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At least 343 records · Page 19

Human cytochrome P450 17A1 structures with metabolites of prostate cancer drug abiraterone reveal substrate-binding plasticity and a second binding site

Abiraterone acetate is a first-line therapy for castration-resistant prostate cancer. This prodrug is deacetylated in vivo to abiraterone, which is a potent and specific inhibitor of cytochrome P450 17A1 (CYP17A1). CYP17A1 performs two sequential steps that are required for the biosynthesis of androgens that drive prostate cancer proliferation, analogous to estrogens in breast cancer. Abiraterone can be further metabolized in vivo on the steroid A ring to multiple metabolites that also inhibit CYP17A1. Despite its design as an active-site-directed substrate analog, abiraterone and its metabolites demonstrate mixed competitive/noncompetitive inhibition. To understand their binding, we solved the X-ray structures of CYP17A1 with three primary abiraterone metabolites. Despite different conformations of the steroid A ring and substituents, all three bound in the CYP17A1 active site with the steroid core packed against the I helix and the A ring C3 keto or hydroxyl oxygen forming a hydrogen bond with N202 similar to abiraterone itself. The structure of CYP17A1 with 3-keto, 5α-abiraterone was solved to 2.0 Å, the highest resolution to date for a CYP17A1 complex. This structure had additional electron density near the F/G loop, which is likely a second molecule of the inhibitor and which may explain the noncompetitive inhibition. Mutation of the adjacent Asn52 to Tyr positions its side chain in this space, maintains enzyme activity, and prevents binding of the peripheral ligand. Collectively, our findings provide further insight into abiraterone metabolite binding and CYP17A1 function.

59 BASIC BIOLOGICAL SCIENCES↗

Metabolism of Syringyl Lignin-Derived Compounds in Pseudomonas putida Enables Convergent Production of 2-Pyrone-4,6-Dicarboxylic Acid

Valorization of lignin, an abundant component of plant cell walls, is critical to enabling the lignocellulosic bioeconomy. Biological funneling using microbial biocatalysts has emerged as an attractive approach to convert complex mixtures of lignin depolymerization products to value-added compounds. Ideally, biocatalysts would convert aromatic compounds derived from the three canonical types of lignin: syringyl (S), guaiacyl (G), and p-hydroxyphenyl (H). Pseudomonas putida KT2440 (hereafter KT2440) has been developed as a biocatalyst owing in part to its native catabolic capabilities but is not known to catabolize S-type lignin-derived compounds. Here, we demonstrate that syringate, a common S-type lignin-derived compound, is utilized by KT2440 only in the presence of another energy source or when vanAB was overexpressed, as syringate was found to be O-demethylated to gallate by VanAB, a two-component monooxygenase, and further catabolized via extradiol cleavage. Unexpectedly, the specificity (kcat/KM) of VanAB for syringate was within 25% that for vanillate and O-demethylation of both substrates was well-coupled to O2 consumption. However, the native KT2440 gallate-cleaving dioxygenase, GalA, was potently inactivated by 3-O-methylgallate. To engineer a biocatalyst to simultaneously convert S-, G-, and H-type monomers, we therefore employed VanAB from Pseudomonas sp. HR199, which has lower activity for 3MGA, and LigAB, an extradiol dioxygenase able to cleave protocatechuate and 3-O-methylgallate. This strain converted 93% of a mixture of lignin monomers to 2-pyrone-4,6-dicarboxylate, a promising bio-based chemical. Overall, this study elucidates a native pathway in KT2440 for catabolizing S-type lignin-derived compounds and demonstrates the potential of this robust chassis for lignin valorization.

2-pyrone-4,6-dicarboxylic acid↗

Towards chloroplastic nanofactories: formation of proteinaceous scaffolds for metabolic engineering

The evolution of eukaryotic lipid-bound organelles allows for specialized metabolism to occur within spatially distinct metabolic landscapes within the same cell. However, this strategy of compartmentalization is not unique to eukaryotic organisms. Many bacteria, spread across 45 different phyla, contain loci that encode for specialized bacterial microcompartments (BMCs) (Sutter et al., 2021). The formation of a BMC involves self-assembly from three families of shell proteins to form the outer shell membrane, in addition to the encapsulation of an enzymatic core packaged within the lumen of a BMC (Kerfeld et al., 2018). These proteinaceous organelles provide a competitive growth advantage by enabling organisms to process inaccessible substrates by sequestering metabolic intermediates (i.e. aldehydes) that would otherwise be toxic within the cytoplasm. While BMCs perform specific metabolic functions in their native organism, synthetic, empty BMC shells can form without the requirement of native cargo inside (Doron and Kerfeld, 2024). This provides a transferable and tunable platform of protein scaffolding for guiding metabolic engineering within a host organism of choice (Raba and Kerfeld, 2022).

59 BASIC BIOLOGICAL SCIENCES↗

Diffusion-assisted molecular beam epitaxy of CuCrO 2 thin films

Using molecular beam epitaxy (MBE) to grow multielemental oxides (MEOs) is generally challenging, partly due to difficulty in stoichiometry control. Occasionally, if one of the elements is volatile at the growth temperature, stoichiometry control can be greatly simplified using adsorption-controlled growth mode. Otherwise, stoichiometry control remains one of the main hurdles to achieving high-quality MEO film growths. Here, in this paper, we report another kind of self-limited growth mode, dubbed diffusion-assisted epitaxy, in which excess species diffuses into the substrate and leads to the desired stoichiometry, in a manner similar to the conventional adsorption-controlled epitaxy. Specifically, we demonstrate that using diffusion-assisted epitaxy, high-quality epitaxial CuCrO 2 films can be grown over a wide growth window without precise flux control using MBE.

36 MATERIALS SCIENCE↗

Design of a Nanophotonic Hybrid Coupler

This project aims to design and simulate a nanophotonic hybrid coupler for detecting vacuum ultraviolet (VUV) light with higher efficiency. VUV light is of significant interest because of its applications ranging from high energy physics to space science and electronic industry. However, current VUV photodetectors have very low efficiencies because most materials absorb in the VUV region (100-200 nm). To address this challenge, I have designed a plasmonic-dielectric coupler with wavelength shifting properties, enabling high Purcell enhancement and far-field confinement. The coupler consists of a cylindrical cSi resonator on top of a thin ZnO layer, and Ag and SiO2 are used as substrates. Simulations are done using the finite-difference time domain method to solve Maxwell’s equations, and specifically with Meep and Lumerical. The effectiveness of the coupler is characterized by the Purcell factor and far-field radiation. The Purcell factor reaches a maximum near 390 nm and is in the o rder of 10^4. Furthermore, the coupler also allows partial control of the directionality of the far-field radiation. With the presence of the resonator, the radiation is directed towards the coupled metalens. Overall, our design combines the advantages of plasmonic and dielectric couplers, along with the intrinsic wavelength shifting properties of materials to enhance VUV detection significantly, and such a device can be used in, for example, the DUNE project.

Zhou, Jiayang↗

PIE-Enabled Study of Aqueous Corrosion & Zr Hydriding in Cr-Coated Cladding: M3GV-23PN0101132

Chromium-coated zirconium alloy cladding is under investigation as an accident-tolerant fuel (ATF) concept to extend performance to higher burnups via improved oxidation resistance and reduced hydrogen pickup. However, hydrothermal corrosion behavior and hydrogen transport mechanisms governing in-service hydriding of these coatings remain poorly understood. In a collaborative study between Pacific Northwest National Laboratory (PNNL), Idaho National Laboratory (INL), and the University of Huddersfield, cold spray (CS) and physical vapor deposition (PVD) Cr-coated Optimized ZIRLO™ cladding samples were characterized after exposure to PWR-simulated water chemistry under both in-core (neutron irradiation) and out-of-core (aqueous-only) conditions at the MIT Research Reactor. Multi-scale characterization was performed independently at PNNL and INL to evaluate coating integrity, microstructural evolution, Cr/Zr interface chemistry, and hydride formation. Both laboratories observed a consistent divergence in hydriding behavior: out-of-core CS Cr-coated cladding exhibited elevated hydride concentrations exceeding those of uncoated cladding, whereas in-core CS samples showed substantially suppressed hydriding. In-core specimens also displayed irradiation-specific features, including nanoscale voids within the Cr coating and radiation-induced segregation clusters in the Zr substrate. CS coatings retained an interdiffusion-free Cr/Zr bond with no intermetallic layer, whereas PVD coatings exhibited inferior quality with visible cracks and pores. An automated image-based hydride quantification method systematically overestimated bulk hydrogen content relative to inert gas fusion measurements, underscoring the need for standardized sample preparation and reference standards. Interpretation of hydride nucleation and growth is complicated by the open inner-diameter of the specimens, which provides additional hydrogen pathways. The results motivate further foundational studies to support predictive models of hydrothermal corrosion and hydrogen transport in unirradiated and irradiated Cr-coated cladding.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗

Enhancing Coherence Limits in Superconducting Quantum Systems for Computing and Sensing

This talk will highlight recent efforts at the SQMS Center to develop qudit-based quantum computing architectures using superconducting three-dimensional (3D) cavities, as well as the use of these ultra-coherent cavities for quantum sensing. I will present systematic studies of materials and devices aimed at identifying and mitigating the dominant sources of decoherence—including two-level systems (TLS), quasiparticles, and other noise mechanisms—in both transmons and 3D cavities. These investigations include microwave loss characterization of niobium, tantalum, aluminum, their native oxides, and substrate materials such as silicon and sapphire. By combining measurements on qubits and cavities, we disentangle subsystem-specific loss mechanisms and establish a hierarchy of mitigation strategies, leading to transmon coherence times exceeding one millisecond. I will also discuss studies of quasiparticle dynamics, including quasiparticle bursts observed in qubits operated both above ground and at the Gran Sasso underground laboratory, and the observation that applied magnetic fields can suppress temporal T₁ fluctuations. Building on these advances, we demonstrate a record-coherence two-cell cavity-qudit system with coherence times exceeding 20 milliseconds. Leveraging tunable sideband interactions together with error-resilient protocols, including measurement-based error correction and post-selection, we achieve high-fidelity quantum state control, including the preparation of Fock states up to N=20 with fidelities above 95% and the generation of high-fidelity two-mode entangled states. Finally, I will discuss how these ultra-coherent quantum systems are enabling emerging quantum sensing applications, including searches for dark matter and gravitational waves.

Roy, Tanay [Fermilab] (ORCID:000000019442862X)↗

System and method for high power diode based additive manufacturing

The present disclosure relates to a system for performing an Additive Manufacturing (AM) fabrication process on a powdered material (PM) forming a substrate. The system uses a first optical subsystem to generate an optical signal comprised of electromagnetic (EM) radiation sufficient to melt or sinter a PM of the substrate. The first optical subsystem is controlled to generate a plurality of different power density levels, with a specific one being selected based on a specific PM forming a powder bed being used to form a 3D part. At least one processor controls the first optical subsystem and adjusts a power density level of the optical signal, taking into account a composition of the PM. A second optical subsystem receives the optical signal from the first optical subsystem and controls the optical signal to help facilitate melting of the PM in a layer-by-layer sequence of operations.

El-Dasher, Bassem S.↗

Elastomeric reflection suppressor

Various embodiments of the present technology generally relate to reflection suppressors. More specifically, some embodiments use elastomeric materials doped with optical absorbers for temporary suppression of Fresnel reflections for multiple substrates spanning wide spectral and angular bandwidth. The refractive index of the elastomer can be tuned to match a substrate and thereby minimize reflection. Some embodiments can use the addition of different absorptive dopants to allow for either broadband or wavelength-selective reflection suppression. As performance is limited only by index mismatch, both spectral and angular performance significantly exceed that of anti-reflection coatings. After use, these light traps may be removed and reused without damaging the substrate. These films have uses in spectroscopic ellipsometry, holography, and lithography.

Miller, David↗

Spatial Study 2021: Sensor-Based Time Series of Surface Water Temperature, Specific Conductance, Total Dissolved Solids, pH, and Dissolved Oxygen from across Multiple Watersheds in the Yakima River Basin, Washington, USA (v3)

This dataset supports a broader study examining the drivers of spatial variability in sediment respiration rates in the Yakima River Basin. The dataset provides two-hour time series hydrological and water chemistry sensor data, manual chamber open channel respiration data, handheld sensor water chemistry data, river substrate grain size photos, general environmental context photos, and field metadata (including qualitative information on instream and river corridor characteristics) collected during the same two-week period at 47 sites within multiple rivers throughout the Yakima River Basin in Washington, USA. Grain size photos can be used to improve estimates of channel substrate D50 data. Related sample-based water chemistry data are published separately at https://data.ess-dive.lbl.gov/datasets/doi:10.15485/1898914.This dataset is comprised of four main folders, one containing three sensor-specific subfolders and the others containing photographs. The SFA_SpatialStudy_2021_SensorData main data folder includes file-level metadata (FLMD), data dictionary (dd), installation methods, field metadata, Ultrameter water chemistry data, field data collection protocols, international generic sample number (IGSN) mapping file, and a readme file. The “Sensor_Manual_Specifications” subfolder contains pdf files from the manufacturer of each sensor with details on the sensor specifications. Each sensor subfolder (BarotrollAtm, MantaRiver, and MinidotManualChamber) contains a sensor data subfolder for timeseries data and a subfolder for plots and summary statistics. The BarotrollAtm Data subfolder contains In Situ Rugged BaroTROLL pressure and temperature data. The MantaRiver Data subfolder contains Eureka Manta+ 35B multisonde temperature, specific conductance, and pH data. The MinidotManualChamber Data subfolder contains PME MiniDOT Logger dissolved oxygen (mg/L and percent saturation) and temperature data. The folder SFA_SpatialStudy_2021_EnvironmentalContextPhotos contains environmental context photographs and videos. The folders SFA_SpatialStudy_2021_SedimentQuadratPhotos_Part1 and SFA_SpatialStudy_2021_SedimentQuadratPhotos_Part2 contain sediment quadrat photographs. All files are .csv, .pdf, .R, .jpg, .jpeg, .mp4, or .mov. This data package was originally published September 2022. It was updated January 2023 (modified files) and June 2024 (new and modified files). See the change history in data package readme for more details.We acknowledge the Yakama Nation as owners and caretakers of the lands where we collected these data. We thank the Confederated Tribes and Bands of the Yakama Nation Tribal Council and Yakama Nation Fisheries for working with us to facilitate sample collection and optimization of data usage according to their values and worldview.

54 ENVIRONMENTAL SCIENCES↗

Dual-Responsive Turn-On T 1 Imaging-Guided Mild Photothermia for Precise Apoptotic Cancer Therapy

Apoptosis has gained increasing attention in cancer therapy as an intrinsic signaling pathway, which leads to minimal leakage of waste products from a dying cell to neighboring normal cells. Among various stimuli to trigger apoptosis, mild hyperthermia is attractive but confronts limitations of non-specific heating and acquired resistance from elevated expression of heat shock proteins. Here, a dual-stimulation activated turn-on T 1 imaging-based nanoparticulate system (DAS) is developed for mild photothermia (≈43 °C)-mediated precise apoptotic cancer therapy. In the DAS, a superparamagnetic quencher (ferroferric oxide nanoparticles, Fe 3 O 4 NPs) and a paramagnetic enhancer (Gd-DOTA complexes) are connected via the N6-methyladenine (m 6 A)-caged, Zn 2+ -dependent DNAzyme molecular device. The substrate strand of the DNAzyme contains one segment of Gd-DOTA complex-labeled sequence and another one of HSP70 antisense oligonucleotide. When the DAS is taken up by cancer cells, overexpressed fat mass and obesity-associated protein (FTO) specifically demethylates the m 6</-sup>A group, thereby activating DNAzymes to cleave the substrate strand and simultaneously releasing Gd-DOTA complex-labeled oligonucleotides. The restored T 1 signal from the liberated Gd-DOTA complexes lights up the tumor to guide the location and time of deploying 808 nm laser irradiation. Afterward, locally generated mild photothermia works in concert with HSP70 antisense oligonucleotides to promote apoptosis of tumor cells. This highly integrated design provides an alternative strategy for mild hyperthermia-mediated precise apoptotic cancer therapy.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Strain-Mediated Sn Incorporation and Segregation in Compositionally Graded Ge 1– x Sn x Epilayers Grown by MBE at Different Temperatures

We investigated the process of Sn incorporation and surface segregation for compositionally graded Ge 1–x Sn x epilayers grown on high-quality Ge (001) substrates. Here, the growth resulted in pseudomorphic GeSn layers with a ~6% maximal Sn fraction at a constant substrate temperature. The maximal fraction of Sn was increased to 9.0% when the growth temperature was continuously lowered while increasing the Sn flux. The analysis of surface droplets and SIMS profiles of elemental composition give evidence of Sn rejection during the growth, potentially associated with a critical energy of elastic strain. The intentional reduction of the coherent strain by decreasing the Sn flux near the sample surface has been shown to trap a higher fraction of Sn in the Ge 1–x Sn x layer and lower surface segregation. Our results demonstrate that strain relief by misfit dislocations in the compositionally graded layer is inhibited, which leads to Sn segregation. Specifically, the compressive strain in the graded Ge 1–x Sn x epilayer is effectively “zero” near the interface with the Ge substrate and increases up to about –1.5 × 10 –2 near the surface. Thus, although the nucleation of a dislocation may reduce the compressive strain for the top region of the epilayer, it is not beneficial for the bottom region.

42 ENGINEERING↗

Coupling to short linear motifs creates versatile PME-1 activities in PP2A holoenzyme demethylation and inhibition

Protein phosphatase 2A (PP2A) holoenzymes target broad substrates by recognizing short motifs via regulatory subunits. PP2A methylesterase 1 (PME-1) is a cancer-promoting enzyme and undergoes methylesterase activation upon binding to the PP2A core enzyme. Here, we showed that PME-1 readily demethylates different families of PP2A holoenzymes and blocks substrate recognition in vitro. The high-resolution cryoelectron microscopy structure of a PP2A-B56 holoenzyme–PME-1 complex reveals that PME-1 disordered regions, including a substrate-mimicking motif, tether to the B56 regulatory subunit at remote sites. They occupy the holoenzyme substrate-binding groove and allow large structural shifts in both holoenzyme and PME-1 to enable multipartite contacts at structured cores to activate the methylesterase. B56 interface mutations selectively block PME-1 activity toward PP2A-B56 holoenzymes and affect the methylation of a fraction of total cellular PP2A. The B56 interface mutations allow us to uncover B56-specific PME-1 functions in p53 signaling. Our studies reveal multiple mechanisms of PME-1 in suppressing holoenzyme functions and versatile PME-1 activities derived from coupling substrate-mimicking motifs to dynamic structured cores.

59 BASIC BIOLOGICAL SCIENCES↗

Protective effects of non–catalytic proteins on endoglucanase activity at air and lignin interfaces

The manner in which added non-catalytic proteins during enzymatic hydrolysis of lignocellulosic substrates enhances hydrolysis mechanisms is not completely understood. Prior research has indicated that a reduction in the non-specific adsorption of enzymes on lignin, and deactivation of enzymes exposed to air–liquid interface provide rationale. This work investigated root causes including effects of the air–liquid interface on non-catalytic proteins, and effects of lignin on endoglucanase. Three different experimental designs and three variables (air–liquid interfacial area, the types of lignin (acid or enzymatic lignin), and the presence of non-enzymatic protein (bovine serum albumin [BSA] or soy proteins ) were used. The results showed that acid isolated lignin adsorbed almost all endoglucanase activity initially present in supernatant, independent of air interface conditions (25 or 250 ml flasks) with the presence of BSA preventing this effect. Endoglucanase lost 30%–50% of its activity due to an air–liquid interface in the presence of lignin while addition of non-enzymatic protein helped to preserve this enzyme's activity. Langmuir and Freundlich models applied to experimental data indicated that the adsorption increases with increasing temperature for both endoglucanase and BSA. Adsorption of the enzyme and protein were endothermic with an increase in entropy. Finally, these results, combined, show that hydrophobicity plays a strong role in the adsorption of both endoglucanase and BSA on lignin.

59 BASIC BIOLOGICAL SCIENCES↗

In situ oxidation of reduced graphene oxide membranes by peracetic acid for dye desalination

Graphene oxide (GO) membranes with tunable interlayer spacings are of interest for dye removal from salty textile wastewater, and the membranes are often reduced to improve their stability, which inevitably lowers water permeance. Herein, we demonstrate that reduced GO (rGO) membranes can be facilely modified using peracetic acid (PAA) in situ to dramatically enhance water permeance while retaining dye rejection. Specifically, PAA-modified membranes (PrGO) are synthesized by vacuum-filtering hydrazine-reduced rGO nanosheets onto Nylon substrate and then exposing them to PAA solutions. The effects of the rGO layer thickness, PAA content, and PAA exposure time on the membrane chemistry, nanostructures, and salt/dye separation properties are thoroughly examined. For example, the PAA oxidation of a 100 nm-thick rGO membrane for 10 min increases water permeance by 180 %, from 35 to 93 Liter m −2 h −1 bar −1 , and decreases Na 2 SO 4 rejection from 10 % to 3.3 % while retaining the rejection of Congo red at ≈99.7 %. The PrGO membranes exhibit stable water permeance and >99 % dye rejection in multi-cycle tests in a crossflow system, surpassing state-of-the-art GO membranes and showcasing their potential for practical applications.

Dye desalination↗

Using Novosphingobium aromaticivorans for Concurrent Production of Intracellular and Extracellular Products from Aromatics Extracted from Poplar Biomass

Achieving high biochemical production in biotransformations of renewable resources requires using concentrated cultures that not only generate the product of interest but also produce abundant microbial cell waste. We explored the concept of gaining value from microbial cells by producing intracellular products in tandem with a desired extracellular product. Specifically, we engineered a strain ofNovosphingobium aromaticivorans to extracellularly produce 2-pyrone-4,6-dicarboxylic acid (PDC) from aromatic substrates and to intracellularly accumulate astaxanthin along with coenzyme Q 10 , all of which are products of industrial interest. Achieving the goal of concurrent production of intracellular and extracellular products required the creative application of bioreactor engineering principles. Although a continuously fed membrane bioreactor (MBR) maximized extracellular product biosynthesis, it had a negative effect on intracellular product accumulation. However, operating the MBR as a sequencing batch reactor (MBR-SBR) with a step-feed resulted in stable concurrent production of both extracellular and intracellular products. With aromatics extracted from poplar biomass, we achieved productivities of 1.14 g of PDC/L-h for the extracellular product and 0.04 mg of astaxanthin/L-h and 0.64 mg of CoQ 10 /L-h for intracellular products, respectively. Our findings demonstrate that the mode of operation of a bioreactor impacts the simultaneous production of intracellular and extracellular products byN. aromaticivorans.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Oriented Electrostatic Effects on O 2 and CO 2 Reduction by a Polycationic Iron Porphyrin

Next-generation energy technologies require improved methods for rapid and efficient chemical-to-electrical energy transformations. One new approach has been to include atomically-positioned, electrostatic motifs in molecular catalysts to stabilize high-energy, charged intermediates. For example, an iron porphyrin bearing four cationic, ortho-N,N,N-trimethylanilinium groups (o-[N(CH 3 ) 3 ] + ) has recently been used to catalyze the complex, multi-step O 2 and CO 2 reduction reactions (ORR and CO 2 RR) with fast rates and at low overpotentials. The success of this catalyst is attributed, at least in part, to specific charge-charge interactions between the atomically-positioned o-[N(CH 3 ) 3 ] + groups and the bound substrate. However, by nature of the mono-ortho substitution pattern, there are four possible atropisomers of this metalloporphyrin and thus four unique electrostatic environments. This work reports that each of the four individual atropisomers catalyzes both the ORR and CO 2 RR with fast rates and low overpotentials. The maximum turnover frequencies (TOF max ) vary among the atropisomers, by a factor of 60 for the ORR and a factor of 5 for CO 2 RR. For the ORR, the αβαβ isomer is the fastest and has the highest overpotential, while for the CO 2 RR, the order is reversed and the αααα isomer is the fastest and has the highest overpotential. The role of charge-positioning is complex and can affect more than a single step such as CO 2 binding. These data offer a first-of-a-kind perspective on atomically positioned charge and highlight the significance of high charge density, rather than orientation, on the thermodynamics and kinetics of multistep molecular electrochemical transformations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗