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At least 37 records · Page 2
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

From quantitative trait loci towards mechanisms: Linkage Integration Hypothesis Testing (LIgHT) sheds light on the mechanisms of genetically modulated stress tolerance

The goal of this work is to assess the mechanistic bases of natural genetic variations in plant responses of photosynthesis to stress. To achieve this goal, we devised the Linkage Integration Hypothesis Testing (LIgHT) approach, comparing chromosomal locations of quantitative trait loci (QTLs) for multiple phenotypes to distinguish between hypothetical mechanisms. As a use case, we explored genetic variations in photosynthesis-related processes under chilling stress in recombinant inbred lines of cowpea ( Vigna unguiculata L. Walp.). We focused on photosynthesis-related parameters measurable in high throughput and indicative of proposed chilling responses, including the states of PSI and PSII, photoprotective non-photochemical quenching, PSII photodamage, and nyctinastic leaf movements (NLMs). The patterns of QTL linkages indicated that chilling stress tolerance is genetically controlled by avoiding PSII photodamage rather than PSI damage or NLMs. This model was validated in a separate experiment measuring the rates of PSII photodamage and repair. Additional linkages suggest that chilling-induced damage to PSII is controlled by the thylakoid proton motive force and redox state of PSII. This regulation appears to be modulated by thylakoid fatty acid composition, previously associated with the same genetic loci and now supported by broader mechanistic evidence. We propose that the LIgHT approach can be broadly applied to test mechanisms underlying genetic variations.

MultispeQ↗
DOE OSTI2020

Glycosidic linkage, N -acetyl side-chain, and other structural properties of methyl 2-acetamido-2-deoxy-β- D -glucopyranosyl-(1→4)-β- D -mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2-acetamido-2-deoxy-β-D-glycopyranosyl-(1→4)-β-D-mannopyranoside monohydrate, C 15 H 27 NO 11 ·H 2 O, was determined and its structural properties compared to those in a set of mono- and disaccharides bearing N -acetyl side-chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N -acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen-bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis – trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter-residue hydrogen bonding and some bond angles in or proximal to β-(1→4) O -glycosidic linkages on linkage torsion angles φ and ψ. Hypersurfaces correlating φ and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.

Chemistry↗
DOE OSTI2020

Nucleophilic Thiols Reductively Cleave Ether Linkages in Lignin Model Polymers and Lignin

Lignin may serve as a renewable feedstock for the production of chemicals and fuels if mild, scalable processes for its depolymerization can be devised. The use of small organic thiols represents a bioinspired strategy to cleave the β–O–4 bond, the most common linkage in lignin. In the present study, synthetic β–O–4 linked polymers were treated with organic thiols, yielding up to 90 % cleaved monomer products. Lignin extracted from poplar was also treated with organic thiols resulting in molecular weight reductions as high as 65 % (Mn) in oxidized lignin. Thiol–based cleavage of other lignin linkages was also explored in small–molecule model systems to uncover additional potential pathways by which thiols might depolymerize lignin. The success of thiol–mediated cleavage on model dimers, polymers, and biomass–derived lignin illustrates the potential utility of small redox–active molecules to penetrate complex polymer matrices for depolymerization and subsequent valorization of lignin into fuels and chemicals.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Single-Crystal Optical Actuation Generated by 100% SO 2 Linkage Photoisomerization in a Ruthenium-Based Coordination Complex

Single-crystal optical actuators are emerging as a new field of materials chemistry because of their wide-ranging potential applications, from light-induced molecular motors to photosensing technologies. Ruthenium-based coordination complexes that contain sulfur dioxide linkage photoisomers have shown particular promise as optical actuators, given that they may exhibit either optical switching or nano-optomechanical transduction in their single-crystal form. The type of single-crystal optical actuation observed in a specific compound within this family of complexes depends upon the nature of the ligand that lies trans to this SO 2 linkage photoisomer, since this governs the type and extent of photoisomer (η 2 -(OS)O or η 1 -OSO) that will form upon the application of light. We report the discovery of a new complex, trans-[Ru(SO 2 )(NH 3 ) 4 (3-iodopyridine)]tosylate 2 (1), which forms an η 1 -OSO photoisomer with 100% photoconversion upon the application of 505 nm light. The photoisomerization process in the ruthenium-based cation of 1 stimulates rotation and translation of the toluenic constituent of its neighboring anion, thereby affording nano-optomechnical transduction. We show that this η 1 -OSO photoisomer transitions to its more thermally stable η 2 -(OS)O photoisomer with an activation energy, E a , of 11(2) kJ/mol using thermally activated single-crystal optical absorption spectroscopy. The application of external light with different wavelengths to 1 is also shown to cause a variation in its optical absorption spectral characteristics. Here, this suggests that the photophysical properties of 1 may be tunable with light.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2026

Influence of linkage chemistry and side-chain polarity on Ion 2 transport in click-functionalized polymerized ionic liquids.

Post-polymerization functionalization offers precise molecular weight control and enables the high-throughput investigation of structure−property relationships in polymer research. However, post-polymerization functionalization strategies often introduce additional linkage chemistry, and its role in the physical properties of polymerized ionic liquids (PILs) has yet to be explored. In this work, a series of PILs were synthesized using Cu(I)-catalyzed azide−alkyne cycloaddition (CuAAC), with comparison made to N-alkylation substitution chemistry. The triazole ring introduced by CuAAC chemistry was found to induce extensive ion aggregation and deteriorate ion transport. The impact of linkage chemistry on ion transport can be alleviated by incorporating polar ethylene glycol spacers in the side chain, achieving an ionic conductivity of 2.1 × 10−4 S/cm at 30 °C. Furthermore, the effect of polar spacer placement was explored, revealing that overall side-chain polarity, rather than polarity in the vicinity of the ionic group, governs ion aggregation and ion transport in PILs.

Shan, Naisong↗
DOE OSTI2024

Emergence of decadal linkage between Western Australian coast and Western–central tropical Pacific

Abstract The impact of interbasin linkage on the weather/climate and ecosystems is significantly broader and profounder than that of only appearing in an individual basin. Here, we reveal that a decadal linkage of sea surface temperature (SST) has emerged between western Australian coast and western–central tropical Pacific since 1985, associated with continuous intensification of decadal variabilities (8–16 years). The rapid SST changes in both tropical Indian Ocean and Indo-Pacific warm pool in association to greenhouse gases and volcanoes are emerging factors resulting in enhanced decadal co-variabilities between these two regions since 1985. These SST changes induce enhanced convection variability over the Maritime Continent, leading to stronger easterlies in the western–central tropical Pacific during the warm phase off western Australian coast. The above changes bring about cooling in the western–central tropical Pacific and strengthened Leeuwin Current and anomalous cyclonic wind off western Australian coast, and ultimately resulting in enhanced coupling between these two regions. Our results suggest that enhanced decadal interbasin connections can offer further understanding of decadal changes under future warmer conditions.

Science & Technology - Other Topics↗
DOE OSTI2022

CUF-Links: Continuous and Ubiquitous FAIRness Linkages for Reproducible Research

Despite much creative work on methods and tools, reproducibility— the ability to repeat the computational steps used to obtain a research result—remains elusive. One reason for these difficulties is that extant tools for capturing research processes, while powerful, often fail to capture vital connections as research projects grow in extent and complexity. We explain here how these interstitial connections can be preserved via simple methods that integrate easily with current work practices to capture basic information about every data product consumed or produced in a project. By thus extending the scope of findable, accessible, interoperable, and reusable (FAIR) data in both time and space to enable the creation of a continuous chain of Continuous and Ubiquitous FAIRness linkages (CUFlinks) from inputs to outputs, such mechanisms can facilitate capture of the provenance linkages that are essential to reproducible research. Herein we give examples of mechanisms that can facilitate the use of these methods, and review how they have been applied in practice.

97 MATHEMATICS AND COMPUTING↗
DOE OSTI2024

A Million Person Study Innovation: Evaluating Cognitive Impairment and other Morbidity Outcomes from Chronic Radiation Exposure Through Linkages with the Centers for Medicaid and Medicare Services Assessment and Claims Data

Here, the study of One Million U.S. Radiation Workers and Veterans, the Million Person Study (MPS), examines the health consequences, both cancer and non-cancer, of exposure to ionizing radiation received gradually over time. Recently the MPS has focused on mortality patterns from neurological and behavioral conditions, e.g., Parkinson's disease, Alzheimer's disease, dementia, and motor neuron disease such as amyotrophic lateral sclerosis. A fuller picture of radiation-related late effects comes from studying both mortality and the occurrence (incidence) of conditions not leading to death. Accordingly, the MPS is identifying neurocognitive diagnoses from fee-for-service insurance claims from the Centers for Medicare and Medicaid Services (CMS), among Medicare beneficiaries beginning in 1999 (the earliest date claims data are available). Linkages to date have identified ∼540,000 workers with available health information. Such linkages provide individual information on important co-factor and confounding variables such as smoking, alcohol consumption, blood pressure, obesity, diabetes and many other health and demographic characteristics. The total person-level set of time-dependent variables, outcomes, organ-specific dose measures, co-factors, and demographics will be massive and much too large to be evaluated with standard software. Thus, development of specialized open-source software designed for large datasets (Colossus) is nearly complete. The wealth of information available from CMS claims data, coupled with individual dose reconstructions, will thus greatly enhance the quality and precision of health evaluations for this new field of low-dose radiation and neurocognitive effects.

Dauer, Lawrence T.↗
DOE OSTI2025

Higher levels of mixed-linkage (1,3;1,4)-β-glucan in transgenic grasses may impact soil C processing

Carbohydrates, including mixed-linkage glucan (MLG), in grass cell walls make them a valuable potential feedstock for biofuel production. Hence, the development of transgenic grasses with elevated levels of MLG is being actively pursued worldwide. Changes in chemical and physical root characteristics of MLG-overproducing transgenic plants can affect processing of the root-derived carbon (C) by soil microorganisms, impacting soil C cycling. Here, this study is the first attempt to elucidate the impact of MLG-related genetic modifications on root traits, root decomposition, and soil C processing. We explored four genotypes of Brachypodium ( Brachypodium distachyon ): a wildtype, a loss-of-function mutant with low MLG, an MLG overexpressing line, and a line lacking MLG hydrolase (with high MLG), incubating their roots in soils of two contrasting vegetation histories: monoculture switchgrass and polyculture restored prairie. The four genotypes exhibited contrasting root MLG and soluble sugar concentrations, and different growth phenotypes. Roots with the highest MLG content resulted in a ∼55 % increase in microbial biomass C compared to wildtype in both soils. However, the genotype effects on C mineralization rates were influenced by the vegetation history, with significant effects observed only in the soil from switchgrass but not prairie origin. While further work is required to understand the full impact of MLG-overproducing plants on soil C accrual, our findings suggest that their influence on soil C processes cannot be discounted.

Brachypodium distachyon↗
DOE OSTI2021

Tunning the linkage of structure units to enable stable spinel-based cathode in the wide potential window

The low practical capacity (<140 mA h g –1 ) of spinel phase LiMn 2–x Ni x O 4 (0 < x < 1) excludes it from high energy density lithium ion batteries (LIBs) for powering electric vehicles. Extending the operating potential window from 3.0 to 4.8 V to 2.0–4.8 V can double the capacity, but result in fast capacity decay due to the drastic cubic-tetragonal phase transition below 3.0 V, induced by serious Jahn-Teller (J-T) distortion of structure units (Mn 3+ )O 6 octahedra. Herein, we propose a novel strategy to suppress J-T distortion by tuning the linkage of structure units MnO 6 octahedra. The original full-vertex-sharing LiO 4 tetrahedra around MnO 6 octahedra in spinel phase are partially replaced by edge-sharing LiO 6 octahedra, which relate Mn-O bonds along the dz 2 direction with those along the d xy plane, thus significantly mitigating J-T distortion and suppressing the phase transition when discharged to 2.0 V. Following this strategy, the prepared spinel-based cathode achieves a high reversible capacity of about 290 mA h g –1 and an energy density up to 957 W h kg –1 with improved cycling stability. Furthermore, this work finds a new opportunity for the traditional spinel cathode towards applications in high energy density LIBs in a low cost and sustainable manner.

25 ENERGY STORAGE↗
DOE OSTI2023

Mixed-Linkage Glucan Is the Main Carbohydrate Source and Starch Is an Alternative Source during Brachypodium Grain Germination

Seeds of the model grass Brachypodium distachyon are unusual because they contain very little starch and high levels of mixed-linkage glucan (MLG) accumulated in thick cell walls. It was suggested that MLG might supplement starch as a storage carbohydrate and may be mobilised during germination. In this work, we observed massive degradation of MLG during germination in both endosperm and nucellar epidermis. The enzymes responsible for the MLG degradation were identified in germinated grains and characterized using heterologous expression. By using mutants targeting MLG biosynthesis genes, we showed that the expression level of genes coding for MLG and starch-degrading enzymes was modified in the germinated grains of knocked-out cslf6 mutants depleted in MLG but with higher starch content. Our results suggest a substrate-dependent regulation of the storage sugars during germination. These overall results demonstrated the function of MLG as the main carbohydrate source during germination of Brachypodium grain. More astonishingly, cslf6 Brachypodium mutants are able to adapt their metabolism to the lack of MLG by modifying the energy source for germination and the expression of genes dedicated for its use.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Rewritable Surface‐Grafted Polymer Brushes with Dynamic Covalent Linkages

Abstract Surface grafting of polymer brushes drastically modifies surface properties, including wettability, compatibility, responsiveness, etc. A broad variety of functionalities can be introduced to the surface via different types of polymers. Bringing together properties of two or more types of polymer brushes to one surface opens up even more possibilities in brush‐modified materials. However, while it is generally feasible to introduce several chemical compositions along the brushes via copolymerization, it is challenging to vary the types of polymer brushes along a surface. Although previous studies have demonstrated binary brushes via orthogonal polymerization techniques or partial deactivation/regrafting, they commonly limit the number of polymer types to two. Here, we propose a strategy to introduce dynamic covalent diketoenamine linkages at the root of polymer brushes. The grafting density could be precisely tuned during surface functionalization. The surface‐anchored polymer brushes were cleaved by the addition of small molecule amines. New polymer brushes can be regrafted from the surface following refunctionalization of exposed sites. The maneuverability allows tuning of the types and densities of the polymer brushes, pointing the way to the preparation of a new generation of well‐defined brush‐modified materials with mixed grafts, with potential applications in the design of smart materials and surfaces.

Cui, Feichen↗
DOE OSTI2022

Leveraging Nitrogen Linkages in the Formation of a Porous Thorium–Organic Nanotube Suitable for Iodine Capture

We report the synthesis, characterization, and iodine capture application of a novel thorium–organic nanotube, TSN-626, [Th 6 O 4 (OH) 4 (C 6 H 4 NO 2 ) 7 (CHO 2 ) 5 (H 2 O) 3 ]·3H 2 O. The classification as a metal–organic nanotube (MONT) distinguishes it as a rare and reduced dimensionality subset of metal–organic frameworks (MOFs); the structure is additionally hallmarked by low node connectivity. TSN-626 is composed of hexameric thorium secondary building units and mixed O/N-donor isonicotinate ligands that demonstrate selective ditopicity, yielding both terminating and bridging moieties. Because hard Lewis acid tetravalent metals have a propensity to bind with electron donors of rival hardness (e.g., carboxylate groups), such Th–N coordination in a MOF is uncommon. However, the formation of key structural Th–N bonds in TSN-626 cap some of the square antiprismatic metal centers, a position usually occupied by terminal water ligands. TSN-626 was characterized by using complementary analytical and computational techniques: X-ray diffraction, vibrational spectroscopy, N 2 physisorption isotherms, and density functional theory. TSN-626 satisfies design aspects for the chemisorption of iodine. The synergy between accessibility through pores, vacancies at the metal–oxo nodes, and pendent N-donor sites allowed a saturated iodine loading of 955 mg g –1 by vapor methods. Furthermore, the crystallization of TSN-626 diversifies actinide–MOF linker selection to include soft electron donors, and these Th–N linkages can be leveraged for the investigation of metal-to-ligand bonding and unconventional topological expressions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

Mechanistic Studies of Ligand Substitution, Linkage Isomerism, and Insertion Reactions in Electron Rich Pd(II) Complexes of a Zwitterionic Diimine Ligand

We have prepared cationic palladium complexes possessing a new zwitterionic ligand bis-N,N’–1-(2,4,6-triphenylpyridyl) oxalamide [(N ^ N)Pd(Me)(L)] + [BArF] - , (BArF=3,5-(CF 3 ) 2 C 6 H 3 , L=NCMe, CO). The structure of [(N ^ N)Pd(Me)(CO)] + [BArF] - was determined by X-ray diffraction analysis. Energy Decomposition Analysis (EDA) indi-cates this N ^ N zwitterionic ligand is more electron-donating relative to bidentate diimine ligands. Low temperature NMR analysis shows the existence of linkage isomers with the N ^ N isomer the most stable. Structures were assigned using NMR and DFT analysis. Barriers to interconversion of isomers are ΔG ‡ = 10-12 kcal/mol. Kinetics of acetoni-trile displacement from [(N ^ N)Pd(Me)(NCCH 3 )] + [BArF] - by CD 3 CN, ethylene and t Bu 3 P were measured and mechanisms of exchange determined. The ethylene complex, [(N ^ N)Pd(Me)(C 2 H 4 )] + was generated at -45 °C, and the barrier of migrato-ry insertion determined at 0 °C (ΔG ‡ = 23.4 kcal/mol) and compared to related diimine complexes. The methyl carbonyl complex undergoes migratory insertion in the presence of CO at -70 to -55 °C (ΔG ‡ = ca. 15.7 kcal/mol) to yield the acyl carbonyl complex. Furthermore, the neutral bis-trimethylsilylmethyl complex [(N ^ N)Pd(CH 2 SiMe 3 ) 2 was prepared and characterized by X-ray diffraction analysis. It displays dynamic behavior at very low temperatures in the NMR spectrum (-90 °C, ΔG ‡ =7.9 kcal/mol) which, supported by DFT analysis, is ascribed to rotation of the bulky -CH 2 SiMe 3 groups.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Linkages Between Mineral Element Composition of Soils and Sediments With Hyporheic Zone Dissolved Organic Matter Chemistry Across the Contiguous United States

The hyporheic zone is a hotspot for biogeochemical cycling where interactions with mineral metals preserve the release and biodegradation of organic matter (OM). A small fraction of OM can still be exchanged between localized sediments and the overlying water column, and recent evidence suggests there exists a longitudinal structuring in sediment dissolved OM (DOM) chemistry across the continental United States (CONUS). In this study, we tested a hypothesis that water extractable sediment DOM chemistry could be explained by sediment metal contents and integrative watershed scale features at the CONUS scale. Crowdsourced samples were characterized for high resolution mass spectrometry and coupled with sediment metals determined via x-ray fluorescence as well as with land cover and soil elemental information obtained from national databases. Our results highlight weak relationships between DOM chemistry and elemental composition at the CONUS scale indicating limited transferability of organo-metal linkages into multi-scale hydrobiogeochemical models.

58 GEOSCIENCES↗
DOE OSTI2021

Modeling dark- and light-induced crystal structures and single-crystal optical absorption spectra of ruthenium-based complexes that undergo SO 2 -linkage photoisomerization

A family of coordination complexes of the type [Ru(SO 2 )(NH 3 ) 4 X] m+ Y n – (m, n = 1 or 2) exhibit optical switching capabilities in their single-crystal states. This striking effect is caused by the light-induced formation of SO 2 -linkage photoisomers, which are metastable if kept at suitably cool temperatures. We modeled the dark- and light-induced states of these large crystalline complexes via plane-wave (PW)- and molecular-orbital (MO)-based density functional theory (DFT) and time-dependent DFT in order to calculate their structural and optical properties; the calculated results are compared with experimental data. We show that the PW-DFT-based periodic models replicate the structural properties of these complexes more effectively than the MO-DFT-based molecular-fragment models, observing only small deviations in key bond lengths relative to the experimentally derived crystal structures. The periodic models were also found to more effectively simulate trends seen in experimental optical absorption spectra, with optical absorbance and coverage of the visible region increasing with the formation of the photoinduced geometries. The contribution of the metastable photoisomeric species more heavily focuses on the lower-energy end of the spectra. Spectra generated from the molecular-fragment models are limited by the geometry of the fragment used and the number of excited-state roots considered in those calculations. In general, periodic models outperform the molecular-fragment models owing to their ability to better appreciate the periodic phenomena that are present in these crystalline materials as opposed to MO approaches, which are finite methods. We thus demonstrate that PW-DFT-based periodic models should be considered as a more than viable method for simulating the optical and electronic properties of these single-crystal optical switches.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Landscape analysis of environmental data sources for linkage with SEER cancer patients database

Abstract One of the challenges associated with understanding environmental impacts on cancer risk and outcomes is estimating potential exposures of individuals diagnosed with cancer to adverse environmental conditions over the life course. Historically, this has been partly due to the lack of reliable measures of cancer patients’ potential environmental exposures before a cancer diagnosis. The emerging sources of cancer-related spatiotemporal environmental data and residential history information, coupled with novel technologies for data extraction and linkage, present an opportunity to integrate these data into the existing cancer surveillance data infrastructure, thereby facilitating more comprehensive assessment of cancer risk and outcomes. In this paper, we performed a landscape analysis of the available environmental data sources that could be linked to historical residential address information of cancer patients’ records collected by the National Cancer Institute’s Surveillance, Epidemiology, and End Results Program. The objective is to enable researchers to use these data to assess potential exposures at the time of cancer initiation through the time of diagnosis and even after diagnosis. The paper addresses the challenges associated with data collection and completeness at various spatial and temporal scales, as well as opportunities and directions for future research.

60 APPLIED LIFE SCIENCES↗