser induced breakdown spectroscopy (LIBS), large geometry secondary ion mass spectrometry (LG-SIMS), laser ablation—multi collector—inductively coupled plasma—mass spectrometry (LA-MC-ICP-MS), and trace elemental compositions obtained by bulk digestion from a suite of commercially available carbon sticky tabs to determine if subtle variations in the tab’s composition can be tied to shifts in the observed uranium isotopic composition of the IRMM-2020 standard relative to its ‘true’ value. The results suggest that, although clear differences exist in the relative abundances of carbon and hydrogen across the various carbon sticky tabs examined, as well as differences in their trace elemental and total uranium concentrations, these differences do not appear to influence the LG-SIMS or LA-MC-ICP-MS uranium isotope ratio measurements, or the appearance of the uranium mass spectrum scans. Instead, the quality (i.e., precision and accuracy) of the LG-SIMS and LA-MC-ICP-MS results are directly proportional to the observed signal intensity at the time of analysis. For the LG-SIMS measurements, there does appear to be a direct correlation between 235U1H hydride formation rates and vacuum conditions within the instrument’s analytical chamber. Furthermore, none of the carbon sticky tabs examined by LG-SIMS displayed evidence of elevated background uranium content. While a preliminary correlation was observed between the uranium isotope background signal during LA-MC-ICP-MS and the total uranium concentrations determined by isotope dilution, none of the tabs displayed a high enough analytical background to affect the isotope ratio measurements.

Zirakparvar, Alex [ORNL] (ORCID:0000000337797730)↗

Systematic Influence of Electronic Modification of Ligands on the Catalytic Rate of Water Oxidation by a Single-Site Ru-Based Catalyst

Catalytic water oxidation is an important process for the development of clean energy solutions and energy storage. Despite the significant number of reports on active catalysts, systematic control of the catalytic activity remains elusive. In this study, descriptors are explored that can be correlated with catalytic activity. [Ru(tpy)(pic) 2 (H 2 O)](NO 3 ) 2 and [Ru(EtO-tpy)(pic) 2 (H 2 O)](NO 3 ) 2 (where tpy=2,2': 6',2“-terpyridine, EtO-tpy=4'-(ethoxy)-2,':6',2”-terpyridine, pic=4-picoline) are synthesized and characterized by NMR, UV/Vis, EPR, resonance Raman, and X-ray absorption spectroscopy, and electrochemical analysis. Addition of the ethoxy group increases the catalytic activity in chemically driven and photocatalytic water oxidation. Thus, the effect of the electron-donating group known for the [Ru(tpy)(bpy)(H 2 O)] 2+ family is transferable to architectures with a tpy ligand trans to the Ru-oxo unit. Under catalytic conditions, [Ru(EtO-tpy)(pic) 2 (H 2 O)](NO 3 ) 2 displays new spectroscopic signals tentatively assigned to a peroxo intermediate. In conclusion, reaction pathways were analyzed by using DFT calculations. [Ru(EtO-tpy)(pic) 2 (H 2 O)](NO 3 ) 2 is found to be one of the most active catalysts functioning by a water nucleophilic attack mechanism.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Light-triggered electrochemical biosensor using singlet oxygen for self-powered operation and glucose detection

This study introduces a light-activated sensing strategy that integrates photosensitization with electrochemical detection. The sensor employs Eosin Y, a photosensitizer that generates singlet oxygen ( 1 O 2 ) via type II photosensitization. Immobilized within a thin polymer matrix on a carbon working electrode, Eosin Y produces 1 O 2 , under green light (520 nm) illumination, initiating a redox process that yields a measurable current. To incorporate biosensing capabilities and enable self-powered operation, this 1 O 2 – mediated process was coupled with glucose oxidase (GOx) to construct a fully operational glucose biosensor. The addition of glucose reverses the current flow by causing GOx to compete for electrons, with the resulting current magnitude correlating with glucose concentration providing a sensitive measure of glucose. The biosensor, as proof-of-principle, demonstrated excellent performance over a range of glucose concentrations (0–73 mM), achieving a detection limit (LOD) of 2.8 mM for steady state photocurrent under oxygen-saturated conditions. This platform leverages light and 1 O 2 as stimuli for tunable, on-demand signal control, offering a novel approach for adaptive, real-time biosensing technologies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Sensitivity of Anthropogenic Cloud Droplet Number Change to Preindustrial Emission Inventories and Physics Parameterizations

Understanding the preindustrial (PI) to present-day (PD) change in cloud droplet number concentration (ΔNd) is important to constrain the anthropogenic influence on clouds and aid future model projections. Perturbed parameter ensemble simulations of PI and PD conditions in the Energy Exascale Earth System Model (E3SMv3) reveal two locations with consistent negative ΔNd signal across parameter space–the Southeastern US and the United Kingdom–despite a trend of positive ΔNd globally from increased fossil fuel consumption. These negative ΔNd signals are driven by higher anthropogenic biofuel emissions in the PI. By varying the PI aerosol mass and/or number emissions across these data sets' uncertainty ranges, we can change the magnitude and sign of ΔNd and the effective radiative forcing from aerosol-cloud interactions (ERFaci) regionally and globally, with near-zero ΔNd leading to near-zero ERFaci. These results highlight the need to constrain PI emission uncertainty to better understand Earth system responses to aerosol-cloud interactions.

Brown, Hunter Y. [University of Wyoming, Laramie, ↗

Enhancing traffic safety analysis with digital twin technology: integrating vehicle dynamics and environmental factors into microscopic traffic simulation

Traffic safety is a critical concern in transportation engineering and urban planning. Traditional traffic safety analysis requires trained observers to collect data in the field, which is time-consuming, labor-intensive, and sometimes inaccurate. In recent years, microscopic traffic simulation, which simulates individual vehicles’ movements within a transportation network, have been utilized to study traffic safety. However, microscopic traffic simulation only focuses on traffic-related factors, such as traffic volume, traffic signals, and lane configurations, neglecting vehicle dynamics and environment-related factors like weather and lighting conditions, which can significantly impact traffic safety. In light of this, this paper explores the application of digital twin technology in traffic safety analysis, integrating vehicle simulators, which consider vehicle dynamics and environmental factors, and microscopic traffic simulators, which simulate the operations of traffic flow, for enhanced safety evaluations. Various scenarios, including different weather conditions and visibility levels, are simulated using a digital twin of a road segment in Tuscaloosa, Alabama. The simulations employ Surrogate Safety Measures (SSMs) like Time to Collision (TTC) and Deceleration Rate to Avoid a Crash (DRAC) to assess safety under varying conditions. The results demonstrate that traffic digital twin can identify potential safety issues that traditional microscopic simulation cannot, providing insights for improving traffic control strategies and transportation infrastructure to enhance traffic safety.

Civil engineering↗

Carrier dynamics in blue, cyan, and green InGaN/GaN LEDs measured by small-signal electroluminescence

We study the carrier dynamics for c-plane InGaN/GaN light-emitting diodes (LEDs) with various emission wavelengths near the green gap using a small-signal electroluminescence method. The LEDs were grown by Lumileds using state-of-the-art growth conditions. Radiative and non-radiative recombination rates are numerically separated, and the carrier recombination lifetime and carrier density are obtained. Experiment shows that the causes of efficiency reduction at longer wavelength in the present structures are injection efficiency decrease, radiative recombination rate decrease, and imbalance of the increase in Auger–Meitner and radiative terms due to the interplay between the carrier–current density relationship and the quantum-confined Stark effect (QCSE). Here, the effects of QCSE, phase-space filling, and the carrier–current density relationship on efficiency reduction at longer wavelengths are examined separately with experimental data and Schrödinger–Poisson calculations. In addition, we confirm the scaling law between C(n) and B(n) under electrical injection and find that the increase in carrier density at a given current density is the primary cause for lower radiative efficiency at high current density in longer wavelength LEDs. Conversely, we do not observe a significant efficiency reduction at longer wavelengths from extrinsic material degradation.

42 ENGINEERING↗

Design and performance of parallel-channel nanocryotrons in magnetic fields

We introduce a design modification to conventional geometry of the cryogenic three-terminal switch, the nanocryotron (nTron). The conventional geometry of nTrons is modified by including parallel current-carrying channels, an approach aimed at enhancing the device's performance in magnetic field environments. The common challenge in nTron technology is to maintain efficient operation under varying magnetic field conditions. Here, we show that the adaptation of parallel channel configurations leads to an enhanced gate signal sensitivity, an increase in operational gain, and a reduction in the impact of superconducting vortices on nTron operation within magnetic fields up to 1 T. Contrary to traditional designs that are constrained by their effective channel width, the parallel nanowire channels permits larger nTron cross sections, further bolstering the device's magnetic field resilience while improving electro-thermal recovery times due to reduced local inductance. This advancement in nTron design not only augments its functionality in magnetic fields but also broadens its applicability in technological environments, offering a simple design alternative to existing nTron devices.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Constant Frequency ZVS PWM Converter

In this paper, a simple yet novel buck or boost adaptive zero-voltage switching (ZVS) converter topology is proposed for soft switching pulse-width modulation (PWM) dc / dc converters. The converter is designed for the high switching frequency that can achieve high efficiency by reducing switching losses for the entire load range at low and high power. Besides, the output at the load terminals is maintained by a PWM signal at a fixed switching frequency, a phase shift signal between converter ports (legs) controls the system circulating current in order to provide the ZVS condition in all load conditions. With the proposed controller, the converter, thus, is suitable for high switching frequency and high-power applications with the small volume. The proposed dc / dc converter operation is analyzed, designed, and confirmed by simulation results for 240 V input, 400 V / 5 A output, and 200 kHz operating frequency at full load.

Asa, Erdem↗

A temporal hierarchy underpins the transcription factor–DNA interactome of the maize UPR

Adverse environmental conditions reduce crop productivity and often increase the load of unfolded or misfolded proteins in the endoplasmic reticulum (ER). This potentially lethal condition, known as ER stress, is buffered by the unfolded protein response (UPR), a set of signaling pathways designed to either recover ER functionality or ignite programmed cell death. Despite the biological significance of the UPR to the life of the organism, the regulatory transcriptional landscape underpinning ER stress management is largely unmapped, especially in crops. To fill this significant knowledge gap, we performed a large–scale systems–level analysis of the protein–DNA interaction (PDI) network in maize (Zea mays). Using 23 promoter fragments of six UPR marker genes in a high–throughput enhanced yeast one–hybrid assay, we identified a highly interconnected network of 262 transcription factors (TFs) associated with significant biological traits and 831 PDIs underlying the UPR. We established a temporal hierarchy of TF binding to gene promoters within the same family as well as across different families of TFs. Cistrome analysis revealed the dynamic activities of a variety of cis–regulatory elements (CREs) in ER stress–responsive gene promoters. By integrating the cistrome results into a TF network analysis, we mapped a subnetwork of TFs associated with a CRE that may contribute to UPR management. Lastly, we validated the role of a predicted network hub gene using the Arabidopsis system. The PDIs, TF networks, and CREs identified in our work are foundational resources for understanding transcription–regulatory mechanisms in the stress responses and crop improvement.

59 BASIC BIOLOGICAL SCIENCES↗

Seismic Elastic Double-Beam Characterization of Faults and Fractures for CO₂ Storage Site Selection

Site characterization for underground injection and storage of gigatonne-scale CO₂ requires reliable and cost-effective methods to detect and characterize faults and fractures and to assess their stress state and fault activation potential. This is critical, as wastewater injection and disposal have been shown to activate faults and induce earthquakes, and CO₂ leakage remains a key concern for long-term storage. In this project, we developed seismic methods to detect and characterize large-scale sedimentary and crystalline basement faults and associated small-scale fractures below conventional seismic imaging resolution using multicomponent (9C) surface seismic data. Machine learning was used to automatically interpret large-scale faults, providing key information for estimating the maximum magnitude of potential induced earthquakes. High-fidelity imaging was achieved by exploiting redundancy across multiple elastic wave modes, where independent images from different modes and frequencies cross-validate each other. We also used our nonlinear signal comparison (NLSC) method for ground roll removal, improving data quality in complex near-surface conditions. The methods were validated using field data acquired in central Montana. Results show that basement faults extend into the sedimentary section and that small-scale fractures are widespread above the basement. The inferred stress orientation is consistent with regional stress data, and the estimated maximum induced earthquake magnitude is small (Mw ~2.3). The developed workflow provides a practical approach for fault and fracture characterization and for assessing induced seismicity and leakage risk. It is directly applicable to CO₂ storage site selection and to other subsurface systems.

02 PETROLEUM↗

Global decline in ocean memory over the 21st century

Ocean memory, the persistence of ocean conditions, is a major source of predictability in the climate system beyond weather time scales. We show that ocean memory, as measured by the year-to-year persistence of sea surface temperature anomalies, is projected to steadily decline in the coming decades over much of the globe. This global decline in ocean memory is predominantly driven by shoaling of the upper-ocean mixed layer depth in response to global surface warming, while thermodynamic and dynamic feedbacks can contribute substantially regionally. As the mixed layer depth shoals, stochastic forcing becomes more effective in driving sea surface temperature anomalies, increasing high-frequency noise at the expense of persistent signals. Reduced ocean memory results in shorter lead times of skillful persistence-based predictions of sea surface thermal conditions, which may present previously unknown challenges for predicting climate extremes and managing marine biological resources under climate change.

54 ENVIRONMENTAL SCIENCES↗

Two-color, intracavity pump–probe, cavity ringdown spectroscopy

Here, we report a proof-of-principle demonstration of intracavity pump–probe, cavity ringdown (CRD) detection in a three-mirror, traveling-wave cavity. With cavity-enhanced pump power and probe absorption path length, the technique is a generally applicable, high-sensitivity, high-selectivity detection method. In our experiments, the pump radiation is switched off during every other probe ringdown, which allows uncorrelated measurements of analyte and background cavity decay rates. The net, two-color signal from the difference between the pump-on and pump-off decay rates is immune to empty-CRD drifts and spectral overlaps from non-target molecular transitions. The immunity to the ringdown drifts allows longer signal-averaging and, thus, higher detection sensitivity. The ability to compensate for the background absorption enhances the detection selectivity in spectrally congested regions. Our technique is well-suited for trace-detection in the mid-IR region, where pump–probe schemes based on strong rovibrational transitions can be applied. In this work, two-color CRD detection is implemented on a ladder-type, three-level system based on the N 2 O, ν 3 = 1 ← 0, P(19) (pump) and ν 3 = 2 ← 1, R(18) (probe), rovibrational transitions. By frequency-locking two-quantum cascade lasers to the p-polarization (pump, Finesse = 5280) and s-polarization (probe, Finesse = 67 700) cavity modes, we achieve high intracavity pump power (36 W) and high probe ringdown rates (>2 kHz). The observed two-color spectra are simulated by a density-matrix, three-level system model that is solved under the constraints of the cavity resonance conditions. In addition to its background compensation capability, experimental flexibility in the selection of pump–probe schemes and signal insensitivity to intracavity laser power are further features that enhance the utility of our technique for mid-IR trace-detection.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Atmospheric effects on the laser-driven avalanche-based remote detection of radiation

Here, the effect of realistic atmospheric conditions on mid-IR (λ = 3.9 µm) and long-wave-IR (λ = 10 µm) laser-induced avalanche breakdown for the remote detection of radioactive material is examined experimentally and with propagation simulations. Our short-range in-lab mid-IR laser experiments show a correlation between increasing turbulence level and a reduced number of breakdown sites associated with a reduction in the portion of the focal volume above the breakdown threshold. Simulations of propagation through turbulence are in excellent agreement with these measurements and provide code validation. We then simulate propagation through realistic atmospheric turbulence over a long range (0.1–1 km) in the long-wave-IR regime (λ = 10 µm). The avalanche threshold focal volume is found to be robust even in the presence of strong turbulence, only dropping by ~50% over a propagation length of ~0.6 km. We also experimentally assess the impact of aerosols on avalanche-based detection, finding that, while background counts increase, a useful signal is extractable even at aerosol concentrations 10 5 times greater than what is typically observed in atmospheric conditions. Our results show promise for the long-range detection of radioactive sources under realistic atmospheric conditions.

54 ENVIRONMENTAL SCIENCES↗

Seismoacoustic Analysis of the Large Surface Explosion Coupling Experiment Using a Large- N Seismic Array

Seismoacoustic signals at local distance (<~10 km) are widely used as important constraints on source parameters for near-surface events, yet the seismoacoustic wave generation and energy partitioning are not fully understood. Spatially dense sensors could provide observations in high resolution to capture the full wavefield for better understanding wave propagation and improving source estimation. Recently, spatially dense observations of the local seismoacoustic wavefield produced by a pair of 1-ton surface explosions have been recorded using a large-N seismic array. This large-N array consists of 446 geophones and covers an area of approximately 2×2.5 km 2 . The two surface explosions occur at the same location but at different times with different atmospheric conditions. Both seismic and air–ground coupled acoustic waves from the two surface explosions are well observed. Analyses of signals recorded by the large-N seismic array show different acoustic wave speed and amplitude for the two explosions. A strong spatial variability in acoustic wave speed and amplitude for each explosion is also observed. Finally, the observations suggest the important role of local atmosphere state on wave propagation and source estimation and demonstrate how the use of a large-N capability can improve characterization of the propagation medium and source.

58 GEOSCIENCES↗

Highly cascaded first-order fiber Bragg gratings in highly multimode optical fibers for distributed temperature sensing under harsh environment conditions

This study presents a pioneering technique for fabricating highly cascaded first-order fiber Bragg gratings (FBGs) using a femtosecond laser-assisted point-by-point inscription method in highly multimode optical fibers, specifically Sapphire crystalline fiber, and pure silica coreless fiber. Notably, it marks the first successful demonstration of a distributed array comprising 10 FBGs within highly multimode fibers. This achievement is facilitated by a high-power laser technique that yields larger reflectors characterized by a Gaussian intensity profile. These first-order FBGs offer various advantages, including enhanced reflectivity, reduced fabrication time, and simplified spectral characteristics, enhancing their accessibility for interpretation when contrasted with higher-order FBGs. In addition to that it encompasses a comprehensive analysis of the robustness and efficacy of these FBGs, with particular emphasis on their ability to endure extreme temperatures. These FBGs demonstrate an advantageous capability for localized multi-point temperature monitoring, reaching temperatures up to 1500°C with sapphire crystalline fiber and 1100°C with pure silica coreless fiber. This resilience makes them suitable for deployment in harsh environmental conditions. This innovative approach substantially broadens the potential applications of highly multimode optical fibers, particularly in the arena of sensing and communication, where challenges related to thermal gradients and harsh environments prevail. Furthermore, these groundbreaking first-order FBGs signify a substantial advancement in the realm of distributed temperature sensing, offering supreme capabilities for temperature monitoring and signal stability. As such, our work holds the promise of a substantial impact on industries and applications that demand unwavering reliability under extreme conditions.

47 OTHER INSTRUMENTATION↗

Signal amplification in a solid-state sensor through asymmetric many-body echo

Electronic spins of nitrogen–vacancy centres in diamond constitute a promising system for micro- and nanoscale magnetic sensing, because of their operation under ambient conditions, ease of placement in close proximity to sensing targets and biological compatibility. At high densities, the electronic spins interact through dipolar coupling, which typically limits but can also potentially enhance sensing performance. Here we report the experimental demonstration of many-body signal amplification in a solid-state, room-temperature quantum sensor. Our approach uses time-reversed two-axis-twisting interactions, engineered through dynamical control of the quantization axis and Floquet engineering in a two-dimensional ensemble of nitrogen–vacancy centres. We observe that optimal amplification occurs when the backward evolution time equals twice the forward evolution time, in sharp contrast to the conventional Loschmidt echo. These observations can be understood as resulting from an underlying time-reversed mirror symmetry of the microscopic dynamics, providing key insights into signal amplification and opportunities for practical entanglement-enhanced quantum sensing.

quantum information↗

Genetic encoding of 3–nitro–tyrosine reveals the impacts of 14–3–3 nitration on client binding and dephosphorylation

14–3–3 proteins are central hub regulators of hundreds of phosphorylated “client” proteins. They are subject to over 60 post–translational modifications (PTMs), yet little is known how these PTMs alter 14–3–3 function and its ability to regulate downstream signaling pathways. An often neglected, but well–documented 14–3–3 PTM found under physiological and immune–stimulatory conditions is the conversion of tyrosine to 3–nitro–tyrosine at several Tyr sites, two of which are located at sites considered important for 14–3–3 function: Y130 (β–isoform numbering) is located in the primary phospho–client peptide–binding groove, while Y213 is found on a secondary binding site that engages with clients for full 14–3–3/client complex formation and client regulation. By genetically encoding 3–nitro–tyrosine, we sought to understand if nitration at Y130 and Y213 effectively modulated 14–3–3 structure, function, and client complexation. The 1.5 Å resolution crystal structure of 14–3–3 nitrated at Y130 showed the nitro group altered the conformation of key residues in the primary binding site, while functional studies confirmed client proteins failed to bind this variant of 14–3–3. But, in contrast to other client–binding deficient variants, it did not localize to the nucleus. Further, the 1.9 Å resolution structure of 14–3–3 nitrated at Y213 revealed unusual flexibility of its C–terminal α–helix resulting in domain swapping, suggesting additional structural plasticity though its relevance is not clear as this nitrated form retained its ability to bind clients. Collectively, our data suggest that nitration of 14–3–3 will alter downstream signaling systems, and if uncontrolled could result in global dysregulation of the 14–3–3 interactome.

14-3-3↗