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At least 145 records · Page 8

All sources NASA NTRS DOE OSTI

DOE OSTI2022

Discovery of unknown posttranslational modifications by top-down mass spectrometry

Post-translational modifications can be important biomarkers of function within biological systems. Top-down mass spectrometry is a valuable tool for the characterization of combinatorial modifications on proteins such as histones that have a range of complex modifications. In this chapter, we present a top-down liquid chromatography-mass spectrometry experimental and data analysis workflow for the identification of novel modifications on proteins. The data analysis workflow presented here is reliant on the combination of proteoform searching using TopPIC and data visualization and fragment ion spectral confirmation using LcMsSpectator, part of the Informed-Proteomics package of software.

Wilson, Jesse W.↗

DOE OSTI2022

Disentangling jet modification in jet simulations and in Z+jet data

The selection of jets in heavy-ion collisions based on their p T after jet quenching is known to bias towards jets that lost little energy in the quark-gluon plasma. In this work, we study and quantify the impact of this selection bias on jet substructure observables so as to isolate effects caused by the modification of the substructure of jets by quenching. We do so at first in a simplified Monte Carlo study in which it is possible to identify the same jet before and after quenching. We show explicitly that jets selected based on their quenched (i.e. observable) p T have substantially smaller fractional energy loss than those selected based on the p T that they would have had in the absence of any quenching. This selection bias has a large impact on jet structure and substructure observables. As an example, we consider the angular separation ΔR of the hardest splitting in each jet, and find that the ΔR distribution of the (biased) sample of jets selected based upon their quenched p T is almost unmodified by quenching. In contrast, quenching causes dramatic modifications to the ΔR distribution of a sample of jets selected based upon their unquenched p T , with a significant enhancement at larger ΔR coming from the soft particles originating from the wake of the jet in the quark-gluon plasma. The jets which contribute to this enhancement are those which have lost the most energy and which were, therefore, left out of the sample selected after quenching. In a more realistic study, we then show that the same qualitative effects can all be observed in Z+jet events. Selecting jets in such events based on either the jet p T or the Z-boson p T provides an experimentally accessible way to quantify the effects of selection biases in jet observables and separate them from the modification of jet substructure caused by quenching. Selecting Z+jet events based upon the jet p T yields a ΔR distribution that appears almost unmodified whereas selecting Z+jet events based upon the Z-boson p T reveals a significant modification to the ΔR-distribution caused by quenching, once again arising from the wakes of those jets that lose more energy.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

DOE OSTI2025

Fortifying the frontier: cell wall modifications during plant immunity

The plant cell wall (CW) was long thought to be a rigid barrier encasing the plant cell and protecting it against biotic and abiotic stressors. Different CW polysaccharides interact with each other, and modifications of either the components or organization of these polysaccharides result in impaired growth or immunity. Emerging evidence suggests that the CW is dynamically modified and reorganized based on internal and external cues. Thus, the CW is both the first barrier that pathogens encounter and the critical final step in defense signaling that leads to fortification of the CW. Here, in this work, we review recent findings on how CW components are remodeled to fortify the CW upon pathogen attack and propose a novel concept: layered CW remodeling as an immune strategy. Within this framework, we categorize three interconnected layers of CW remodeling upon pathogen attack: (i) rapid and reversible CW depositions that provide immediate but transient protection; (ii) flexible modifications with plausible signaling functions that integrate defense and surveillance; and (iii) irreversible fortifications that encase pathogen, delimiting infected cells from uninfected cells. This layered framework provides a cohesive view of how different CW modifications are integrated into, and contribute to, plant defense. We also discuss the challenges in studying CW modifications during biotic stresses and highlight important questions that remain unanswered.

Bhandari, Deepak D. [Michigan State Univ., East La↗

DOE OSTI2026

Site-Selective Modification of Lanthanum Oxychloride to Modulate Halide-Ion Conduction

Design principles for solid-state halide-ion conduction remain poorly defined despite the increasing importance of halide ions as charge carriers in a variety of energy storage and electrochemical computing technologies. Here, we employ a siteselective modification strategy in which aliovalent cations are preferentially introduced at the La 3+ crystallographic site of LaOCl in the 2c Wyckoff position, enabling controlled generation of chloride vacancies and modification of lattice dynamics to enhance chloride-ion conductivity. Aliovalent substitution of La 3+ with Mg 2+ , Ca 2+ , and Sr 2+ generates charge-compensating Cl vacancies while preserving the matlockite crystal structure. X-ray excited optical luminescence measurements with Dy 3+ as a reporter chromophore evidence vacancy-derived midgap electronic states and an extended energy range of radiation-less Auger electron emission corresponding to substantial modification of electronic structure and local electrostatic potentials. Ca alloying at 8−10 at. % increases the chloride-ion conductivity by three- to 4 orders of magnitude as compared to unalloyed LaOCl, whereas comparable amounts of Sr- and Mg-alloying in LaOCl imbue less pronounced conductivity enhancements. Temperature-dependent Raman spectroscopy measurements reveal that Ca- and Sr-alloying substantially soften the La−Cl sublattice and yield a more compliant crystal lattice that can deform to accommodate Cl-ion migration. Structure solutions derived from Rietveld refinements to powder Xray diffraction reveal larger O−La−Cl bond-angle deviations and enhanced out-of-plane cation displacements for Ca- and Sr-alloyed compositions as compared to Mg-alloyed LaOCl. Such local distortions enhance chloride-ion mobility by reshaping and flattening vacancy migration energy landscapes and by modulating lattice dynamics governing anion conduction. We further illustrate that coalloying of Ca with Mg and Sr induces a nonmonotonic conductivity−defect stoichiometry relationship that can be rationalized based on cooperative interactions. Together, these results establish site-selective aliovalent alloying of LaOCl as an effective route to halide-ion solid electrolytes and provide broadly generalizable design principles for site-selective modification to induce vacancy formation and lattice softening to engender facile anion transport

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2015

Understanding the role of NH 4 F and Al 2 O 3 surface co-modification on lithium-excess layered oxide Li 1.2 Ni 0.2 Mn 0.6 O 2

In this work we prepared Li 1.2 Ni 0.2 Mn 0.6 O 2 (LNMO) using a hydroxide co-precipitation method and investigated the effect of co-modification with NH 4 F and Al 2 O 3 . After surface co-modification, the first cycle Coulombic efficiency of Li 1.2 Ni 0.2 Mn 0.6 O 2 improved from 82.7% to 87.5%, and the reversible discharge capacity improved from 253 to 287 mAh g –1 at C/20. Moreover, the rate capability also increased significantly. A combination of neutron diffraction (ND), high-resolution transmission electron microscopy (HRTEM), aberration-corrected scanning transmission electron microscopy (a-STEM)/electron energy loss spectroscopy (EELS), and X-ray photoelectron spectroscopy (XPS) revealed the changes of surface structure and chemistry after NH 4 F and Al 2 O 3 surface co-modification while the bulk properties showed relatively no changes. These complex changes on the material s surface include the formation of an amorphous Al 2 O 3 coating, the transformation of layered material to a spinel-like phase on the surface, the formation of nanoislands of active material, and the partial chemical reduction of surface Mn 4+ . Such enhanced discharge capacity of the modified material can be primarily assigned to three aspects: decreased irreversible oxygen loss, the activation of cathode material facilitated with preactivated Mn 3+ on the surface, and stabilization of the Ni-redox pair. In conclusion, these insights will provide guidance for the surface modification in high-voltage-cathode battery materials of the future.

36 MATERIALS SCIENCE↗

DOE OSTI2025

MXenoids: Generalization of MXene-Inspired Covalent Surface Modifications Across Two-Dimensional Materials

The ability to perform versatile covalent surface modifications in two-dimensional (2D) inorganic materials marks a significant advance in the functionalization of this broad family of materials. One particularly successful example of 2D materials with chemically modifiable surfaces are 2D transition metal carbides and nitrides (MXenes). MXenes' strong in-plane metal-carbon bonds and labile surface metal-halide bonds create altogether unprecedented opportunities for versatile postsynthetic modifications and assembling complex materials, including various organic-inorganic hybrids. Here, we demonstrate the general applicability of this surface modification strategy to non-MXene halide-terminated 2D materials, termed MXenoids. These surface modifications enable compositional and electronic structure engineering, introduce chiral hybrid organic-inorganic structures, and photoluminescence ranging from near-IR to blue. This study highlights the avenue of surface chemistry-driven materials design, enhancing the functional capabilities of 2D materials.

Zhou, Chenkun [University of Chicago, IL (United S↗

DOE OSTI2014

Electrochemical Modification of Indium Tin Oxide Using Di(4-nitrophenyl) Iodonium Tetrafluoroborate

Optoelectronic applications typically rely on indium tin oxide (ITO) as a transparent electrode material. Improvements in the performance of such devices as photovoltaics and light-emitting diodes often requires robust, controllable modification of the ITO surface to enhance interfacial charge transfer properties. Here, modifier films were deposited onto ITO by the electrochemical reduction of di(4-nitrophenyl) iodonium tetrafluoroborate (DNP), allowing for control over surface functionalization. The surface coverage could be tuned from submonolayer to multilayer coverage by either varying the DNP concentration or the number of cyclic voltammetry (CV) grafting scans. Modification of ITO with 0.8 mM DNP resulted in near-monolayer surface coverage (4.95 × 10 14 molecules/cm 2 ). X-ray photoelectron spectroscopy (XPS) analysis confirmed the presence of 4-nitrophenyl (NO 2 Ph) moieties on the ITO surface through the detection of a NO 2 nitrogen signal at 405.6 eV after grafting. Further XPS evidence suggests that the NO 2 Ph radicals do not bond to the surface indium or tin sites, consistent with modification occurring either through bonding to surface hydroxyl groups or through strong physisorption on ITO. CV in the presence of an electroactive probe and electrochemical impedance spectroscopy (EIS) were used to explore the electronic effects that modification via DNP has on ITO. Even at submonolayer coverage, the insulating organic films can reduce the current response to ferrocene oxidation and reduction by more than 25% and increase the charge transfer resistance by a factor of 10.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2020

Improvement of cryo-EM maps by density modification

A density-modification procedure for improving maps from single-particle electron cryogenic microscopy (cryo-EM) is presented here. The theoretical basis of the method is identical to that of maximum-likelihood density modification, previously used to improve maps from macromolecular X-ray crystallography. Key differences from applications in crystallography are that the errors in Fourier coefficients are largely in the phases in crystallography but in both phases and amplitudes in cryo-EM, and that half-maps with independent errors are available in cryo-EM. These differences lead to a distinct approach for combination of information from starting maps with information obtained in the density-modification process. The density-modification procedure was applied to a set of 104 datasets and improved map-model correlation and increased the visibility of details in many of the maps. The procedure requires two unmasked half-maps and a sequence file or other source of information on the volume of the macromolecule that has been imaged.

47 OTHER INSTRUMENTATION↗

DOE OSTI2019

The mechanism of eutectic modification by trace impurities

In the quest toward rational design of materials, establishing direct links between the attributes of microscopic building blocks and the macroscopic performance limits of the bulk structures they comprise is essential. Building blocks of concern to the field of crystallization are the impurities, foreign ingredients that are either deliberately added to or naturally present in the growth medium. While the role of impurities has been studied extensively in various materials systems, the inherent complexity of eutectic crystallization in the presence of trace, often metallic impurities ('eutectic modification') remains poorly understood. In particular, the origins behind the drastic microstructural changes observed upon modification are elusive. Herein, we employ an integrated imaging approach to shed light on the influence of trace metal impurities during the growth of an irregular (faceted-non-faceted) eutectic. Our dynamic and 3D synchrotron-based X-ray imaging results reveal the markedly different microstructural and, for the first time, topological properties of the eutectic constituents that arise upon modification, not fully predicted by the existing theories. Together with ex situ crystallographic characterization of the fully-solidified specimen, our multi-modal study provides a unified picture of eutectic modification: The impurities selectively alter the stacking sequence of the faceted phase, thereby inhibiting its steady-state growth. Consequently, the non-faceted phase advances deeper into the melt, eventually engulfing the faceted phase in its wake. We present a quantitative topological framework to rationalize these experimental observations.

36 MATERIALS SCIENCE↗

DOE OSTI2021

Structurally silent peptide anchor modifications allosterically modulate T cell recognition in a receptor-dependent manner

Presentation of peptides by class I MHC proteins underlies T cell immune responses to pathogens and cancer. The association between peptide binding affinity and immunogenicity has led to the engineering of modified peptides with improved MHC binding, with the hope that these peptides would be useful for eliciting cross-reactive immune responses directed toward their weak binding, unmodified counterparts. Increasing evidence, however, indicates that T cell receptors (TCRs) can perceive such anchor-modified peptides differently than wild-type (WT) peptides, although the scope of discrimination is unclear. We show here that even modifications at primary anchors that have no discernible structural impact can lead to substantially stronger or weaker T cell recognition depending on the TCR. Surprisingly, the effect of peptide anchor modification can be sensed by a TCR at regions distant from the site of modification, indicating a through-protein mechanism in which the anchor residue serves as an allosteric modulator for TCR binding. Our findings emphasize caution in the use and interpretation of results from anchor-modified peptides and have implications for how anchor modifications are accounted for in other circumstances, such as predicting the immunogenicity of tumor neoantigens. Our data also highlight an important need to better understand the highly tunable dynamic nature of class I MHC proteins and the impact this has on various forms of immune recognition.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2016

Gravitational wave tests of quantum modifications to black hole structure—with post-GW150914 update

Here a preliminary discussion is given of the prospects that gravitational-wave observations of binary inspiral of black holes (BHs) could reveal or constrain quantum modifications to BH dynamics, such as are required to preserve postulates of quantum mechanics. Different proposals for such modifications are characterized by different scales, and the size of these scales relative to those probed by observation of inspiral signals is important in determining the feasibility of finding experimental signatures. Certain scenarios with strong quantum modifications in a region extending well outside the horizon are expected to modify classical evolution, and distort the near-peak gravitational wave signal, suggesting a search for departures from waveforms predicted by general relativity. The near agreement of the GW150914 signal with such waveforms is discussed, and indicates constraints on some such scenarios. Important strategies for more precise future tests are (1) to develop more precise predictions from scenarios proposing quantum modifications, and (2) searching for observed deviations from numerical relativity predictions via analysis of gravity wave data, particularly focussing on the signal region corresponding to plunge and merger.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

DOE OSTI2026

Modification of ion-temperature-gradient turbulence by impurities in stellarator plasmas

Recent nonlinear gyrokinetic simulations have shown that impurities can strongly modify the turbulent heat flux in stellarator plasmas. Here, the ion-temperature-gradient (ITG) dispersion relation in a plasma containing impurities is analytically solved in certain limits and an expression for the modification of the ITG growth rate by impurities is derived. The analytical expression is the sum of three terms corresponding to three different physical causes (impurity density gradient, impurity temperature gradient and dilution) of the change in the growth rate. The scalings predicted analytically for the modification of the growth rate are shown to be reproduced by linear gyrokinetic simulations. The conditions for reduction or increase of the ITG growth by impurities are also correctly predicted by the analytical solution to the dispersion relation. Finally, a remarkable correlation is found between the analytical expression for the modification of the growth rate and the modification of the turbulent heat flux obtained from nonlinear gyrokinetic simulations.

Calvo, Iván [Research Centre for Energy, Environme↗

DOE OSTI2022

Measurement of ψ ( 2 S ) nuclear modification at backward and forward rapidity in p + p , p + Al , and p + Au collisions at s N N = 200 GeV

Suppression of the J/ψ nuclear-modification factor has been seen as a trademark signature of final-state effects in large collision systems for decades. In small systems, the nuclear modification was attributed to cold-nuclear-matter effects until the observation of strong differential suppression of the ψ(2S) state in p+A and d+A collisions suggested the presence of final-state effects. Results of J/ψ and ψ(2S) measurements in the dimuon decay channel are presented here for p+p, p+Al, and p+Au collision systems at $\sqrt{^{S}NN}$ = 200 GeV. The results are predominantly shown in the form of the nuclear-modification factor, R pA , the ratio of the ψ(2S) invariant yield per nucleon-nucleon collision in collisions of proton on target nucleus to that in p+p collisions. Finally, measurements of the J/ψ and ψ(2S) nuclear-modification factor are compared with shadowing and transport-model predictions, as well as to complementary measurements at Large-Hadron-Collider energies.

73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗

DOE OSTI2020

Fruit development and epigenetic modifications

Summary Fruit development is a complex process that is regulated not only by plant hormones and transcription factors, but also requires epigenetic modifications. Epigenetic modifications include DNA methylation, histone post‐translational modifications, chromatin remodeling and noncoding RNAs. Together, these epigenetic modifications, which are controlled during development and in response to the environment, determine the chromatin state of genes and contribute to the transcriptomes of an organism. Recent studies have demonstrated that epigenetic regulation plays an important role in fleshy fruit ripening. Dysfunction of a DNA demethylase delayed ripening in tomato, and the application of a DNA methylation inhibitor altered ripening process in the fruits of several species. These studies indicated that manipulating the epigenome of fruit crops could open new ways for breeding in the future. In this review, we highlight recent progress and address remaining questions and challenges concerning the epigenetic regulation of fruit development and ripening.

Tang, Dengguo↗

DOE OSTI2017

Significance of a Posttranslational Modification of the PilA Protein of Geobacter sulfurreducens for Surface Attachment, Biofilm Formation, and Growth on Insoluble Extracellular Electron Acceptors

Geobacter sulfurreducens , an anaerobic metal-reducing bacterium, possesses type IV pili. These pili are intrinsic structural elements in biofilm formation and, together with a number of c -type cytochromes, are thought to serve as conductive nanowires enabling long-range electron transfer (ET) to metal oxides and graphite anodes. Here, we report that a posttranslational modification of a nonconserved amino acid residue within the PilA protein, the structural subunit of the type IV pili, is crucial for growth on insoluble extracellular electron acceptors. Matrix-assisted laser desorption ionization (MALDI) mass spectrometry of the secreted PilA protein revealed a posttranslational modification of tyrosine-32 with a moiety of a mass consistent with a glycerophosphate group. Mutating this tyrosine into a phenylalanine inhibited cell growth with Fe(III) oxides as the sole electron acceptor. In addition, this amino acid substitution severely diminished biofilm formation on graphite surfaces and impaired current output in microbial fuel cells. These results demonstrate that the capability to attach to insoluble electron acceptors plays a crucial role for the cells' ability to utilize them. The work suggests that glycerophosphate modification of Y32 is a key factor contributing to the surface charge of type IV pili, influencing the adhesion of Geobacter to specific surfaces. Type IV pili are bacterial appendages that function in cell adhesion, virulence, twitching motility, and long-range electron transfer (ET) from bacterial cells to insoluble extracellular electron acceptors. The mechanism and role of type IV pili for ET in Geobacter sulfurreducens is still a subject of research. In this study, we identified a posttranslational modification of the major G. sulfurreducens type IV pilin, suggested to be a glycerophosphate moiety. We show that a mutant in which the glycerophosphate-modified tyrosine-32 is replaced with a phenylalanine has reduced abilities for ET and biofilm formation compared with those of the wild type. The results show the importance of the glycerophosphate-modified tyrosine for surface attachment and electron transfer in electrode- or Fe(III)-respiring G. sulfurreducens cells.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2017

Identification of Glutaminyl Cyclase Genes Involved in Pyroglutamate Modification of Fungal Lignocellulolytic Enzymes

The breakdown of plant biomass to simple sugars is essential for the production of second-generation biofuels and high-value bioproducts. Currently, enzymes produced from filamentous fungi are used for deconstructing plant cell wall polysaccharides into fermentable sugars for biorefinery applications. A post-translational N-terminal pyroglutamate modification observed in some of these enzymes occurs when N-terminal glutamine or glutamate is cyclized to form a five-membered ring. This modification has been shown to confer resistance to thermal denaturation for CBH-1 and EG-1 cellulases. In mammalian cells, the formation of pyroglutamate is catalyzed by glutaminyl cyclases. Using the model filamentous fungus Neurospora crassa , we identified two genes ( qc-1 and qc-2 ) that encode proteins homologous to mammalian glutaminyl cyclases. We show that qc-1 and qc-2 are essential for catalyzing the formation of an N-terminal pyroglutamate on CBH-1 and GH5-1. CBH-1 and GH5-1 produced in a Δqc-1 Δqc-2 mutant, and thus lacking the N-terminal pyroglutamate modification, showed greater sensitivity to thermal denaturation, and for GH5-1, susceptibility to proteolytic cleavage. QC-1 and QC-2 are endoplasmic reticulum (ER)-localized proteins. The pyroglutamate modification is predicted to occur in a number of additional fungal proteins that have diverse functions. The identification of glutaminyl cyclases in fungi may have implications for production of lignocellulolytic enzymes, heterologous expression, and biotechnological applications revolving around protein stability.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2015

Notification of General Class 1 Permit Modification for the Los Alamos National Laboratory (LANL) Hazardous Waste Facility Permit, EPA ID # NM0890010515

This document contains a notification for a Class 1 Permit Modification to modify the Los Alamos National Laboratory (LANL) Hazardous Waste Facility Permit (Permit). The text modifications are provided herein and have been made to the Permit by the Department of Energy (DOE) and Los Alamos National Security, LLC (LANS), collectively the Permittees. The modifications to the text of the Permit have been identified using red text and red lines through the texts for deletions. Description: This modification includes three changes. One change includes an address change within the Attachment D, Contingency Plan, and the remaining changes correct two typographical errors in Permit Section 2.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

DOE OSTI2017

Study of Perfluorophosphonic Acid Surface Modifications on Zinc Oxide Nanoparticles

In this study, perfluorinated phosphonic acid modifications were utilized to modify zinc oxide (ZnO) nanoparticles because they create a more stable surface due to the electronegativity of the perfluoro head group. Specifically, 12-pentafluorophenoxydodecylphosphonic acid, 2,3,4,5,6-pentafluorobenzylphosphonic acid, and (1H,1H,2H,2H-perfluorododecyl)phosphonic acid have been used to form thin films on the nanoparticle surfaces. The modified nanoparticles were then characterized using infrared spectroscopy, X-ray photoelectron spectroscopy, and solid-state nuclear magnetic resonance spectroscopy. Dynamic light scattering and scanning electron microscopy-energy dispersive X-ray spectroscopy were utilized to determine the particle size of the nanoparticles before and after modification, and to analyze the film coverage on the ZnO surfaces, respectively. Zeta potential measurements were obtained to determine the stability of the ZnO nanoparticles. It was shown that the surface charge increased as the alkyl chain length increases. This study shows that modifying the ZnO nanoparticles with perfluorinated groups increases the stability of the phosphonic acids adsorbed on the surfaces. Thermogravimetric analysis was used to distinguish between chemically and physically bound films on the modified nanoparticles. The higher weight loss for 12-pentafluorophenoxydodecylphosphonic acid and (1H,1H,2H,2H-perfluorododecyl)phosphonic acid modifications corresponds to a higher surface concentration of the modifications, and, ideally, higher surface coverage. While previous studies have shown how phosphonic acids interact with the surfaces of ZnO, the aim of this study was to understand how the perfluorinated groups can tune the surface properties of the nanoparticles

perfluorophosphonic acid↗