Glycosyl residue composition of cell wall extracts from tillers of switchgrass WT and PvGAUT4-KD plants
Glycosyl residue composition of cell wall extracts from tillers of switchgrass WT and PvGAUT4-KD plants
bio engineered↗
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Glycosyl residue composition and total carbohydrate in cell wall extracts from WT and PvGAUT4-KD lines
Glycosyl residue composition and total carbohydrate in cell wall extracts from WT and PvGAUT4-KD lines
bio engineered↗
Glycosyl residue composition of cell wall extracts from stems of P. deltoides WT, vector control and PdGAUT4-KD plants
Glycosyl residue composition of cell wall extracts from stems of P. deltoides WT, vector control and PdGAUT4-KD plants
bio engineered↗
Glycosyl residue composition and total carbohydrate of cell wall extracts from WT and PdGAUT4-KD lines
Glycosyl residue composition and total carbohydrate of cell wall extracts from WT and PdGAUT4-KD lines
bio engineered↗
Glycosyl linkage analysis of fractionated cell walls from switchgrass WT and PvGAUT4-KD lines
Glycosyl linkage analysis of fractionated cell walls from switchgrass WT and PvGAUT4-KD lines
bio engineered↗
Glycosyl linkage analysis of fractionated cell walls from P.deltoides WT and PdGAUT4-KD lines.
Glycosyl linkage analysis of fractionated cell walls from P.deltoides WT and PdGAUT4-KD lines.
bio engineered↗
Robustness of topological persistence in knowledge distillation for wearable sensor data
Topological data analysis (TDA) has shown great success in various applications involving wearable sensor data. However, there are difficulties in leveraging topological features in machine learning and wearable sensors because of the large time consumption and computational resources required to extract the features. To address this problem, knowledge distillation (KD) is utilized to generate a small model and accommodate topological features with persistence image (PI) representations from the raw time series data. Deploying topological knowledge in KD enables the student to achieve better performance compared to the one trained solely on raw time series data. However, it is not yet known if there are coherent characteristics for topological features in PI, which can aid in improving the performance during KD. In this paper, we investigate the suitability and challenges of utilizing topological features in KD for wearable sensor data, thereby contributing to the advancement of the field. Our study explores the impact of transferred topological features by comparing the Teacher-to-Student framework with Multiple Teachers-to-Student where teachers utilize both time series data and persistence images obtained by TDA as inputs. Additionally, we conduct a rigorous examination of topological knowledge effects by testing under various corruptions, knowledge types, and learning strategies in the context of human activity recognition tasks. Our analysis of topological features in KD presents the optimal strategy for incorporating these features. This study includes datasets of varying scales, window lengths, and activity classes, providing a comprehensive evaluation. Our results demonstrate that leveraging topological features in KD to enhance performance across databases.
97 MATHEMATICS AND COMPUTING↗
Resolving SPARC–HSA binding kinetics with an ultrasensitive photonic sensor based on bound states in the continuum
Secreted protein acidic and rich in cysteine (SPARC) is critical in cell-matrix interactions and tissue remodeling. It influences tumor progression through its affinity for human serum albumin (HSA) - the most abundant plasma protein, which also plays a crucial role in drug delivery. Strong molecular binding leads to a dissociation constant KD in the nanomolar range. Thus, determining KD requires detecting sub-nanomolar concentrations with ultrasensitive methods. This may be crucial for elucidating the nature of SPARC-HSA binding, as their interaction remains a subject of debate. Capturing these interactions accurately requires a platform capable of resolving rapid binding kinetics at extremely low analyte concentrations. In this work, we report on a microfluidics-integrated photonic nanostructure that supports bound states in the continuum (BICs) and is optimized for studying the fast kinetics of high-affinity protein-protein interactions. The unprecedented capability of detecting sub-nanomolar concentrations allows quantifying KD between SPARC and HSA beyond the state of the art. We leverage an all-dielectric photonic crystal slab (PhCS) sustaining two BIC branches arising from gapped Dirac cone dispersion. HSA is covalently immobilized on the PhCS bonded to a PDMS microfluidic chamber. SPARC dissociation is carried out using PBS buffer (pH 7.4), ensuring complete protein release through precise control of the flow rate and continuous spectral monitoring of the BICs. The measured KD=8.2±0.8 nM confirms the strong affinity of SPARC for HSA. This study highlights the potential of BIC-based sensing as a versatile tool for investigating protein interactions. These results also have implications for the optimization of drug delivery systems and cancer treatment strategies.
Albumin↗
Fyn–Saracatinib Complex Structure Reveals an Active State-like Conformation
Fyn is a Src-family tyrosine kinase implicated in synaptic dysfunction and neuroinflammation across multiple neurodegenerative disorders, including Alzheimer’s disease (AD) and Parkinson’s disease (PD). Saracatinib (AZD0530) is a potent Src-family inhibitor that has been explored as a repurposed therapeutic; however, its clinical utility is limited by poor kinase selectivity caused by high sequence conservation within Src-family ATP-binding sites. Here, we combine surface plasmon resonance (SPR) and X-ray crystallography to define saracatinib recognition by the Fyn kinase domain (KD). SPR single-cycle kinetics shows that saracatinib binds the isolated Fyn KD and full-length Fyn with low-nanomolar affinity, whereas dasatinib binds with subnanomolar affinity and markedly slower dissociation. We determined the crystal structure of the Fyn KD-saracatinib complex at 2.22 Å resolution. The kinase adopts an active-like conformation with the DFG motif and αC-helix in the ‘in’ state and a conserved β3 αC Lys-Glu salt bridge. Saracatinib occupies the adenine and ribose pockets, and engages the hinge through direct and water-mediated hydrogen bonding while complementing a hydrophobic back pocket by van der Waals contacts. Comparison with reported saracatinib-bound structures of other kinases suggests that the active-state geometry observed for Fyn creates a pocket not observed in inactive-like complexes, providing a structural handle for designing Fyn-selective inhibitors. Comparison with all saracatinib-bound kinase co-structures currently available in the PDB (ALK2 and PKMYT1) indicates a conserved monodentate hinge binding mode but kinase-dependent αC-helix conformations, providing a structural rationale for designing Fyn-selective analogues.
AZD0530↗
Sorption of Metals and Radionuclides in Cementitious Leachate Impacted Sediments from the Savannah River Site
Performance assessments (PAs) are calculations used to establish the risk posed by radioactive waste disposal facilities in the Savannah River Site (SRS). The distribution coefficient (Kd; solid/liquid concentration ratio; Csolid/liquid) is one of the key geochemical parameters used in the PA to provide a measure of how strongly the dissolved contaminants bind to solid phases; the greater the Kd value, the greater the tendency to bind to the solids. The overall purpose of this study was to measure this key parameter for several constituents of concern in the cementitious leachate impacted SRS sediment environments. Particular attention was directed at quantifying the influence of cementitious leachate from various stages of cement aging on the sorption of radioactive waste and heavy metals on SRS sediments.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Fundamental Data Supporting Novel Radiochemical Separations
Rapid chemical separation of actinide, lanthanide, and other radioactive elements is an important pursuit in the field of radioanalytical and nuclear chemistry. Vital to the development of advanced systems to achieve such separations is the determination of elements’ distribution coefficients (Kd values) for chromatographic resins. In this study, batch contacts of 68 elements were performed with various commercially available resins, and the resulting distribution coefficients were determined by Inductively Coupled Plasma – Mass Spectrometry Analysis (ICP-MS). An evaluation of the resulting Kd data for elements on the resins was performed. Finally, this work presents prototype flowsheets for streamlined separation of radioisotopes from a variety of complex matrices.
Distribution Coefficient↗
Hydrogen permeation in iron-chromium-aluminum (FeCrAl) alloys and the effects of microstructure and surface oxide
Iron–chromium–aluminum (FeCrAl) class alloys are candidates for use as cladding for accident-tolerant fuels and moderators. In this context, hydrogen isotope permeation in FeCrAl alloys is an important material property. Here, in the present work, the apparent permeability, effective diffusivity, and apparent solubility of hydrogen in the FeCrAl alloys C26M and Kanthal D (KD) were measured with gas-driven hydrogen permeation. Permeation measurements were conducted at temperatures of 400 to 700 °C and at gas-driven pressures from 1 to 100 kPa. In particular, the effect of grain size on hydrogen transport was studied with KD samples with three different microstructures: nanocrystalline (NC), ultra-fine grained (UFG), and coarse-grained (CG). The UFG and NC specimens had higher apparent activation energies (73.4 kJ mol -1 and 65.2 kJ mol -1 , respectively) for hydrogen permeability than the CG sample (46.9 kJ mol -1 ). An aluminum oxide layer formed on the primary- and secondary-side surfaces of all samples subjected to permeation experiments which demonstrated the propensity of FeCrAl alloys to form these innate oxide permeation barriers.
11 NUCLEAR FUEL CYCLE AND FUEL MATERIALS↗
Combining computational modeling and experimental library screening to affinity-mature VEEV-neutralizing antibody F5
Engineered monoclonal antibodies have proven to be highly effective therapeutics in recent viral outbreaks. However, despite technical advancements, an ability to rapidly adapt or increase antibody affinity and by extension, therapeutic efficacy, has yet to be fully realized. We endeavored to stand-up such a pipeline using molecular modeling combined with experimental library screening to increase the affinity of F5, a monoclonal antibody with potent neutralizing activity against Venezuelan Equine Encephalitis Virus (VEEV), to recombinant VEEV (IAB) E1E2 antigen. We modeled the F5/E1E2 binding interface and generated predictions for mutations to improve binding using a Rosetta-based approach and dTERMen, an informatics approach. The modeling was complicated by the fact that a high-resolution structure of F5 is not available and the H3 loop of F5 exceeds the length for which current modeling approaches can determine a unique structure. A subset of the predicted mutations from both methods were incorporated into a phage display library of scFvs. This library and a library generated by error-prone PCR were screened for binding affinity to the recombinant antigen. Results from the screens identified favorable mutations which were incorporated into 12 human-IgG1 variants. The best variant, containing eight mutations, improved KD from 0.63 nM (parental) to 0.01 nM. While this did not improve neutralization or therapeutic potency of F5 against IAB, it did increase cross-reactivity to other closely related VEEV epizootic and enzootic strains, demonstrating the potential of this method to rapidly adapt existing therapeutics to emerging viral strains.
affinity-maturation↗
Sorption kinetics and stability of conventional adsorbents for mercury remediation
In-situ remediation of mercury at numerous contaminated sites worldwide is a challenging and costly endeavor due to the persistency of this contaminant. In this study, we evaluated eight commercially available sorbent media ranging from carbon-, clays- and silica-based materials (PBC– Biochar, eSorb – Sorbster, nsPAC – Powdered Activated Carbon, fsPAC – Powdered Activated Carbon with Mackinawite, F300 – Filtrasorb 300, Si-SH – Silica Thiol, eBind – RemBind, Q-Clay – Organoclay PM-199), for their effectiveness in sorbing mercury (Hg 2+ ) and mercury complexed with dissolved organic matter (Hg-DOM). Under the chosen experimental conditions of this study, results showed that in the absence of DOM, the kinetic rates of Hg 2+ sorption onto the evaluated sorbents were in the order of 0.31 min-1 (Si-SH) to 2.98 min -1 (nsPAC), whereas in the presence of DOM, the rates varied from 0.16 min-1 (F300) to 0.95 min -1 (nsPAC). The measured sorption capacity for Hg 2+ in the absence of DOM varied from 3.02 mg/g (Q-Clay) to 35.15 mg/g (Si-SH), whereas in the presence of DOM, calculated partition coefficient (KD) ranged from 69.7 mL/g (Q-Clay) to 41,510 mL/g (Si-SH). Furthermore, kinetic data suggest liquid film diffusion was the rate-limiting steps governing mercury sorption onto the studied media. Overall, the obtained study parameters (kinetics/isotherm) are particularly important in informing robust engineering designs for deployment of the vast majority of evaluated sorbents. Thus, sorbent-based strategies offer viable solutions for cost-effective cleanup of mercury at industrially contaminated sites.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Deuteration removes quantum dipolar defects from KDP crystals
Abstract Dielectric properties of the hydrogen-bonded ferroelectric crystal KH 2 PO 4 (KDP) differ significantly from those of KD 2 PO 4 (DKDP). It is well established that deuteration affects the interplay of hydrogen-bond switches and heavy ion displacements that underlie the emergence of macroscopic polarization, but a detailed microscopic model is missing. We show that all-atom path integral molecular dynamics simulations can predict the isotope effects, revealing the microscopic mechanism that differentiates KDP and DKDP. Proton tunneling generates phosphate configurations that do not contribute to the polarization. At low temperatures, these quantum dipolar defects are substantial in KDP but negligible in DKDP. These intrinsic defects explain why KDP has lower spontaneous polarization and transition entropy than DKDP. The prominent role of quantum fluctuations in KDP is related to the unusual strength of the hydrogen bonds and should be equally important in other crystals of the KDP family, which exhibit similar isotope effects.
Yang, Bingjia (ORCID:0000000340749553)↗
Structure-driven development of a biomimetic rare earth artificial metalloprotein
The 2011 discovery of the first rare earth–dependent enzyme in methylotrophic Methylobacterium extorquens AM1 prompted intensive research toward understanding the unique chemistry at play in these systems. This enzyme, an alcohol dehydrogenase (ADH), features a La 3+ ion closely associated with redox-active coenzyme pyrroloquinoline quinone (PQQ) and is structurally homologous to the Ca 2+ -dependent ADH from the same organism. AM1 also produces a periplasmic PQQ-binding protein, PqqT, which we have now structurally characterized to 1.46-Å resolution by X-ray diffraction. This crystal structure reveals a Lys residue hydrogen-bonded to PQQ at the site analogously occupied by a Lewis acidic cation in ADH. Accordingly, we prepared K 142 A- and K 142 D-PqqT variants to assess the relevance of this site toward metal binding. Isothermal titration calorimetry experiments and titrations monitored by UV–Vis absorption and emission spectroscopies support that K 142 D-PqqT binds tightly (Kd = 0.6 ± 0.2 μM) to La 3+ in the presence of bound PQQ and produces spectral signatures consistent with those of ADH enzymes. These spectral signatures are not observed for WT- or K 142 A-variants or upon addition of Ca 2+ to PQQ ⸦ K 142 D-PqqT. Addition of benzyl alcohol to La 3+ -bound PQQ ⸦ K 142 D-PqqT (but not Ca 2+ -bound PQQ ⸦ K 142 D-PqqT, or La 3+ -bound PQQ ⸦ WT-PqqT) produces spectroscopic changes associated with PQQ reduction, and chemical trapping experiments reveal the production of benzaldehyde, supporting ADH activity. By creating a metal binding site that mimics native ADH enzymes, we present a rare earth-dependent artificial metalloenzyme primed for future mechanistic, biocatalytic, and biosensing applications.
Science & Technology - Other Topics↗
M3SF-25LL010302052 - Radionuclide Interaction with Hydrothermally Altered Repository Materials
This progress report (Level 3 Milestone Number M3SF-25LL010302052) summarizes research conducted at Lawrence Livermore National Laboratory (LLNL) within the Crystalline Host Rock Properties & Processes - LLNL Number SF-25LL01030205. Observed changes in radionuclide sorption after bentonite/clay heating have implications for radionuclide diffusive transport through engineered barriers and must be considered when designing waste disposal repositories. Recent research performed at Los Alamos National Laboratory (LANL) has provided key insights regarding the hydrothermal alteration behavior of bentonite backfill in the presence of repository materials (steel, concrete, etc.). We are examining how this mineral alteration affects retardation behavior of a suite of radionuclides of interest to repository performance assessment. Sorption experiments and data analysis for 233 U were initiated in FY24 following earlier experiments performed on 243 Am, 90 Sr, 137 Cs. In FY25, we completed the 233 U study and initiated and completed a study of 237 Np sorption. Below, we summarize the results and potential impacts of hydrothermal alteration on radionuclide retardation and assess the importance of this process to radionuclide migration from a GHRDC. We also use statistical tools (i.e. PCA) to help us determine the major drivers in affecting changes in measured Kd values induced by hydrothermal alteration. These experiments also allow us to test the predictive ability of our component additivity approach to surface complexation and ion exchange. Our guiding hypothesis is that a robust surface complexation/ion exchange model and associated database can effectively predict changes in radionuclide sorption behavior resulting from the hydrothermal alteration of mineralogy in a repository near field. In November 2024 the paper “Selenium interaction with iron minerals: Quantitative comparison of sorption and coprecipitation impacts on mobility” was published in Applied Geochemistry. A short update of results to date is presented below. In FY25, we also actively supported the DITUSC project, which is part of the EURADII initiative, as associate partners. We are executing the Migration2025 conference and support associated the NEA-TDB and Thermochimie workshops that will provide critical international engagements and develop consensus and synergy in thermodynamics as it relates to supporting the US nuclear waste repository program.
12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
Sugar Relese Supplementary Text and Figures
Phylogenetic tree of GAUT Protein Family and gene model, RNAi construct, and relative transcript abundance of GAUT4 in switchgrass, rice and poplar knockdown (KD) lines.
bio engineered↗