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DOE OSTI2023

Chemo-mechanical-microstructural coupling in the tarsus exoskeleton of the scorpion Scorpio palmatus

The multiscale structure of biomaterials enables their exceptional mechanical robustness, yet the impact of each constituent at their relevant length scale remains elusive. Here, we used SAXD analysis to expose the intact chitin-fiber architecture within the exoskeleton on a scorpion's claw, revealing varying orientations, including Bouligand and unidirectional regions different from other arthropod species. We uncovered the contribution of individual components’ constituent behavior to its mechanical properties from the micro- to the nanoscale. At the microscale, in-situ micromechanical experiments were used to determine site-specific stiffness, strength, and failure of the biocomposite due to fiber orientation, while metal-crosslinking of proteins is characterized via fluorescence maps. At the constituent level, combined with FEA simulations, we uncovered the behavior of fiber-matrix deformation with fiber diameter <53.7 nm and protein modulus in the range 1.4–11 MPa. The unveiled microstructure-mechanics relationship sheds light on the evolved structural functionalities and constituents' interactions within the scorpion cuticle.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

The oleaginous yeast Cutaneotrichosporon oleaginosum modifies corn stover alkali lignin

The current paradigm in synthetic biology for lignin bioconversion platforms includes primarily bacteria and filamentous fungi. Yeast are notoriously understudied for their role in lignin degradation and utilization, despite their ubiquity in saprophytic microbial communities. A few publications report lignin-modifying yeasts, but investigations to date have relied on model aromatic compounds or lignin-containing substrates replete with other carbon sources. In this work, we use a suite of analytical tools to evaluate interactions between corn stover-extracted lignin and the oleaginous yeast Cutaneotrichosporon oleaginosum. Notably, 2D-NMR analysis showed a significant decrease in the H-lignin component as well as resinol (β-β) and phenylcoumaran (β-5) linkages. Using super-resolution fluorescence microscopy, we demonstrated that this yeast may uptake polymeric lignin and/or undertakes interactions at the cellular envelope. To explore mechanisms of lignin modification, transport, and aromatics catabolism, extensive secretomics and proteomics analyses were conducted. Compared to carbon-limited glucose and “No Carbon” controls, several putative laccases, quinone reductases, superoxide dismutases, and glyoxal/oxalate oxidases were upregulated in the lignin condition. Excitingly, two ferric reductases and an oxalate exchanger were only observed in the lignin condition. These results indicate that C. oleaginosum may perform extracellular quinone redox cycling to generate lignin-modifying reactive oxygen species. These findings enhance our understanding of yeast-lignin interactions and provide valuable insights for validation studies and metabolic engineering.

09 BIOMASS FUELS↗

DOE OSTI2023

Rapid CO2 changes cause oscillations in photosynthesis that implicate PSI acceptor-side limitations

Abstract Oscillations in CO2 assimilation rate and associated fluorescence parameters have been observed alongside the triose phosphate utilization (TPU) limitation of photosynthesis for nearly 50 years. However, the mechanics of these oscillations are poorly understood. Here we utilize the recently developed dynamic assimilation techniques (DATs) for measuring the rate of CO2 assimilation to increase our understanding of what physiological condition is required to cause oscillations. We found that TPU-limiting conditions alone were insufficient, and that plants must enter TPU limitation quickly to cause oscillations. We found that ramps of CO2 caused oscillations proportional in strength to the speed of the ramp, and that ramps induce oscillations with worse outcomes than oscillations induced by step change of CO2 concentration. An initial overshoot is caused by a temporary excess of available phosphate. During the overshoot, the plant outperforms steady-state TPU and ribulose 1,5-bisphosphate regeneration limitations of photosynthesis, but cannot exceed the rubisco limitation. We performed additional optical measurements which support the role of PSI reduction and oscillations in availability of NADP+ and ATP in supporting oscillations.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Enhanced intersystem crossing of boron dipyrromethene by TEMPO radical

Radical enhanced intersystem crossing (EISC) of organic chromophores is an important approach to generate a long-lived triplet state for various electronic and optoelectronic applications. However, structural factors and design rules to promote EISC are not entirely clear. In this work, we report a series of boron dipyrromethene (BODIPY) derivatives covalently linked with a 2,2,6,6-tetramethyl-1-piperidinyloxyl (TEMPO) radical with varying distances and topologies. We show that the incorporation of the TEMPO radical to BODIPY results in strong fluorescence quenching by up to 85% as a result of EISC and enhanced internal conversion. In BDP-2AR [2-(4-methyleneamino-TEMPO) BODIPY], a dyad with the shortest BODIPY–TEMPO through-bond distance, we observe the fastest EISC rate (τ isc = 1.4 ns) and the longest triplet excited state lifetime (τ T = 32 μs) compared to other distance and geometry variations. Contrary to previous reports and a general presumption, the BODIPY–TEMPO through-bond distance in this system does not play a significant role on the triplet formation rate and yield. Finally, density functional theory suggests a folding of the TEMPO radical to form a sandwich-like structure with a BODIPY ring that leads to a decrease in the through-space distance, providing a new and an interesting insight for the radical enhanced intersystem.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2025

Influence of Water, Vacuum, and Temperature on Surface Conditions of a Zeolite‐based Molecular Sieve

Molecular sieves such as zeolite-based materials are ubiquitous in industrial separation processes. However, there is a significant gap in understanding the surface properties and adsorption mechanisms for commercial zeolites, as most research focuses on pure zeolite powders rather than industrially relevant forms. Here, this work addresses this gap in understanding by employing advanced characterization techniques, including positron annihilation spectroscopy, X-ray diffraction, scanning electron microscopy, X-ray fluorescence spectroscopy, X-ray photoelectron spectroscopy, liquid nitrogen sorption, and Fourier-transform infrared spectroscopy, to investigate the adsorption and desorption behavior of water in commercial zeolite 13X. Our research reveals insights into the pore-filling mechanisms, the impact of material binders on adsorption properties, and the dynamics of hydration and drying processes for zeolites. Monitoring changes on a minute scale allowed the distinction between fast and slow processes leading to sample drying. The identification of positronium bound to Na + ions indicated that water molecules remain in the vicinity of Na + ions after air-drying zeolite 13X. These findings highlight the importance of various environmental conditions in restoring zeolite properties to baseline after hydration, with significant implications for optimizing industrial processes. This work sets the direction for further research aimed at developing more efficient and robust separation techniques.

Beads Binder↗

DOE OSTI2024

Detection of the BICT State in a Borafluorene with High Stokes Shift Fluorescence

Four-coordinate aryl borafluorenes with boron–oxygen and boron–nitrogen dative bonds can exhibit very large fluorescence Stokes shifts. The large Stokes shifts are hypothesized to arise from cleavage of the boron-donor dative bond in the excited state, via a mechanism called bond-cleavage-induced intramolecular charge transfer (BICT). The primary goal of this current investigation is to directly observe the BICT state by performing transient absorption spectroscopy (TAS) on four-coordinate borafluorenes, which have improved optical stability. A novel four-coordinate aryl borafluorene was synthesized which features a dative B–O bond and two tert-butyl moieties on the aryl ring. TAS of the new borafluorene is consistent with the existence of a single, three-coordinate species in the excited state, as predicted by the BICT hypothesis. In conclusion, the TAS data is supported by fluorescence lifetime measurements and DFT calculations.

Absorption↗

DOE OSTI2022

The Assembly and Jamming of Nanoparticle Surfactants at Liquid–Liquid Interfaces

Abstract Using the interactions between nanoparticles (NPs) and polymeric ligands to generate nanoparticle surfactants (NPSs) at the liquid–liquid interface, the binding energy of the NP to the interface can be significantly increased, irreversibly binding the NPSs to the interface. By designing a simplified NPS model, where the NP size can be precisely controlled and the characteristic fluorescence of the NPs be used as a direct probe of their spatial distribution, we provide new insights into the attachment mechanism of NPSs at the liquid–liquid interface. We find that the binding energy of NPSs to the interface can be reduced by competitive ligands, resulting in the dissociation and disassembly of NPSs at the interface, and allowing the construction of responsive, reconfigurable all‐liquid systems. Smaller NPSs that are loosely packed (unjammed) and irreversibly bound to the interface can be displaced by larger NPSs, giving rise to a size‐dependent assembly of NPSs at the interface. However, when the smaller size NPSs are densely packed and jam at the interface, the size‐dependent assembly of NPSs at the interface can be completely suppressed.

Wang, Beibei↗

DOE OSTI2022

The Assembly and Jamming of Nanoparticle Surfactants at Liquid–Liquid Interfaces

Wang, Beibei↗

DOE OSTI2023

Plants cope with fluctuating light by frequency‐dependent nonphotochemical quenching and cyclic electron transport

Summary In natural environments, plants are exposed to rapidly changing light. Maintaining photosynthetic efficiency while avoiding photodamage requires equally rapid regulation of photoprotective mechanisms. We asked what the operation frequency range of regulation is in which plants can efficiently respond to varying light. Chlorophyll fluorescence, P700, plastocyanin, and ferredoxin responses of wild‐types Arabidopsis thaliana were measured in oscillating light of various frequencies. We also investigated the npq1 mutant lacking violaxanthin de‐epoxidase, the npq4 mutant lacking PsbS protein, and the mutants crr2‐2 , and pgrl1ab impaired in different pathways of the cyclic electron transport. The fastest was the PsbS‐regulation responding to oscillation periods longer than 10 s. Processes involving violaxanthin de‐epoxidase dampened changes in chlorophyll fluorescence in oscillation periods of 2 min or longer. Knocking out the PGR5/PGRL1 pathway strongly reduced variations of all monitored parameters, probably due to congestion in the electron transport. Incapacitating the NDH‐like pathway only slightly changed the photosynthetic dynamics. Our observations are consistent with the hypothesis that nonphotochemical quenching in slow light oscillations involves violaxanthin de‐epoxidase to produce, presumably, a largely stationary level of zeaxanthin. We interpret the observed dynamics of photosystem I components as being formed in slow light oscillations partially by thylakoid remodeling that modulates the redox rates.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

19-LW-045 Full Length Final Report. Molecular Mechanisms of Bacterial Pathogenesis: Waging the Arms Race with Superbugs

As the current global pandemic makes abundantly clear, we need a better understanding of infectious disease to safeguard human health, the economy and global security. Modern omics techniques hold the promise of providing a comprehensive understanding of the molecular mechanisms of life, including causes of pathogenesis from infectious disease at the molecular level, but we there is a serious gap in annotation of gene function. For as much as half of the genes and gene products encoded in genomes the molecular and/or cellular function is unknown or only partially understood. Recent innovations in fluorescence microscopy for live cell imaging and genetic engineering make it possible to determine the temporal correlation between molecular events, such as a gene being expressed due to host-pathogen interaction, and cellular events, such as bacterial invasion of immune cells. This is turn allows us to gain new insight as to the molecular and cellular role of individual genes and will enable the discovery and validation of new molecular mechanisms essential for infectious disease. Knowing the molecular mechanisms of disease processes will provide new therapeutic targets or novel countermeasure strategies. We aimed to develop a lattice light sheet fluorescence microscope as a unique resource at LLNL for long time course live cell imaging experiments; to develop the reagents and cell lines needed to monitor molecular events during the course pathogenic bacteria infecting mammalian immune cells; and to demonstrate that we could capture molecular events during an infection. We fully commissioned the LLNL lattice light sheet microscope and conducted initial proof of principle imaging experiments on mammalian immune cells and pathogenic bacteria. It is clear from the experience gained that long time course live cell imaging has tremendous potential to help elucidate molecular mechanisms of host-pathogen interactions and to help annotate gene function, which would establish a basis for new countermeasures. It is also clear that if live cell imaging is to realize its full potential new data processing and analysis tools will need to be developed to facilitate analysis of molecular events within cells; new sample chambers and stages could facilitate studies with a wider range of cell and tissue types; and alternative molecular tagging methods need to be explored to enable more facile engineering of cells labeled with molecular specificity.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Degradation in photovoltaic encapsulation strength of attachment: Results of the first PVQAT TG5 artificial weathering study

Delamination of the encapsulant in photovoltaic (PV) module technology results in immediate optical loss and may enable subsequent corrosion or mechanical damage. The effects of artificial weathering were not previously known; therefore, an empirical study was performed to survey the factors most affecting adhesion, including the ultraviolet (UV) source (ie, Xe or fluorescent lamp[s]), the optical filters for the lamp, the chamber temperature, and the relative humidity. Natural weathering was also performed at locations, including the following: Golden, Colorado; Miami, Florida; Phoenix, Arizona; QiongHai, China; Riyadh, Saudi Arabia; and Turpan, China. Specimens were constructed using a laminated glass/poly (ethylene-co-vinyl acetate)/glass geometry. The compressive shear test (CST) was used to quantify the mechanical strength of attachment, taken as a proxy for adhesion. The fractography of select specimens (including cross-sectional optical microscopy) was used to verify the failure mode (delamination or decohesion). Additional analysis of the local solar spectrum as well as the specimen temperature was performed to interpret the results of natural weathering. The goals of this study include to identify the most significant stressors, clarify where strong coupling may occur between stressors, and validate accelerated test results relative to natural weathering. The importance of specimen conditioning (for moisture) and hygrometric degradation as well as the effects of UV degradation are identified in this paper.

14 SOLAR ENERGY↗

DOE OSTI2024

Cationic and Anionic Redox of Battery Cathodes Investigated by Advanced Synchrotron‐Based Mapping of Resonant Inelastic X‐ray Scattering

Abstract Redox reaction builds the foundation stone for the energy density of rechargeable battery cathodes. Probing and understanding the redox reaction behavior is crucial, but also extremely formidable, which requires individual and reliable detection of cationic and anionic redox states. Fortunately, the recently developed ultra‐high‐efficiency mapping of resonant inelastic X‐ray scattering (mRIXS) has emerged as a powerful tool to probe the battery chemistry states. Here, the latest advances of employing advanced mRIXS is summarized to investigate the cationic and anionic redox mechanism of battery cathodes during electrochemical operation. Owing to the new dimension of information along the emission energy and high sensitivity to valence 3d states, 3d transition‐metal L ‐edge (TM‐ L ) mRIXS can eliminate the lineshape distortion in conventional 3d TM‐ L fluorescence X‐ray absorption spectra and investigate the cationic redox quantitatively. Moreover, O‐ K mRIXS could fingerprint the intrinsic oxidized lattice oxygen states and quantify the oxygen redox (OR) reversibility, thus demystifying the controversy in traditional wisdom. In addition, different modification strategies coupled with underlying mechanisms for regulating the activity and reversibility of OR utilizing mRIXS are also summarized. This review provides valuable guidance for further exploration of underlying reaction mechanisms of battery cathodes by mRIXS, along with both technological and scientific improvements.

Cheng, Chen↗

DOE OSTI2022

Multiple pathways mediate chloroplast singlet oxygen stress signaling

Chloroplasts can respond to stress and changes in the environment by producing reactive oxygen species (ROS). Aside from being cytotoxic, ROS also have signaling capabilities. For example, the ROS singlet oxygen ( 1 O 2 ) can initiate nuclear gene expression, chloroplast degradation, and cell death. Here to unveil the signaling mechanisms involved, researchers have used several 1 O 2 -producing Arabidopsis thaliana mutants as genetic model systems, including plastid ferrochelatase two (fc2), fluorescent in blue light (flu), chlorina 1 (ch1), and accelerated cell death 2 (acd2). Here, we compare these 1 O 2 -producing mutants to elucidate if they utilize one or more signaling pathways to control cell death and nuclear gene expression. Using publicly available transcriptomic data, we demonstrate fc2, flu, and ch1 share a core response to 1 O 2 accumulation, but maintain unique responses, potentially tailored to respond to their specific stresses. Subsequently, we used a genetic approach to determine if these mutants share 1 O 2 signaling pathways by testing the ability of genetic suppressors of one 1 O 2 producing mutant to suppress signaling in a different 1 O 2 producing mutant. Our genetic analyses revealed at least two different chloroplast 1 O 2 signaling pathways control cellular degradation: one specific to the flu mutant and one shared by fc2, ch1, and acd2 mutants, but with life-stage-specific (seedling vs. adult) features. Overall, this work reveals chloroplast stress signaling involving 1 O 2 is complex and may allow cells to finely tune their physiology to environmental inputs.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2025

Time-resolved detectors for quantum ghost imaging

Quantum ghost imaging is a method that utilizes the correlated detection of two photons to generate an image. One photon is detected by an imaging sensor and the other by a single-element bucket detector. The selection of the imaging sensor and its capabilities relative to the bucket detector impact the quality of the ghost images. This work examines a SPAD array and a photocathode detector as imaging sensors for quantum ghost imaging. We discuss how to achieve optimal images using these two technologies. We also demonstrate that these devices are able to generate ghost images at 1Hz frame rates, expanding the technique to biologically relevant time scales.

36 MATERIALS SCIENCE↗

DOE OSTI2022

Crystal Structure of CYP3A4 Complexed with Fluorol Identifies the Substrate Access Channel as a High-Affinity Ligand Binding Site

Cytochrome P450 3A4 (CYP3A4) is a major human drug-metabolizing enzyme, notoriously known for its extreme substrate promiscuity, allosteric behavior, and implications in drug–drug interactions. Despite extensive investigations, the mechanism of ligand binding to CYP3A4 is not fully understood. We determined the crystal structure of CYP3A4 complexed with fluorol, a small fluorescent dye that can undergo hydroxylation. In the structure, fluorol associates to the substrate channel, well suited for the binding of planar polyaromatic molecules bearing polar groups, through which stabilizing H-bonds with the polar channel residues, such as Thr224 and Arg372, can be established. Mutagenesis, spectral, kinetic, and functional data confirmed the involvement but not strict requirement of Thr224 for the association of fluorol. Collectively, our data identify the substrate channel as a high-affinity ligand binding site and support the notion that hydrophobic ligands first dock to the nearby peripheral surface, before migrating to the channel and, subsequently, into the active site.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2024

Lattice light-sheet microscopy allows for super-resolution imaging of receptors in leaf tissue

Plant leaf tissues are difficult to image via fluorescent microscopy, largely due to the presence of chlorophyll and other pigments that provide large background fluorescence. An advantage of Lattice Light-Sheet microscopy is its use of Bessel beams that illuminate a thin focal region of interest for microscopy, allowing for the excitation of fluorescent molecules within this region without surrounding chlorophyll-like objects outside of the region of interest. Here, we apply STORM Super-resolution techniques to observe Receptor-Like Kinases in Arabidopsis thaliana leaf cells. By applying this technique with the Lattice Light-Sheet, we can localize immune response proteins in sub-100 nm length scales and reconstruct three-dimensional locations of proteins within individual leaf cells. Using this technique, we observed the effect of the elicitors ATP and flg22, where we observed a significant degree of internalization of cognate receptors P2K1 and FLS2. We were also able to similarly observe differences in colocalization due to stimulation with these elicitors, where we observe proteins on the membrane becoming less colocalized as a result of stimulation, suggesting an immune response mechanism involving receptors internalizing via pathways distinct to the receptor. Further, these data show the Lattice Light-Sheet’s capabilities for imaging tissue with problematic background fluorescence that otherwise makes super-resolution fluorescence microscopy difficult.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2026

Imaging from Macro to Nanoscale: Multimodal Advances in Chemical and Biomedical Imaging

Imaging increasingly serves as a multiscale framework for linking molecular mechanisms to cellular behavior, tissue architecture, and organ phenotypes in biology and unraveling fundamental processes in chemistry, physics and materials science. This Perspective highlights recent advances in chemical and biomedical imaging across macro-, micro-, and nanoscales, using representative examples published in Chemical and Biomedical Imaging (CBMI). At the macroscale, we discuss chemically selective MRI, including endogenous and exogenous CEST strategies, together with photoacoustic imaging as a hybrid modality with functional and chemical contrast. At the microscale, we consider fluorescence, label-free optical and vibrational imaging, and selected X-ray approaches that expand sensitivity, specificity, and temporal resolution in biological and materials systems. At the nanoscale, we highlight super-resolution fluorescence microscopy, single-molecule methods, tip-enhanced Raman spectroscopy, and correlative imaging strategies that resolve local heterogeneity and molecular organization. Across scales, a common theme emerges that advances in probes, contrast mechanisms, instrumentation, and sample handling are enabling chemically informed imaging that connects molecular specificity with biological context.

multiscale imaging↗

DOE OSTI2022

Linking the Salmonella enterica 1,2-Propanediol Utilization Bacterial Microcompartment Shell to the Enzymatic Core via the Shell Protein PduB

Bacterial microcompartments (MCPs) are protein-based organelles that house the enzymatic machinery for metabolism of niche carbon sources, allowing enteric pathogens to outcompete native microbiota during host colonization. While much progress has been made toward understanding MCP biogenesis, questions still remain regarding the mechanism by which core MCP enzymes are enveloped within the MCP protein shell. Here, we explore the hypothesis that the shell protein PduB is responsible for linking the shell of the 1,2-propanediol utilization (Pdu) MCP from Salmonella enterica serovar Typhimurium LT2 to its enzymatic core. Using fluorescent reporters, we demonstrate that all members of the Pdu enzymatic core are encapsulated in Pdu MCPs. We also demonstrate that PduB is critical for linking the entire Pdu enzyme core to the MCP shell. Using MCP purifications, transmission electron microscopy, and fluorescence microscopy, we find that shell assembly can be decoupled from the enzymatic core, as apparently empty MCPs are formed in Salmonella strains lacking PduB. Mutagenesis studies reveal that PduB is incorporated into the Pdu MCP shell via a conserved, lysine-mediated hydrogen bonding mechanism. Finally, growth assays and system-level pathway modeling reveal that unencapsulated pathway performance is strongly impacted by enzyme concentration, highlighting the importance of minimizing polar effects when conducting these functional assays. Together, these results provide insight into the mechanism of enzyme encapsulation within Pdu MCPs and demonstrate that the process of enzyme encapsulation and shell assembly are separate processes in this system, a finding that will aid future efforts to understand MCP biogenesis.

1, 2-propanediol utilization↗