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At least 541 records · Page 30

Comparative genomics provides insights into the cold adaptation of endophytic fungi associated with Deschampsia antarctica

Endophytic fungi from Deschampsia antarctica , the southernmost flowering plant, provide insights into the cold adaptation mechanisms of plant-associated fungi in extreme environments. This study presents the genome sequences and comparative analysis of eight fungal isolates from D. antarctica leaves. These Antarctic fungal isolates were analyzed alongside 121 plant-associated fungal genomes to uncover signatures of adaptation and endophytic specialization. Antarctic endophytes show striking patterns, including reduced genome size (∼26.3 Mb on average), streamlined gene content (∼8844 genes), and notably small secretomes (∼288 proteins). Despite this reduced gene repertoire, they maintain a robust set of genes encoding carbohydrate-active enzymes (CAZymes) but lack those for lignin and bacterial cell wall degradation, indicating a symbiotic lifestyle that avoids host damage and predation. One isolate, Alternaria sp. UNIPAMPA017 stood out, with 26% of its genome occupied by transposable elements. Lifestyle, rather than phylogeny, was the main driver of CAZyme and secretome profiles, underscoring ecological convergence. Compared to endophytes from Arabidopsis and Populus, D. antarctica endophytes harbor fewer pectin-degrading enzymes, reflecting their adaptation to the cell wall structure of their monocot host. Together, these fungi reveal a pattern of genomic reduction and functional fine-tuning, hallmarks of life adapted to persist in cold, nutrient-scarce niches.

Ascomycota↗

Single-ion hydration thermodynamics from clusters to bulk solutions: Recent insights from molecular modeling

The importance of single-ion hydration thermodynamic properties for understanding the driving forces of aqueous electrolyte processes, along with the impossibility of their direct experimental measurement, have prompted a large number of experimental, theoretical, and computational studies aimed at separating the cation and anion contributions. Here we provide an overview of historical approaches based on extrathermodynamic assumptions and more recent computational studies of single-ion hydration in order to evaluate the approximations involved in these methods, quantify their accuracy, reliability, and limitations in the light of the latest developments. Finally, we also offer new insights into the factors that influence the accuracy of ion–water interaction models and our views on possible ways to fill this substantial knowledge gap in aqueous physical chemistry.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Chickpea protein hydrolysate as a novel plant-based cryoprotectant in frozen surimi: Insights into protein structure integrity and gelling behaviors

Chickpea protein (CP) and its enzymatic hydrolysates are one of the most widely consumed pulse ingredients manifesting versatile applications in food industry, such as binders, emulsifiers, and meat protein substitutes. Other than those well-known functionalities, however, the use of CP as a cryoprotectant remained unexplored. Here, in this study, we prepared the chickpea protein hydrolysate (CPH) and investigated its cryoprotective effects to frozen surimi in terms of the protein structure integrity and gelling behaviors. Results indicated that CPH could inhibit myofibrillar protein (MP) denaturation and oxidation during the freeze–thaw cycling, as evidenced by their increased solubility, Ca 2+ -ATPase activity, sulfhydryl concentration, and declined content of disulfide bonds, carbonyl concentration and surface hydrophobicity. Freezing-induced changes on MP secondary structures were also retarded. Moreover, gels prepared from CPH-protected frozen surimi demonstrated more stabilized microstructure, uniform water distribution, enhanced elasticity, gel strength and water holding capacity. The CPH alone, at a reducing addition content of 4% (w/w), exhibited comparable cryoprotective performance to that of the commercial formulation (4% sucrose and 4% sorbitol). Therefore, this study provides scientific insights for development of pulse proteins as novel and high-performance food cryoprotectants.

59 BASIC BIOLOGICAL SCIENCES↗

A deep insight on the coal ash-to-slag transformation behavior during the entrained flow gasification process

Recent research provided deep insight on the coal ash-to-slag transformation characterization during the entrained flow gasification process, with experimentation on a 40 kg/hr (dry basis) coal-fed opposed multi-burner (OMB) entrained flow gasifier and simulation via FactSage™ software. A general mechanism is presented to relate the gasifier design temperature, ash fluid temperature, and operating temperature with the degree of the slag polymerization. The change of the high temperature zone, the corresponding particle residence time in the high temperature zone, and syngas composition have obvious effects on the slag mineral transformation behavior. Mineral types formed on the wall of the gasifier chamber were mainly anorthite (CaAl 2 Si 2 O 8 ), aluminum oxide (Al 2 O 3 ), and calcium sulfide (CaS). These minerals transformed to anorthite and diopside (CaMgSi 2 O 6 ) at the slag hole zone, while the minerals at the lock hopper were anorthite, orthoclase (KAlSi 3 O 8 ), quartz (SiO 2 ), gypsum (CaSO 4 ), calcite (CaCO 3 ), and halite (NaCl). FactSage™ predicted minerals as anorthite, diopside, orthoclase, and albite (NaAlSi 3 O 8 ), etc., where the slag temperature was below the ash fluid temperature and when the ratios of CO/CO 2 and (CO + H 2 )/CO 2 were lower than 1.0 and 2.0, respectively. By simulation, residual carbon was found to be the dominant factor over syngas composition to cause mineral transformation, and this was verified experimentally. The Ca-based crystals, typically anorthite, was shifted to diopside, near the slag hole zone, and a linear relationship was found between the content ratios of diopside/(anorthite + diopside), CaO/SiO 2 , and (CaO + MgO)/SiO 2 . A dimensionless number, θ, was defined to characterize the changing chemical composition and the degree of slag polymerization, with temperature deviation from the design condition. Three zones of θ were identified and related to the deviation between the actual gasification condition from the design condition. Finally, a low slag polymerization degree corresponded with a higher temperature deviation between the actual condition and design condition, and this proved that increased residual carbon content and changing iron valence state increased the mineral types when the slag temperature was below the ash fluid temperature.

01 COAL, LIGNITE, AND PEAT↗

Understanding Spatial Genome Organization: Methods and Insights

Abstract The manner by which eukaryotic genomes are packaged into nuclei while maintaining crucial nuclear functions remains one of the fundamental mysteries in biology. Over the last ten years, we have witnessed rapid advances in both microscopic and nucleic acid-based approaches to map genome architecture, and the application of these approaches to the dissection of higher-order chromosomal structures has yielded much new information. It is becoming increasingly clear, for example, that interphase chromosomes form stable, multilevel hierarchical structures. Among them, self-associating domains like so-called topologically associating domains (TADs) appear to be building blocks for large-scale genomic organization. This review describes features of these broadly-defined hierarchical structures, insights into the mechanisms underlying their formation, our current understanding of how interactions in the nuclear space are linked to gene regulation, and important future directions for the field.

Ramani, Vijay (ORCID:0000000333455960)↗

Insights from FEED studies for retrofitting existing fossil power plants with carbon capture technology

Recent United States Department of Energy (DOE) sponsored front-end engineering design (FEED) studies for retrofitting existing fossil-fueled power plants with state-of-the-art carbon capture technology contain previously overlooked real-world design considerations for near-term deployment of carbon capture. Insights from examining seven recently published FEED study reports are summarized in this paper. This includes a discussion of the design, performance, and cost implications associated with (1) location-specific considerations such as water availability, land availability, and accessibility; (2) host-plant-specific factors such as flue gas specifications, allowable degree of integration between the capture system and host plant, and operational mode; and (3) miscellaneous factors such as market conditions, permitting requirements, and business case incentives. In conclusion, this manuscript highlights (1) water availability as a key design and cost driver, with host plant steam extraction increasing capture system cooling water availability, (2) modularization and constructability impacts on the number of capture trains, (3) the impacts of host plant operational mode and capacity factor on the business case for installing capture, and (4) the merit of continued research, development, and demonstration efforts addressing steam extraction, host plant tie-in at the stack, solvent reclamation and air emissions control.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Excipient screening by lyophilization provides insights into spray drying formulations for nanoparticle vaccines

Nanoparticles have shown great promise as delivery platforms in the development of tunable and safe vaccines. Nanolipoprotein particles (NLPs), also known as nanodiscs, are discoidal nanoparticles composed of a lipid bilayer stabilized at their periphery by apolipoproteins. Under the right conditions, the NLP self-assembly process is highly customizable in terms of lipids and apolipoprotein constituents, allowing for tunable physical and chemical characteristics. This flexibility allows a wide range of vaccine antigens and adjuvants to be incorporated onto the NLP platform for tailored vaccine design. The stability of NLPs during long term storage is a very important factor in developing a vaccine delivery platform suitable for widespread global use. When stored in a solution for extended periods of time, NLPs dissociate into their corresponding lipids and protein constituents, leading to particle degradation. Proper stabilization of NLPs can often be achieved by lyophilization (i.e. freeze-drying), a method widely used for various applications including pharmaceuticals. This process, however, can be damaging to particles without the presence of lyoprotectants or excipients that help maintain particle stability during lyophilization. Another method used to stabilize vaccines and pharmaceuticals is spray drying, a process that converts liquid formulations into dry powders through controlled heating and airflow. While spray drying is rapid, scalable, and cost-effective, lyophilization is typically a gentler process that better retains biomolecule structure and function. Both processes use excipients for particle stabilization, so lyophilization can be used as a surrogate to test stability of NLPs, to down-select formulations that may withstand the harsher conditions of spray drying. To screen different formulations, NLPs were synthesized and purified to homogeneity by size exclusion chromatography (SEC) and samples were prepared with a wide range of lyoprotectants and/or excipients. To assess the protective effects of excipients on NLPs upon spray drying, both pre- and post-lyophilized samples were analyzed by SEC. To assess the protective effects upon heating (encountered during the spray drying process), NLP samples were incubated at elevated temperatures prior to SEC analysis. The lyoprotectants and excipients evaluated in this study had different efficiencies in protecting NLPs during lyophilization and heating tests. Trehalose, for example, exhibits stabilization on NLPs both upon lyophilization and heating whereas leucine accelerated NLP dissociation. Although some lyoprotectants are effective by themselves, different combinations can decrease the stabilization of NLPs. Shelf-stable vaccines that do not require cold-chain storage are essential for global accessibility and our findings provide fundamental insight into how to advance NLP-based vaccines for these applications.

Serrano, Litzay J [Lawrence Livermore National Lab↗

Modulating Cu electrode microenvironments with MOF coatings: insights from molecular dynamics and electrochemical experiments of CO reduction

Metal-organic frameworks (MOFs) present a compelling strategy for tuning electrochemical interfaces by reshaping interfacial solvent structure. In this study, we examine how MOF coatings influence the microenvironment at copper electrodes during the CO electroreduction reaction (CORR) using a combined approach of molecular dynamics (MD) simulations and electrochemical experiments. Two MOFs, NU-901 and ZIF-8, are selected to explore the impact of pore size and channel hydrophobicity on electrochemical activity and interfacial concentration in acetonitrile (ACN) and dimethyl sulfoxide (DMSO) electrolytes. Electrochemical measurements reveal that MOF@Cu electrodes exhibit lower Faradaic efficiencies for CO hydrogenation products (ethylene and methane) compared to bare copper but have dramatic impacts on the interfacial microenvironment. NU-901, with its larger pores and strong interactions with DMSO, traps DMSO molecules and enhances CO coordination in DMSO but suppresses CORR selectivity in favor of the hydrogen evolution reaction (HER). ZIF-8, with smaller pores and hydrophobic channels, limits the interfacial water concentration, and, in ACN, promotes CO coordination. The simulations provide insights into how MOFs can act as physical modulators of reactant delivery and interfacial structure to control electrochemical microenvironments. This work highlights the value of molecular dynamics in uncovering how structural features of MOFs influence interfacial phenomena, even when catalytic performance is not directly improved.

Copper electrode microenvironments↗

Scattering insights into shear-induced scission of rod-like micelles

Understanding the scission of rod-like micelles under mechanical forces is crucial for optimizing their stability and behavior in industrial applications. This study investigates how micelle length, flexibility, and external forces interact, offering insights into the design of micellar systems in processes influenced by mechanical stress. Although significant, direct experimental observations of flow-induced micellar scission using scattering techniques remain scarce. Small angle neutron scattering (SANS) is used to explore the shear response of aqueous cetyltrimethylammonium bromide (CTAB) solutions with sodium nitrate. Rheological tests show shear thinning with no shear banding, ensuring a uniform flow field for reliable interpretation of scattering data. As shear rate increases, the scattering spectra show angular distortion, which is analyzed using spherical harmonic decomposition to characterize flow-induced scission and micelle orientation under shear. Two analysis steps are used: a model-independent spectral eigendecomposition reveals a decrease in micellar length, while regression analysis quantifies the evolution of the length distribution and mean length with shear rate. Additionally, micelle alignment increases with shear, quantified by the orientational distribution function. In conclusion, these findings provide experimental evidence for flow-induced alignment and scission, offering a new framework for understanding shear-induced phenomena in micellar systems.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Insights into Ti doping for stabilizing the Na 2/3 Fe 1/3 Mn 2/3 O 2 cathode in sodium ion battery

Iron- and manganese-based layered metal oxides, as cathodes for sodium ion batteries, have received widespread attention because of the low cost and high specific capacity. However, the Jahn-teller effect of Mn 3+ ions and the resulted unstable structure usually lead to continuously capacity decay. Herein, Titanium (Ti) has been successfully doped into Na 2/3 Fe 1/3 Mn 2/3 O 2 to suppress the Jahn-Teller distortion and improve both cycling and rate performance of sodium ion batteries. In situ high-energy synchrotron X-ray diffraction study shows that Ti-doped compound (Na 2/3 Fe 1/3 Mn 0.57 Ti 0.1 O 2 ) can maintain the single P2 phase without any phase transition during the whole charging/discharging process. Further, various electrochemical characterizations are also applied to explore the better kinetics of sodium ions transfer in the Na 2/3 Fe 1/3 Mn 0.57 Ti 0.1 O 2 . This work provides a comprehensive insight into the Ti-doping effects on the performance from both structural and electrokinetic perspectives.

25 ENERGY STORAGE↗

Enhancing low-temperature sintering in the MgO-LiF system: Mechanistic insights

In the present article, we provide compelling evidence that minor (1 wt%) additions of micron and nanometre-sized LiF particles in MgO decompose leading to free Li diffusing into MgO surfaces enhancing vacancy production during direct current sintering. The addition of nanometre-sized LiF particles leads to a > 500 °C reduction in the sintering temperature and over 99 % theoretical density of final consolidated compacts. Correlating differential scanning calorimetry with in-situ x-ray diffraction, together with Schottky calculations, post sintering electron microscopy and laser induced breakdown spectroscopy, we uncover critical insights into this impressive reduction in sintering temperature. Our quantitative analysis reveals that MgO and LiF interact at low temperatures with the diffusion of Li into the surface of MgO particles due to the intrinsic structural disorder of the LiF and MgO crystallites. Nanometre-sized LiF particles were found to react the most at low temperatures due to their increased structural disorder. Our multimodal characterization points to a Li-promoted densification and sintering mechanism. This impressive reduction in sintering temperature can be harnessed to promote low-temperature fabrication of MgO-based composites for technological applications.

36 MATERIALS SCIENCE↗

Transformation of heavy metal speciation during sludge drying: mechanistic insights

Speciation can fundamentally affect on the stability and toxicity of heavy metals in sludge from wastewater treatment plants. This research investigated the speciation of heavy metals in sludge from both municipal and industrial sources, and metal speciation change as a result of drying process to reduce sludge volume. The changes in sludge properties including sludge moisture content, temperature, density, and electrical conductivity were also monitored to provide insights into the mechanisms causing the change in heavy metal speciation. The results show that the drying process generally stabilized the Cr, Cu, Cd and Pb in sludge by transforming acid-soluble, reducible and oxidizable species into structurally stable forms. Such transformation and stabilization occurred regardless of the sludge source and type, and were primarily caused by the changes in sludge properties associated with decomposition of organic matter and sulfide. The results enhanced our understanding of the geochemical behavior of heavy metals in municipal sludge, and are useful for designing a treatment system for environment-friendly disposal of sludge.

Weng, Huanxin↗

Dynamics of streamflow permanence in a headwater network: Insights from catchment-scale model simulations

The hillslope and channel dynamics that govern streamflow permanence in headwater systems have important implications for ecosystem functioning and downstream water quality. Recent advancements in process-based, semi-distributed hydrologic models that build upon empirical studies of streamflow permanence in well-monitored headwater catchments show promise for characterizing the dynamics of streamflow permanence in headwater systems. However, few process-based models consider the continuum of hillslope-stream network connectivity as a control on streamflow permanence in headwater systems. The objective of this study was to expand a process-based, catchment-scale hydrologic model to better understand the spatiotemporal dynamics of headwater streamflow permanence and to identify controls of streamflow expansion and contraction in a headwater network. Further, we aimed to develop an approach that enhanced the fidelity of model simulations, yet required little additional data, with the intent that the model might be later transferred to catchments with limited long-term and spatially explicit measurements. This approach facilitated network-scale estimates of the controls of streamflow expansion and contraction, albeit with higher degrees of uncertainty in individual reaches due to data constraints. Our model simulated that streamflow permanence was highly dynamic in first-order reaches with steep slopes and variable contributing areas. The simulated stream network length ranged from nearly 98±2% of the geomorphic channel extent during wet periods to nearly 50±10% during dry periods. The model identified a discharge threshold of approximately 1 mm d –1 , above which the rate of streamflow expansion decreases by nearly an order of magnitude, indicating a lack of sensitivity of streamflow expansion to hydrologic forcing during high-flow periods. Overall, we demonstrate that process-based, catchment-scale models offer important insights on the controls of streamflow permanence, despite uncertainties and limitations of the model. We encourage researchers to increase data collection efforts and develop benchmarks to better evaluate such models.

54 ENVIRONMENTAL SCIENCES↗

The X-Ray Crystal Structure of the Keratin 1-Keratin 10 Helix 2B Heterodimer Reveals Molecular Surface Properties and Biochemical Insights into Human Skin Disease

Keratins 1 (K1) and 10 (K10) are the primary keratins expressed in differentiated epidermis. Mutations in K1/K10 are associated with human skin diseases. We determined the crystal structure of the complex between the distal (2B) helices of K1 and K10 to better understand how human keratin structure correlates with function. The 3.3 Å resolution structure confirms many features inferred by previous biochemical analyses, but adds unexpected insights. It demonstrates a parallel, coiled-coil heterodimer with a predominantly hydrophobic intermolecular interface; this heterodimer formed a higher order complex with a second K1-K10-2B heterodimer via a Cys401K10 disulfide link, although the bond angle is unanticipated. The molecular surface analysis of K1-K10-2B identified several pockets, one adjacent to the disulfide linkage and conserved in K5-K14. The solvent accessible surface area of the K1-K10 structure is 20–25% hydrophobic. The 2B region contains mixed acidic and basic patches proximally (N-terminal), whereas it is largely acidic distally (C-terminal). Mapping of conserved and nonconserved residues between K1-K10 and K5-K14 onto the structure demonstrated the majority of unique residues align along the outer helical ridge. Finally, the structure permitted a fresh analysis of the deleterious effects caused by K1/K10 missense mutations found in patients with phenotypic skin disease.

59 BASIC BIOLOGICAL SCIENCES↗

Structure of an APC3–APC16 Complex: Insights into Assembly of the Anaphase-Promoting Complex/Cyclosome

The anaphase-promoting complex/cyclosome (APC/C) is a massive E3 ligase that controls mitosis by catalyzing ubiquitination of key cell cycle regulatory proteins. The APC/C assembly contains two subcomplexes: the “Platform” centers around a cullin-RING-like E3 ligase catalytic core; the “Arc Lamp” is a hub that mediates transient association with regulators and ubiquitination substrates. The Arc Lamp contains the small subunits APC16, CDC26, and APC13, and tetratricopeptide repeat (TPR) proteins (APC7, APC3, APC6, and APC8) that homodimerize and stack with quasi-2-fold symmetry. Within the APC/C complex, APC3 serves as center for regulation. APC3's TPR motifs recruit substrate-binding coactivators, CDC20 and CDH1, via their C-terminal conserved Ile-Arg (IR) tail sequences. Human APC3 also binds APC16 and APC7 and contains a > 200-residue loop that is heavily phosphorylated during mitosis, although the basis for APC3 interactions and whether loop phosphorylation is required for ubiquitination are unclear. Here, we map the basis for human APC3 assembly with APC16 and APC7, report crystal structures of APC3Δloop alone and in complex with the C-terminal domain of APC16, and test roles of APC3's loop and IR tail binding surfaces in APC/C-catalyzed ubiquitination. The structures show how one APC16 binds asymmetrically to the symmetric APC3 dimer and, together with biochemistry and prior data, explain how APC16 recruits APC7 to APC3, show how APC3's C-terminal domain is rearranged in the full APC/C assembly, and visualize residues in the IR tail binding cleft important for coactivator-dependent ubiquitination. Overall, the results provide insights into assembly, regulation, and interactions of TPR proteins and the APC/C.

59 BASIC BIOLOGICAL SCIENCES↗

Structural Insights into the Interaction of Coronavirus Papain-Like Proteases and Interferon-Stimulated Gene Product 15 from Different Species

Severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV) encode multifunctional papain-like proteases (PLPs) that have the ability to process the viral polyprotein to facilitate RNA replication and antagonize the host innate immune response. The latter function involves reversing the post-translational modification of cellular proteins conjugated with either ubiquitin (Ub) or Ub-like interferon-stimulated gene product 15 (ISG15). Ub is known to be highly conserved among eukaryotes, but surprisingly, ISG15 is highly divergent among animals. The ramifications of this sequence divergence to the recognition of ISG15 by coronavirus PLPs at a structural and biochemical level are poorly understood. Therefore, the activity of PLPs from SARS-CoV, MERS–CoV, and mouse hepatitis virus was evaluated against seven ISG15s originating from an assortment of animal species susceptible, and not, to certain coronavirus infections. Excitingly, our kinetic, thermodynamic, and structural analysis revealed an array of different preferences among PLPs. Included in these studies is the first insight into a coronavirus PLP’s interface with ISG15 via SARS-CoV PLpro in complex with the principle binding domain of human ISG15 (hISG15) and mouse ISG15s (mISG15s). Here, the first X-ray structure of the full-length mISG15 protein is also reported and highlights a unique, twisted hinge region of ISG15 that is not conserved in hISG15, suggesting a potential role in differential recognition. Taken together, this new information provides a structural and biochemical understanding of the distinct specificities among coronavirus PLPs observed and addresses a critical gap of how PLPs can interact with ISG15s from a wide variety of species.

59 BASIC BIOLOGICAL SCIENCES↗

Insights into the thermal decomposition of plutonium(IV) oxalate – a DFT study of the intermediate structures

The thermal decomposition of plutonium oxalate to oxide is one of the most studied reactions in actinide chemistry but the intermediates have been the subject of debate for decades. Recent experimental data suggest that the decomposition of Pu(IV) oxalate in air undergoes dehydration first, then reduction to Pu(III) oxalate. The precise structural modifications that take place are unknown as experiments have not been able to fully characterize the intermediates at the microscopic level. To rectify this, we employed solid state density functional theory calculations at the PBE-D3 level with a Hubbard U correction to model the structures and energetics of potential dehydrated Pu(IV) and Pu(III) oxalate intermediate compounds. Based on the theoretical study presented here, the anhydrous analogues of the known hydrated Pu(IV) and Pu(III) oxalates are the preferred crystal structures formed through an overall exothermic reaction process. However, decomposition could proceed through the formation of a higher energy, more complicated 3D lattice structure with frustrated oxalate binding. It is expected that the intermediates presented here could be identified using spectroscopic techniques to enable further insight into the reaction mechanism.

38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗

Computational insights into the structure of anhydrous Pu(III) oxalate

Despite the plutonium oxalate method's wide use in plutonium reprocessing, the method's mechanistic details remain unclear, particularly the identity of the plutonium oxidation state during conversion from an oxalate hydrate to the oxide. Recently, the optical vibrational spectra of Pu(III) oxalate during calcination were measured, providing an experimental reference for computational studies aimed at elucidating the oxalate structure. Here, in this work, we compare the vibrational and electronic properties of two candidate anhydrous Pu(III) oxalate structures calculated using density functional theory with recent experiments. We find that both structures are plausible and may coexist at experimental temperatures, providing insights into the broad features measured in the Raman and infrared spectra.

11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗