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At least 1,297 records · Page 72
All sourcesNASA NTRSDOE OSTI
DOE OSTI2020

Exploring the role of electronic structure on photo-catalytic behavior of carbon-nitride polymorphs

A fully self-consistent density-functional theory (DFT) with improved functionals is used herein to provide a comprehensive account of structural, electronic, and optical properties of C 3 N 4 polymorphs. Using our recently developed van Leeuwen-Baerends (vLB) corrected local-density approximation (LDA), we implemented LDA + vLB within full-potential N th -order muffin-tin orbital (FP-NMTO) method and show that it improves structural properties and band gaps compared to semi-local functionals (LDA/GGA). We demonstrate that the LDA + vLB predicts band-structure and work-function for well-studied 2D-graphene and bulk-Si in very good agreement with experiments, and more exact hybrid functional (HSE) calculations as implemented in the Quantum-Espresso (QE) package. The structural and electronic-structure (band gap) properties of C 3 N 4 polymorphs calculated using FP-NMTO-LDA + vLB is compared with more sophisticated hybrid-functional calculations. We also perform detailed investigation of photocatalytic behavior using QE-HSE method of C 3 N 4 polymorphs through work-function, band (valence and conduction) position with respect to water reduction and oxidation potential. Our results show $γ$-C 3 N 4 as the best candidate for photocatalysis among all the C 3 N 4 polymorphs but it is dynamically unstable at ‘zero’ pressure. We show that $γ$-C 3 N 4 can be stabilized under hydrostatic-pressure, which improves its photocatalytic behavior relative to water reduction and oxidation potentials.

36 MATERIALS SCIENCE↗
DOE OSTI2025

The pectin puzzle: Decoding the fine structure of rhamnogalacturonan-I (RG-I) in Arabidopsis thaliana uncovers new pectin features

Pectin is generally divided into four distinct structural categories, namely homogalacturonan, xylogalacturonan, rhamnogalacturonan I (RG-I) and rhamnogalacturonan II. While much of the structural diversity of homogalacturonan, xylogalacturonan and rhamnogalacturonan II has been elucidated, the structural features of RG-I are less well understood. In this work, we employed multiple complementary analytical techniques to present a detailed structural analysis of RG-I in the model species Arabidopsis thaliana . Starting with highly purified RG-I from different Arabidopsis tissues, we employed comparative linkage and nuclear magnetic resonance analysis along with mass spectrometry analysis of enzymatically digested RG-I oligosaccharides. Besides the presence of the canonical α-1,5-arabinan, β-1,4-galactan, β-1,6-galactan and arabinogalactan RG-I side chains of varying lengths, we show that a large portion of the β-1,6-galactan is terminated by either 4-O-methyl β-glucuronic acid (GlcA) residues or, to a smaller degree, β-GlcA that lacks the Me-ether group. Importantly, O-acetylation of RG-I GalA residues is a minor modification while 10 % of the backbone Rha residues are 3-O-acetylated, and most of the acetylated Rha is additionally branched with β-galactose substituents. Taken together, the combined results of these different analytical techniques present the most comprehensive structural overview of Arabidopsis thaliana RG-I to date.

25 ENERGY STORAGE↗
DOE OSTI2025

Kinetic and structural evidence for specific DMSO interference with reversible binding of uncharged bis-oximes to hAChE and their reactivation kinetics of OP-hAChE

The structural basis of inhibitory effect of organic solvent dimethyl sulfoxide (DMSO) on human acetylcholinesterase (EC 3.1.1.7; hAChE) was inferred from the effect of DMSO on kinetics of reversible inhibition of uncharged, heterocyclic bis-oximes to hAChE, from DMSO effect on rates of reactivation of inactive organophosphate (OP)-hAChE conjugates by bis-oximes and by X-ray structures of bis-oxime and DMSO binding to hAChE. Here, the reversible inhibition constant of DMSO for hAChE in 0.1 M phosphate buffer pH 7.4 at 22 °C, was K i = (0.32 ± 0.04) % (or 45 ± 5 mM). The K i of the bis-oxime LG-703 for hAChE was 3.2-fold larger in 1 % DMSO, consistent with direct competition between LG-703 and DMSO. The X-ray structure of the LG-703∗hAChE complex (PDB ID: 6U3P) shows DMSO and LG-703 bound to individual hAChE monomers, LG-703 in the chain A and DMSO in the chain B. In the co-crystallization both small molecules were present at a similar excess over their corresponding K i values for hAChE (7.8-fold for DMSO and 6.5-fold for LG-703) and formation of two different complexes (DMSO∗hAChE and LG-703∗hAChE), in the same crystal, appears consistent with inhibition kinetics. Furthermore, rates of reactivation of paraoxon-inhibited hAChE (POX-hAChE) and of VX-hAChE by LG-703 and by a novel heterocyclic bis-oxime LG-1922 were reduced 2 – 3-fold in DMSO, consistent with observation of the active-center-bound DMSO molecules in the newly solved structure of the LG-1922∗POX-hAChE complex presented here and in our POX-hAChE structure (PDB ID: 8DT2) showing obstruction of the reactivator access to the conjugated P atom.

Acetylcholinesterase inhibition↗
DOE OSTI2021

Formation, structure, and thermal stability evolution of ternesite based on a single-stage sintering process

Highlights: • The synthesis of high-purity ternesite based on a single-stage sintering process was firstly studied. • The formation mechanism and crystallization behaviour of ternesite during sintering were investigated. • The structure perfection and symmetry of ternesite crystals were increased with its growth. • The growth and structural development of ternesite crystals during sintering resulted in a higher thermal stability of itself. Ternesite was prepared via a single-stage solid-state reaction from stoichiometric quantities of the CaCO{sub 3}, SiO{sub 2} and CaSO{sub 4}·2H{sub 2}O precursors. In this paper, the formation, structure, and thermal stability evolution of ternesite during sintering were investigated ex situ after quenching. The optimal sintering temperature for the formation of high-purity ternesite was approximately 1200 °C for 12 h, of which the purity level can reach as high as 96.3%. The results from scanning electron microscopy analysis suggest that the formation of ternesite benefited from the preformation of the intermediate silicate phase. Increasing the sintering temperature from 1100 °C to approximately 1250 °C was favourable for the growth of ternesite crystals, and a prolonged duration can also promote this behaviour. The structural perfection and symmetry of ternesite crystals increased with its growth, which was demonstrated by a multimethod approach. By means of thermal analysis, the growth and structural development of ternesite crystals during sintering eventually resulted in a higher thermal stability.

36 MATERIALS SCIENCE↗
DOE OSTI2021

Effects of Co doping on the structure and physicochemical properties of hausmannite (Mn 3 O 4 ) and its transformation during aging

Hausmannite is a common low-valence manganese oxide mineral with a distorted spinel structure in surficial sediments. Although natural Mn oxides often contain various transition metal (TM) impurities, few studies have addressed the substitution mechanisms of TMs, such as cobalt (Co), with hausmannite and induced changes in the mineral physicochemical properties. In this study, Co-doped hausmannites with final Co/Mn molar ratios of 0.05 and 0.11 were synthesized and characterized by wet chemical analysis, powder X-ray diffraction (XRD), Fourier transformed infrared spectra (FTIR), high resolution transmission electron microscope (HRTEM), X-ray photoelectron spectroscopy (XPS) and X-ray absorption fine structure spectroscopy (XAFS). Co-doped samples have larger crystallite sizes and smaller specific surface areas than those of the hausmannite without Co. The Co cations exist in a mixed-valence of +3 and + 2. Powder XRD and acid dissolution experiments indicate that Co incorporates into the mineral structures, and increases the mineral structural stability. Co K-edge extended X-ray adsorption fine structure (EXAFS) analysis demonstrates that Co likely substitutes for lattice Mn(III). After aging at room temperature for three years, 14.1 ± 1.9% of pure hausmannite is transformed to manganite while only 2.6 ± 0.7% of manganite appears in the aged Co-doped sample with an initial Co/Mn molar ratio of 0.10. Finally, these results provide new insights into the incorporation mechanisms of TMs into low valence Mn oxides, and the stability of these minerals in natural environments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2020

Influence of crystal structure on constitutive anisotropy of silica sand at particle-scale

In spite of recent advanced geotechnical research regarding the influence of particle-scale morphology and fabric on the constitutive behavior of silica sands, there is still no published literature that investigated the influence of crystal structure of sand particles on their constitutive behavior. The main constituent of silica sand particles is quartz mineral, which has a trigonal crystal system and hexagonal lattice. This paper investigates the influence of quartz crystal structure on the constitutive response of silica sand particles using 3D X-ray diffraction (3DXRD), synchrotron micro-computed tomography (SMT), and 3D finite element (FE) analysis. Here, unconfined uniaxial compression experiments on single particles of synthetic silica cubes exposed the notion of constitutive anisotropy caused by the crystal structure of quartz. Since the silica cubes have simple regular geometry (1 mm) 3 , they were loaded in different directions with respect to their crystal local planes. The crystal structure was also identified for a natural silica sand specimen composed of 2705 particles and loaded in confined uniaxial compression. Physical limitations of the experimental measurements made a strong case for the use of 3D FE analysis to study how the change in crystal local orientation of individual sand particles can fundamentally produce anisotropy in the constitutive response of natural sand specimens. The 3D FE analysis was validated to accurately model the crystal-based constitutive anisotropy in silica particles using the results of the silica cube experiments. The analysis was then executed on 3D FE meshes that closely matched the physical shape and fabric of the 2705 particles in the natural sand specimen. Both the experiments and 3D FE analysis showed that the crystal structure of quartz essentially causes a directional anisotropy in the constitutive behavior of silica particles.

58 GEOSCIENCES↗
DOE OSTI2021

Room temperature crystallography of human acetylcholinesterase bound to a substrate analogue 4K-TMA: Towards a neutron structure

Acetylcholinesterase (AChE) catalyzes hydrolysis of acetylcholine thereby terminating cholinergic nerve impulses for efficient neurotransmission. Human AChE (hAChE) is a target of nerve agent and pesticide organophosphorus compounds that covalently attach to the catalytic Ser203 residue. Reactivation of inhibited hAChE can be achieved with nucleophilic antidotes, such as oximes. Understanding structural and electrostatic (i.e. protonation states) determinants of the catalytic and reactivation processes is crucial to improve design of oxime reactivators. Here we report X-ray structures of hAChE conjugated with a reversible covalent inhibitor 4K-TMA (4K-TMA:hAChE) at 2.8 Å resolution and of 4K-TMA:hAChE conjugate with oxime reactivator methoxime, MMB4 (4K-TMA:hAChE:MMB4) at 2.6 Å resolution, both at physiologically relevant room temperature, as well as cryo-crystallographic structure of 4K-TMA:hAChE at 2.4 Å resolution. 4K-TMA acts as a substrate analogue reacting with the hydroxyl of Ser203 and generating a reversible tetrahedral hemiketal intermediate that closely resembles the first tetrahedral intermediate state during hAChE-catalyzed acetylcholine hydrolysis. Structural comparisons of room temperature with cryo-crystallographic structures of 4K-TMA:hAChE and published mAChE complexes with 4K-TMA, as well as the effect of MMB4 binding to the peripheral anionic site (PAS) of the 4K-TMA:hAChE complex, revealed only discrete, minor differences. The active center geometry of AChE, already highly evolved for the efficient catalysis, was thus indicative of only minor conformational adjustments to accommodate the tetrahedral intermediate in the hydrolysis of the neurotransmitter acetylcholine (ACh). To map protonation states in the hAChE active site gorge we collected 3.5 Å neutron diffraction data paving the way for obtaining higher resolution datasets that will be needed to determine locations of individual hydrogen atoms.

4K-TMA↗
DOE OSTI2020

Structure and composition of blueberry fiber pectin and xyloglucan that bind anthocyanins during fruit puree processing

Blueberry is a well-known source of antioxidants and prebiotic dietary fiber yet the fate of these health-beneficial ingredients during fruit processing it is not understood. Detailed composition and structure of blueberry pomace (PF) remaining after commercial blueberry fruit puree processing, as well as the water soluble and water insoluble fractions, were determined. The PF was comprised of dietary fiber (60.8%) that was largely insoluble (46.2% vs. 14.6% soluble dietary fiber) pectin, xyloglucan, arabinoxylan and mannan polysaccharides, fructose (11.22%) and glucose (10.37%) free sugars, protein (9%), fat (5%), and anthocyanins (6444.5 μg/g). The most abundant anthocyanins detected in PF were malvidin 3-arabinoside and peonidin 3-glucoside and the pectin was determined to be methyl-esterified and acetylated rhamnogalacturonan I with a 4,5-unsaturated function at the non-reducing end based on oligosaccharide structural analysis. Blueberry PF xyloglucan oligosaccharide side chain structures included xylose, arabinose and galactose consistent with arabino-xyloglucan structure. Additionally, microwave-assisted extraction of blueberry PF (pH 2 for 10 min at 80 °C) was performed to more clearly elucidate pectin structure, and revealed a pectin polymer with high molar mass (1072 kDa) and viscosity that was dependent upon the molar mass. A random coil shape was confirmed for both the blueberry PF and microwave extracted blueberry pectin, which agreed with previous reports that flexible blueberry pectin contributes to strong anthocyanin binding. In summary, the blueberry pomace anthocyanin content was slightly higher than that reported for fresh whole blueberry fruit, which suggests that most blueberry anthocyanins adhered to the pomace fiber, and most likely the insoluble pectin, during and after processing.

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

Lignin-enhanced reduction of structural Fe(III) in nontronite: Dual roles of lignin as electron shuttle and donor

Lignin is a major component of plant-derived soil organic matter (SOM) in soils and sediments. Fe-bearing clay minerals are widely distributed in these environments and often co-exist with lignin. While previous studies have reported the electron shuttling and donating roles of certain redox-active SOM in the dissimilatory reduction of structural Fe(III) in Fe-bearing clay minerals, the role of lignin in this process remains unknown. Here we studied this role by incubating an Fe-rich smectite (nontronite NAu-2) with two types of lignin (soluble and insoluble) in the absence and presence of an Fe(III)-reducing bacterium Shewanella putrefaciens CN32 under anaerobic condition. Labile carbon source (i.e., lactate) was added in some experiments as an extra electron donor. The results demonstrated that both soluble and insoluble lignins abiotically reduced structural Fe(III) in NAu-2. The reduction extent was proportional to lignin concentration. After abiotic reaction, lignin served as either electron shuttle or electron donor in the presence of CN32: (1) When lactate was present, lignin served as an electron shuttle to enhance the rate of Fe(III) reduction; (2) When lactate was absent, lignin served as an electron donor for Fe(III) reduction. Although the biotic Fe(III) reduction extents were similar in the presence of either soluble or insoluble lignin, the reduction rates with soluble lignin were always higher than those with insoluble lignin, likely owing to their different electron transfer mechanisms. After interaction with NAu-2 and/or CN32, soluble lignin structure largely remained intact, but with some decreases of humic/fulvic acid-like and protein-like compounds, aromatic functional groups (e.g., C-H, C=O, COOH), and aliphatic/aromatic compounds. An increase of semiquinone-like organic radicals was observed after lignin interaction with NAu-2. These chemical changes of lignin were likely coupled with reduction of structural Fe(III) in nontronite. The nontronite structure remained largely unchanged without much dissolution and mineral transformation. The findings of this study provide insights into the role of lignin in promoting mineral-microbe interactions and have significant implications for coupled Fe and C biogeochemical cycles in soils and sediments.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2022

Integrative structural and functional analysis of human malic enzyme 3: A potential therapeutic target for pancreatic cancer

Malic enzymes (ME1, ME2, and ME3) are involved in cellular energy regulation, redox homeostasis, and biosynthetic processes, through the production of pyruvate and reducing agent NAD(P)H. Recent studies have implicated the third and least well-characterized isoform, mitochondrial NADP + -dependent malic enzyme 3 (ME3), as a therapeutic target for pancreatic cancers. Here, we utilized an integrated structure approach to determine the structures of ME3 in various ligand-binding states at near-atomic resolutions. ME3 is captured in the open form existing as a stable tetramer and its dynamic Domain C is critical for activity. Catalytic assay results reveal that ME3 is a non-allosteric enzyme and does not require modulators for activity while structural analysis suggests that the inner stability of ME3 Domain A relative to ME2 disables allostery in ME3. With structural information available for all three malic enzymes, the foundation has been laid to understand the structural and biochemical differences of these enzymes and could aid in the development of specific malic enzyme small molecule drugs.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2024

Structural characterization of strawberry pomace

Strawberries are a nutrient dense food rich in vitamins, minerals, non-nutrient antioxidant phenolics, and fibers. Strawberry fiber bioactive structures are not well characterized and limited information is available about the interaction between strawberry fiber and phenolics. Therefore, we analyzed commercial strawberry pomace in order to provide a detailed carbohydrate structural characterization, and to associate structures with functions. The pomace fraction, which remained after strawberry commercial juice extraction, contained mostly insoluble (49.1 % vs. 5.6 % soluble dietary fiber) dietary fiber, with pectin, xyloglucan, xylan, β-glucan and glucomannan polysaccharides; glucose, fructose, xylose, arabinose, galactose, fucose and galacturonic acid free carbohydrates; protein (15.6 %), fat (8.34 %), and pelargonidin 3-glucoside (562 μg/g). Oligosaccharides from fucogalacto-xyloglucan, methyl-esterified rhamnogalacturonan I with branched arabinogalacto-side chains, rhamnogalacturonan II, homogalacturonan and β-glucan were detected by MALDI-TOF MS, NMR and glycosyl-linkage analysis. Previous reports suggest that these oligosaccharide and polysaccharide structures have prebiotic, bacterial pathogen anti-adhesion, and cholesterol-lowering activity, while anthocyanins are well-known antioxidants. A strawberry pomace microwave acid-extracted (10 min, 80 °C) fraction had high molar mass (2376 kDa) and viscosity (3.75 dL/g), with an extended rod shape. A random coil shape, that was reported previously to bind to phenolic compounds, was observed for other strawberry microwave-extracted fractions. These strawberry fiber structural details suggest that they can thicken foods, while the polysaccharide and polyphenol interaction indicates great potential as a multiple-function bioactive food ingredient important for gut and metabolic health.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

Structural dependence of hydrogen evolution reaction on transition metal catalysts sputtered at different temperatures in alkaline media

In the present article, we studied the catalytic activity of magnetron sputtered Mo, V, Ni, and Co thin films for hydrogen evolution reaction (HER) in the alkaline electrolyte. Here, we find that the HER potentials (η 10 ) of the Mo and V thin film catalysts sputtered at 800 °C shift positive with respect to those of the film catalysts sputtered at 25°C. For Mo metal the observed shift of η 10 was 280 mV and for V metal observed shift of η 10 was 390 mV. On the other hand, minimal effect of sputtering temperature on both Ni and Co thin film catalyst activity for HER was observed. Structural analysis reveals that Mo and V prepared at 800 °C have uncommon face centered cubic (fcc, 0.74 packing density) structure as opposed to room-temperature sputtered Mo and V thin films which have common body centered cubic (bcc, 0.68 packing density) structure, resulting in significant increases of the packing densities when they are prepared at 800 °C. On the other hand, the high-temperature prepared thin films of Ni and Co retained fcc structures, resulting in no density changes compared to the room-temperature prepared fcc Ni and hexagonal close packed (hcp, 0.74 packing density) Co. Impedance spectroscopy shows that fcc Mo is a better catalyst than fcc Ni, which is considered an industry standard for non-noble pure metal-based catalysts in alkaline media. Stability tests also suggest that fcc Mo thin film catalysts prepared at 800 °C are more durable than fcc Ni thin films. Our study points out that structure phases of catalysts can be a key factor governing the activities of transition metals for HER in alkaline media.

08 HYDROGEN↗
DOE OSTI2022

Investigation of crossed-twin structure formation in magnesium and magnesium alloys

In this work, the effect of alloying addition on the propensity for twin-twin interactions to transform into crossed-twin structures in magnesium alloys is investigated. A full-field elasto-viscoplastic fast Fourier transform (EVP-FFT) framework combined with a discrete twin model and dislocation density-based hardening law for slip strengths is used to calculate the micromechanical fields in the crystalline matrix around the interacting twins. AZ31 and MgLi alloys are selected along with pure Mg to study the influence of plastic anisotropy in connection with alloying elements. These alloys were selected since their plastic anisotropy measure, which is defined as the ratio between the critical resolved shear stress for pyramidal $\langle$c +a$\rangle$ and basal $\langle$a$\rangle$ slip modes, spanned a wide range. To quantify the role of twin thicknesses, we probe a range of impinging twin thicknesses while fixing the recipient twin thickness. The analysis reveals that: (i) the local driving stress for crossed twin structure formation generated from the interaction of the two twins is lower in a low plastically anisotropic material, like a MgLi alloy, than a high plastically anisotropic material like pure Mg and (ii) the critical impinging twin thickness needed to form the crossed twin structure in pure Mg, AZ31 and MgLi alloys is ~0.5, ~0.75 and ~1.5 times the recipient twin thickness. We propose a relationship between the tendency for crossed twin structure formation and the experimentally observed higher ductility in MgLi alloys compared to pure Mg. Finally, one key implication of the findings is that crossed- twin structure formation can be hindered and the ductility of magnesium alloy thereby improved by properly choosing alloying elements that lower the slip strength for pyramidal $\langle$c + a$\rangle$ slip.

36 MATERIALS SCIENCE↗
DOE OSTI2024

Co 3 Ga 2 Ge 5 : Probing site mixing of the Ru 3 Sn 7 structure type with elements difficult to distinguish by diffraction

Co 3 Ga 2 Ge 5 was synthesized through arc-melting stoichiometric ratios of the elements, and a Ru 3 Sn 7 -type structure was confirmed by X-ray diffraction. Because Co 3 Ga 2 Ge 5 contains Ga and Ge, which have very similar X-ray and neutron scattering factors, any Ga/Ge crystallographic site preference cannot be determined with diffraction alone. The purpose of this study is to highlight the importance of using multiple techniques to characterize otherwise structurally ambiguous intermetallic compounds. Here, we utilize 71 Ga nuclear magnetic resonance spectroscopy and an analysis of the X-ray absorption fine structure to clarify the amount of Ga/Ge site mixing. Our combined use of X-ray diffraction and spectroscopy provides a comprehensive structural analysis of Ga site mixing across the Ge crystallographic sites, enhancing the understanding of the structure and properties of Co 3 Ga 2 Ge 5 .

36 MATERIALS SCIENCE↗
DOE OSTI2022

Structure of a dimeric photosystem II complex from a cyanobacterium acclimated to far-red light

Photosystem II (PSII) is the water-splitting enzyme central to oxygenic photosynthesis. To drive water oxidation, light is harvested by accessory pigments, mostly chlorophyll (Chl) a molecules, which absorb visible light (400–700 nm). Some cyanobacteria facultatively acclimate to shaded environments by altering their photosynthetic machinery to additionally absorb far-red light (FRL, 700–800 nm), a process termed far-red light photoacclimation or FaRLiP. During far-red light photoacclimation, FRL-PSII is assembled with FRL-specific isoforms of the subunits PsbA, PsbB, PsbC, PsbD, and PsbH, and some Chl-binding sites contain Chls d or f instead of the usual Chl a. The structure of an apo-FRL-PSII monomer lacking the FRL-specific PsbH subunit has previously been determined, but visualization of the dimeric complex has remained elusive. Here, we report the cryo-EM structure of a dimeric FRL–PSII complex. The site assignments for Chls d and f are consistent with those assigned in the previous apo-FRL-PSII monomeric structure. All sites that bind Chl d or Chl f at high occupancy exhibit a FRL-specific interaction of the formyl moiety of the Chl d or Chl f with the protein environment, which in some cases involves a phenylalanine sidechain. The structure retains the FRL-specific PsbH2 subunit, which appears to alter the energetic landscape of FRL-PSII, redirecting energy transfer from the phycobiliprotein complex to a Chl f molecule bound by PsbB2 that acts as a bridge for energy transfer to the electron transfer chain. Collectively, these observations extend our previous understanding of the structure-function relationship that allows PSII to function using lower energy FRL.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2023

Structural basis of DNA binding by the WhiB-like transcription factor WhiB3 in Mycobacterium tuberculosis

Mycobacterium tuberculosis (Mtb) WhiB3 is an iron–sulfur cluster-containing transcription factor belonging to a subclass of the WhiB-Like (Wbl) family that is widely distributed in the phylum Actinobacteria. WhiB3 plays a crucial role in the survival and pathogenesis of Mtb. It binds to the conserved region 4 of the principal sigma factor (σ A 4 ) in the RNA polymerase holoenzyme to regulate gene expression like other known Wbl proteins in Mtb. However, the structural basis of how WhiB3 coordinates with σ A 4 to bind DNA and regulate transcription is unclear. Here we determined crystal structures of the WhiB3:σ A 4 complex without and with DNA at 1.5 Å and 2.45 Å, respectively, to elucidate how WhiB3 interacts with DNA to regulate gene expression. These structures reveal that the WhiB3:σ A 4 complex shares a molecular interface similar to other structurally characterized Wbl proteins and also possesses a subclass-specific Arg-rich DNA-binding motif. We demonstrate that this newly defined Arg-rich motif is required for WhiB3 binding to DNA in vitro and transcriptional regulation in Mycobacterium smegmatis. Together, our study provides empirical evidence of how WhiB3 regulates gene expression in Mtb by partnering with σ A 4 and engaging with DNA via the subclass-specific structural motif, distinct from the modes of DNA interaction by WhiB1 and WhiB7.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Developing expert scientific consensus on the environmental and societal effects of marine artificial structures prior to decommissioning

Thousands of artificial (‘human-made’) structures are present in the marine environment, many at or approaching end-of-life and requiring urgent decisions regarding their decommissioning. No consensus has been reached on which decommissioning option(s) result in optimal environmental and societal outcomes, in part, owing to a paucity of evidence from real-world decommissioning case studies. To address this significant challenge, we asked a worldwide panel of scientists to provide their expert opinion. They were asked to identify and characterise the ecosystem effects of artificial structures in the sea, their causes and consequences, and to identify which, if any, should be retained following decommissioning. Experts considered that most of the pressures driving ecological and societal effects from marine artificial structures (MAS) were of medium severity, occur frequently, and are dependent on spatial scale with local-scale effects of greater magnitude than regional effects. The duration of many effects following decommissioning were considered to be relatively short, in the order of days. Overall, environmental effects of structures were considered marginally undesirable, while societal effects marginally desirable. Experts therefore indicated that any decision to leave MAS in place at end-of-life to be more beneficial to society than the natural environment. However, some individual environmental effects were considered desirable and worthy of retention, especially in certain geographic locations, where structures can support improved trophic linkages, increases in tourism, habitat provision, and population size, and provide stability in population dynamics. The expert analysis consensus that the effects of MAS are both negative and positive for the environment and society, gives no strong support for policy change whether removal or retention is favoured until further empirical evidence is available to justify change to the status quo. The combination of desirable and undesirable effects associated with MAS present a significant challenge for policy- and decision-makers in their justification to implement decommissioning options. Decisions may need to be decided on a case-by-case basis accounting for the trade-off in costs and benefits at a local level.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Crystal and magnetic structure of polar oxide HoCrWO 6

In this study, polar magnetic oxide HoCrWO 6 is synthesized and its crystal structure, magnetic structure, and thermodynamic properties are investigated. HoCrWO 6 forms the polar crystal structure (space group Pna 2 1 (#33)) due to the cation ordering of W 6+ and Cr 3+ . There is an antiferromagnetic transition at T N = 24.5 K along with the magnetic entropy change (~5 J.Kg. –1 K –1 at 70 kOe). Neutron diffraction measurement indicates that both Cr and Ho sublattices are ordered with the moment of 2.32(5)μ B and 8.7(4)μ B at 2 K, respectively. While Cr forms A-type collinear antiferromagnetic (AFM) structure with magnetic moment along the b axis, Ho sublattice orders in a non-coplanar AFM arrangement. A comparison with isostructural DyFeWO 6 and DyCrWO 6 indicates that the magnetic structure of this family of compounds is controlled by the presence or absence of e g electrons in the transition metal sublattice.

42 ENGINEERING↗