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At least 1,783 records · Page 99

Global characterization of biosynthetic gene clusters in non-model eukaryotes using domain architectures

Abstract The majority of pharmaceuticals are derived from natural products, bioactive compounds naturally synthesized by organisms to provide evolutionary advantages. Although the rich evolutionary history of eukaryotic algal species implicates a high potential for natural product-based drug discovery, it remains largely untouched. This study investigates 2762 putative biosynthetic gene clusters (BGCs) from 212 eukaryotic algal genomes. To analyze a vast set of structurally diverse BGCs, we employed comparative analysis based on the vectorization of biosynthetic domains, referred to as biosynthetic domain architecture (BDA). By characterizing core biosynthetic machineries through BDA, we identified key BDAs of modular BGCs in diverse eukaryotes and introduced 16 candidate modular BGCs with similar BDAs to previously validated BGCs. This study provides a global characterization of eukaryotic algal BGCs, offering an alternative to laborious manual curation for BGC prioritization.

59 BASIC BIOLOGICAL SCIENCES↗

Multimodal characterization of Te inclusions in Cd 1−x Zn x Te and Cd 1−x Zn x Te 1−y Se y for gamma and X-ray detectors

While CdZnTe (CZT) and CdZnTeSe (CZTS) semiconductors have emerged as compounds for room-temperature gamma and X-ray detection materials, they continue to be constrained by the formation of Te-inclusion defects generated during the growth and post-growth phases of the material, which adversely affect the detector performance. We demonstrate the utility of multimodal microscopic imaging and analysis for the characterization of the optical and electronic properties of Te inclusions in CZT and CZTS crystals at both micron and nanometer length scales. Having first identified regions with micron-scale Te inclusions using confocal Raman microscopy techniques, optically coupled infrared scattering near-field optical microscopic mapping was performed to map the distribution of these inclusions with nanometer spatial resolution and correlate the presence of Te inclusions in the matrix with other properties. Kelvin probe force microscopy was then utilized to characterize the variations of the work function associated with the presence of Te inclusions. Here, we observe an increase of ~ 240 mV in the work function associated with Te inclusions compared to the bulk CZT/CZTS crystals. Additionally, we observe that individual bulk grains in CZT can exhibit slight potential variations. Our findings develop a portrait of the charge trapping mechanisms in CZT and CZTS that act to degrade detector performance, while the demonstration of these combined microscopy techniques provides a new analytical tool that can be utilized for further optimization of the detector performance for these semiconducting compounds.

36 MATERIALS SCIENCE↗

A multi-omic characterization of temperature stress in a halotolerant Scenedesmus strain for algal biotechnology

Microalgae efficiently convert sunlight into lipids and carbohydrates, offering bio-based alternatives for energy and chemical production. Improving algal productivity and robustness against abiotic stress requires a systems level characterization enabled by functional genomics. Here, we characterize a halotolerant microalga Scenedesmus sp. NREL 46B-D3 demonstrating peak growth near 25 °C that reaches 30 g/m 2 /day and the highest biomass accumulation capacity post cell division reported to date for a halotolerant strain. Functional genomics analysis revealed that genes involved in lipid production, ion channels and antiporters are expanded and expressed. Exposure to temperature stress shifts fatty acid metabolism and increases amino acids synthesis. Co-expression analysis shows that many fatty acid biosynthesis genes are overexpressed with specific transcription factors under cold stress. These and other genes involved in the metabolic and regulatory response to temperature stress can be further explored for strain improvement.

09 BIOMASS FUELS↗

Ghost-imaging-enhanced noninvasive spectral characterization of stochastic x-ray free-electron-laser pulses

Abstract High-intensity ultrashort X-ray free-electron laser (XFEL) pulses are revolutionizing the study of fundamental nonlinear x-ray matter interactions and coupled electronic and nuclear dynamics. To fully exploit the potential of this powerful tool for advanced x-ray spectroscopies, a noninvasive spectral characterization of incident stochastic XFEL pulses with high resolution is a key requirement. Here we present a methodology that combines high-acceptance angle-resolved photoelectron time-of-flight spectroscopy and ghost imaging to enhance the quality of spectral characterization of x-ray free-electron laser pulses. Implementation of this noninvasive high-resolution x-ray diagnostic can greatly benefit the ultrafast x-ray spectroscopy community by functioning as a transparent beamsplitter for applications such as transient absorption spectroscopy in averaging mode as well as covariance-based x-ray nonlinear spectroscopies in single-shot mode where the shot-to-shot fluctuations inherent to a self-amplified spontaneous emission (SASE) XFEL pulse are a powerful asset.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Characterization of Adsorption Enthalpy of Novel Water-Stable Zeolites and Metal-Organic Frameworks

Water adsorption is becoming increasingly important for many applications including thermal energy storage, desalination, and water harvesting. To develop such applications, it is essential to understand both adsorbent-adsorbate and adsorbate-adsorbate interactions, and also the energy required for adsorption/desorption processes of porous material-adsorbate systems, such as zeolites and metalorganic frameworks (MOFs). In this study, we present a technique to characterize the enthalpy of adsorption/desorption of zeolites and MOF-801 with water as an adsorbate by conducting desorption experiments with conventional differential scanning calorimetry (DSC) and thermogravimetric analyzer (TGA). With this method, the enthalpies of adsorption of previously uncharacterized adsorbents were estimated as a function of both uptake and temperature. Our characterizations indicate that the adsorption enthalpies of type I zeolites can increase to greater than twice the latent heat whereas adsorption enthalpies of MOF-801 are nearly constant for a wide range of vapor uptakes.

42 ENGINEERING↗

In vitro Characterization of Phenylacetate Decarboxylase, a Novel Enzyme Catalyzing Toluene Biosynthesis in an Anaerobic Microbial Community

Anaerobic bacterial biosynthesis of toluene from phenylacetate was reported more than two decades ago, but the biochemistry underlying this novel metabolism has never been elucidated. Here we report results of in vitro characterization studies of a novel phenylacetate decarboxylase from an anaerobic, sewage-derived enrichment culture that quantitatively produces toluene from phenylacetate; complementary metagenomic and metaproteomic analyses are also presented. Among the noteworthy findings is that this enzyme is not the well-characterized clostridial p-hydroxyphenylacetate decarboxylase (CsdBC). However, the toluene synthase under study appears to be able to catalyze both phenylacetate and p-hydroxyphenylacetate decarboxylation. Observations suggesting that phenylacetate and p-hydroxyphenylacetate decarboxylation in complex cell-free extracts were catalyzed by the same enzyme include the following: (i) the specific activity for both substrates was comparable in cell-free extracts, (ii) the two activities displayed identical behavior during chromatographic separation of cell-free extract s, (iii) both activities were irreversibly inactivated upon exposure to O 2, and (iv) both activities were similarly inhibited by an amide analog of p-hydroxyphenylacetate. Based upon these and other data, we hypothesize that the toluene synthase reaction involves a glycyl radical decarboxylase. This first-time study of the phenylacetate decarboxylase reaction constitutes an important step in understanding and ultimately harnessing it for making bio-based toluene.

59 BASIC BIOLOGICAL SCIENCES↗

In Vitro Characterization and Concerted Function of Three Core Enzymes of a Glycyl Radical Enzyme - Associated Bacterial Microcompartment

Many bacteria encode proteinaceous bacterial microcompartments (BMCs) that encapsulate sequential enzymatic reactions of diverse metabolic pathways. Well-characterized BMCs include carboxysomes for CO 2 -fixation, and propanediol- and ethanolamine-utilizing microcompartments that contain B 12 -dependent enzymes. Genes thus required to form BMCs are typically organized in gene clusters, which promoted their distribution across phyla by horizontal gene transfer. Recently, BMCs associated with glycyl radical enzymes (GREs) were discovered; these are widespread and comprise at least three functionally distinct types. Previously, we predicted one type of these GRE-associated microcompartments (GRMs) represents a B 12 -independent propanediol-utilizing BMC. We functionally and structurally characterize enzymes of the GRM of Rhodopseudomonas palustris BisB18 and demonstrate their concerted function in vitro. The GRM signature enzyme, the GRE, is a dedicated 1,2-propanediol dehydratase with a new type of intramolecular encapsulation peptide. It forms a complex with its activating enzyme and, in conjunction with an aldehyde dehydrogenase, converts 1,2-propanediol to propionyl-CoA. Notably, homologous GRMs are also encoded in pathogenic Escherichia coli strains. Our high-resolution crystal structures of the aldehyde dehydrogenase lead to a revised reaction mechanism. The successful in vitro reconstitution of a part of the GRM metabolism provides insights into the metabolic function and steps in the assembly of this BMC.

59 BASIC BIOLOGICAL SCIENCES↗

Characterization of photocatalytic TiO 2 powder under varied environments using near ambient pressure X-ray photoelectron spectroscopy

Consecutive eight study phases under the successive presence and absence of UV irradiation, water vapor, and oxygen were conducted to characterize surface changes in the photocatalytic TiO2 powder using near-ambient-pressure X-ray photoelectron spectroscopy (XPS). Both Ti 2p and O 1s spectra show hysteresis through the experimental course. Under all the study environments, the bridging hydroxyl (OH br ) and terminal hydroxyl (OH t ) are identified at 1.1–1.3 eV and 2.1–2.3 eV above lattice oxygen, respectively. This enables novel and complementary approach to characterize reactivity of TiO 2 powder. The dynamic behavior of surface-bound water molecules under each study environment is identified, while maintaining a constant distance of 1.3 eV from the position of water vapor. In the dark, the continual supply of both water vapor and oxygen is the key factor retaining the activated state of the TiO 2 powder for a time period. Two new surface peaks at 1.7–1.8 and 4.0–4.2 eV above lattice oxygen are designated as peroxides (OOH/H 2 O 2 ) and H 2 O 2 dissolved in water, respectively. The persistent peroxides on the powder further explain previously observed prolonged oxidation capability of TiO 2 powder without light irradiation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

An overview of selected current approaches to the characterization of aqueous inorganic clusters

This Perspective article highlights some of the traditional and non-traditional analytical tools that are currently used to characterize aqueous inorganic nanoscale clusters and polyoxometalate ions. The techniques discussed in this article include nuclear magnetic resonance spectroscopy (NMR), small angle X-ray scattering (SAXS), dynamic and phase analysis light scattering (DLS and PALS), Raman spectroscopy, and quantum mechanical computations (QMC). For each method we briefly describe how it functions and illustrate how these techniques are used to study cluster species in the solid state and in solution through several representative case studies. In addition to highlighting the utility of these techniques, we also discuss limitations of each approach and measures that can be applied to circumvent such limits as it pertains to aqueous inorganic cluster characterization.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Synthesis and Characterization of Potassium Aryl- and Alkyl-Substituted Silylchalcogenolate Salts

Treatment of either triphenyl(chloro)silane or tert-butyldiphenyl(chloro)silane with potassium metal in THF, followed by addition of 18-crown-6, affords [K(18-crown-6)][SiPh 3 ] (1) and [K(18-crown-6)][SiPh 2 t Bu] (2), respectively, as the reaction products in high yield. Compounds 1 and 2 were fully characterized including by multi-nuclear NMR and IR spectroscopies. Addition of elemental chalcogen to either 1 or 2, results in facile chalcogen insertion into the potassium-silicon bond to afford the silylchalcogenolates, [K(18-crown-6)][E– SiPh2R] (E = S, R = Ph (3); Se, R = Ph (4); E = Te, R = Ph (5); E = S, R = t Bu (6); E = Se, R = t Bu (7); E = Te, R = t Bu (8)), in moderate to good yield. The silylchalcogenolates reported herein were characterized by multi-nuclear NMR and IR spectroscopies, and their solid-state molecular structures were determined by single-crystal X-ray crystallography. Importantly, the reported compounds crystallize as discrete monomers in the solid-state, a structural feature not previously observed in silylchalcogenolates, providing well-defined access routes into systematic metal complexation studies.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Fluorinated bottlebrush polymers based on poly(trifluoroethyl methacrylate): Synthesis and characterizations

Bottlebrush polymers are densely grafted polymers with long side-chains attached to a linear polymeric backbone. Their unusual structures endow them with a number of unique and potentially useful properties in solution, in thin films, and in bulk. Despite the many studies of bottlebrushes that have been reported, the structure–property relationships for this class of materials are still poorly understood. In this contribution, we report the synthesis and characterization of fluorinated bottlebrush polymers based on poly(2,2,2-trifluoroethyl methacrylate). The synthesis was achieved by atom transfer radical polymerization (ATRP) using an α-bromoisobutyryl bromide functionalized norbornene initiator, followed by ring-opening metathesis polymerization (ROMP) using a third generation Grubbs’ catalyst (G3). Rheological characterization revealed that the bottlebrush polymer backbones remained unentangled as indicated by the lack of a rubbery plateau in the modulus. By tuning the size of the backbone of the bottlebrush polymers, near-spherical and elongated particles representing single brush molecular morphologies were observed in a good solvent as evidenced by TEM imaging, suggesting a semi-flexible nature of their backbones in dilute solutions. Thin films of bottlebrush polymers exhibited noticeably higher static water contact angles as compared to that of the macromonomer reaching the hydrophobic regime, where little differences were observed between each bottlebrush polymer. Further investigation by AFM revealed that the surface of the macromonomer film was relatively smooth; in contrast, the surface of bottlebrush polymers displayed certain degrees of nano-scale roughness (R q = 0.8–2.4 nm). The enhanced hydrophobicity of these bottlebrushes likely results from the preferential enrichment of the fluorine containing end groups at the periphery of the molecules and the film surface due to the side chain crowding effect. Furthermore, our results provide key information towards the design of architecturally tailored fluorinated polymers with desirable properties.

36 MATERIALS SCIENCE↗

In-depth investigation on quantitative characterization of pyrolysis oil by 31 P NMR

The characterization of different heteroatom functional groups by employing 31 P NMR has been developed for almost 30 years. In this study, an in-depth investigation of this commonly used method has been accomplished for the analysis of pyrolysis oil. Several commonly used internal standards for 31 P NMR have been examined by in situ monitoring. The results indicated that endo-N-hydroxy-5-norbornene-2,3-dicarboximide (NHND) is not stable after a long period of storage or experiment (>12 hours), but both cyclohexanol and triphenylphosphine oxide (TPPO) can be used as internal standards if a long experiment or storage is required. The pyrolysis oil has also been investigated by both short time (16 hours) in situ monitoring and long time (14 days) ex situ monitoring. The results showed that aliphatic OH, carboxylic acids and water contents are not very stable after 2 hours, and thus a short time of preparation, storage, and experiment need to be considered to ensure a precise quantitative measurement. The decomposition products are still unclear, but some preliminary investigations for different acids, (e.g. formic acid) have been accomplished. The results indicated that the aromatic carboxylic acids (benzoic acid and vanillic acid) are more stable than formic acid and acetic acid. Interestingly, the formic acid will even decompose to some other compounds at the very beginning of the in situ monitoring test. Further characterization found that water is one of the major products for the decomposition of formic acid in the 31 P NMR solution. Finally, as far as we know, this is the first report on such time-dependent changes when using 31 P NMR to analyze the pyrolysis oil, and these results show that proper application of this method is essential to achieve reliable quantitative data.

09 BIOMASS FUELS↗

Synthesis and characterization of (Ga 1-x Zn x )(N 1-x O x ) nanocrystals with a wide range of compositions

We describe the synthesis and characterization of wurtzite (Ga 1-x Zn x )(N 1-x O x ) nanocrystals with a wide range of compositions and a focus on properties relevant for solar fuel generation. (Ga 1-x Zn x )(N 1-x O x ), a solid solution of GaN and ZnO, is an intriguing material because it exhibits composition-dependent visible absorption even though the parent semiconductors absorb in the UV. When functionalized with co-catalysts, (Ga 1-x Zn x )(N 1-x O x ) is also capable of water splitting under visible irradiation. Here, we examine the synthesis of (Ga 1-x Zn x )(N 1-x O x ) nanocrystals to understand how they form by nitridation of ZnO and ZnGa 2 O 4 nanocrystalline precursors. We find that the ZnO precursor is critical for the formation of crystalline (Ga 1-x Zn x )(N 1-x O x ) at 650 °C, consistent with a mechanism in which wurtzite (Ga 1-x Zn x )(N 1-x O x ) nucleates topotactically on wurtzite ZnO at an interface with ZnGa 2 O 4 . Using this information, we expand the range of compositions from previously reported 0.30 ≤ x ≤ 0.87 to include the low-x and high-x ends of the range. The resulting compositions, 0.06 ≤ x ≤ 0.98, constitute the widest range of (Ga 1-x Zn x )(N 1-x O x ) compositions obtained by one synthetic method. We then examine how the band gap depends on sample composition and find a minimum of 2.25 eV at x = 0.87, corresponding to a maximum possible solar-to-H 2 power conversion efficiency of 12%. Finally, we examine the photoelectrochemical (PEC) oxidation behavior of thick films of (Ga 1-x Zn x )(N 1-x O x ) nanocrystals with x = 0.40, 0.52, and 0.87 under visible illumination. (Ga 1-x Zn x )(N 1-x O x ) nanocrystals with x = 0.40 exhibit solar PEC oxidation activity that, while too low for practical applications, is higher than that of bulk (Ga 1-x Zn x )(N 1-x O x ) of the same composition. The highest photocurrents are observed at x = 0.52, even though x = 0.87 absorbs more visible light, illustrating that the observed photocurrents are a result of an interplay of multiple parameters which remain to be elucidated. This set of characterizations provides information useful for future studies of composition-dependent PEC properties of nanoscale (Ga 1-x Zn x )(N 1-x O x ).

36 MATERIALS SCIENCE↗

Synthesis and characterization of a series of nickel( ii ) alkoxide precursors and their utility for Ni(0) nanoparticle production

We synthesized a series of nickel(II) aryloxide ([Ni(OAr) 2 (py) x ]) precursors from an amide-alcohol exchange using [Ni(NR 2 ) 2 ] in the presence of pyridine (py). The H-OAr selected were the mono- and di-ortho-substituted 2-alkyl phenols: alkyl = methyl (H-oMP), iso-propyl (H-oPP), tert-butyl (H-oBP) and 2,6-di-alkyl phenols (alkyl = di-iso-propyl (H-DIP), di-tert-butyl (H-DBP), di-phenyl (H-DPhP)). Furthermore, the crystalline products were solved as solvated monomers and structurally characterized as [Ni(OAr) 2 (py) x ], where x = 4: OAr = oMP (1), oPP (2); x = 3: OAr = oBP (3), DIP (4); x = 2: OAr = DBP (5), DPhP (6). The excited states (singlet or triplet) and various geometries of 1–6 were identified by experimental UV-vis and verified by computational modeling. Magnetic susceptibility of the representative compound 4 was fit to a Curie Weiss model that yielded a magnetic moment of 4.38(3)μ B consistent with a Ni 2+ center. Compounds 1 and 6 were selected for decomposition studied under solution precipitation routes since they represent the two extremes of coordination. The particle size and crystalline structure were characterized using transmission electron microscopy (TEM) and powder X-ray diffraction (PXRD). Finally, the materials isolated from 1 and 6 were found by TEM to form irregular shape nanomaterials (8–15 nm), which by PXRD were found to be Ni 0 hcp (PDF: 01-089-7129) and fcc (PDF: 01-070-0989), respectively.

36 MATERIALS SCIENCE↗

Isolation and characterization of new lignin streams derived from extractive-ammonia (EA) pretreatment

One of the key challenges facing lignin conversion to fuels and chemicals is related to the level of carbohydrate and ash impurities found in extracted lignin. Structural modifications of lignin may also occur as a result of biomass pretreatment and harsh lignin extraction protocols. Extractive-Ammonia (EA) is a new pretreatment technology that uses liquid ammonia to cleave lignin–carbohydrate complexes, decrystallize cellulose, solubilize lignin, and selectively extract lignin from lignocellulosic biomass, enabling better utilization of both lignin and carbohydrate components in a biorefinery. The EA-based biorefinery produces two different lignin-rich streams, with different properties, that could potentially be upgraded to fuels and chemicals using green processes. Here, a water/ethanol-based fractionation method was developed to enrich the ammonia-soluble extractives, resulting in a major product stream containing 92% lignin. Detailed characterization of the various streams resulting from EA treatment, including compositional analysis, structural characterization by nuclear magnetic resonance (NMR) spectrometry, elemental analysis, molecular weight analysis, and thermo-gravimetric analysis provides a broad evaluation of the EA-derived lignin product stream structures and properties, assessing their potential for commercial applications. In conclusion, EA-derived lignins preserve much of lignin's functionality, including the sensitive β-aryl ether units. Furthermore, we observed nitrogen incorporation in the lignin-rich streams, notably due to the presence of hydroxycinnamoyl amides formed during ammonia pretreatment.

09 BIOMASS FUELS↗

Characterization of extreme ultraviolet laser ablation mass spectrometry for actinide trace analysis and nanoscale isotopic imaging

The purpose of this research was to characterize Extreme Ultraviolet Time-of-Flight (EUV TOF) Laser Ablation Mass Spectrometry for high spatial resolution elemental and isotopic analysis. We compare EUV TOF results with Secondary Ionization Mass Spectrometry (SIMS) to orient the EUV TOF method within the overall field of analytical mass spectrometry. Using the well-characterized NIST 61x glasses, we show that the EUV ionization approach produces relatively few molecular ion interferences in comparison to TOF SIMS. We demonstrate that the ratio of element ion to element oxide ion is adjustable with EUV laser pulse energy and that the EUV TOF instrument has a sample utilization efficiency of 0.014%. The EUV TOF system also achieves a lateral resolution of 80 nm and we demonstrate this lateral resolution with isotopic imaging of closely spaced particles or uranium isotopic standard materials.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

A mononuclear nonheme {FeNO} 6 complex: synthesis and structural and spectroscopic characterization

While the synthesis and characterization of {FeNO} 7,8,9 complexes have been well documented in heme and nonheme iron models, {FeNO} 6 complexes have been less clearly understood. Herein, we report the synthesis and structural and spectroscopic characterization of mononuclear nonheme {FeNO} 6 and iron(III)–nitrito complexes bearing a tetraamido macrocyclic ligand (TAML), such as [(TAML)Fe III (NO)] - and [(TAML)Fe III (NO 2 )] 2- , respectively. First, direct addition of NO (g) to [Fe III (TAML)] - results in the formation of [(TAML)Fe III (NO)] - , which is sensitive to moisture and air. The spectroscopic data of [(TAML)Fe III (NO)] - , such as 1 H nuclear magnetic resonance and X-ray absorption spectroscopies, combined with computational study suggest the neutral nature of nitric oxide with a diamagnetic Fe center (S = 0). We also provide alternative pathways for the generation of [(TAML)Fe III (NO)] - , such as the iron–nitrite reduction triggered by protonation in the presence of ferrocene, which acts as an electron donor, and the photochemical iron–nitrite reduction. To the best of our knowledge, the present study reports the first photochemical nitrite reduction in nonheme iron models.

36 MATERIALS SCIENCE↗

Iron carbide nanoplatelets: colloidal synthesis and characterization

Iron carbide nanoplatelets with an orthorhombic Fe 3 C structure were synthesized following a simple liquid chemical approach. The formation of the carbide phases was shown to depend on the presence of a long chain diol and the reaction temperature. Confirmation of the iron carbide phases and structural characterization was made by X-ray diffraction (XRD) and Mössbauer spectroscopy. Particle morphology was characterized by transmission electron microscopy (TEM) and HR-TEM and the magnetic properties were measured with magnetometry (VSM). The sample with the Fe 3 C phase shows a ferromagnetic behavior with a magnetization of 139 emu g -1 under a 30 kOe applied field. The simple methodology presented here for producing iron carbide nanoplatelets has promising application in the biomedical and catalyst industries.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗