Mechanism Of Incorporation Research Articles

Investigation of the effects and mechanism of incorporation of cross-linked/acetylated tapioca starches on the gel properties and in vitro digestibility of kung-wan

The effects and mechanism of incorporation of cross-linked tapioca starch (CTS) or acetylated tapioca starch (ATS) on the gel properties and in vitro digestibility of kung-wan (a Chinese-style meatball) were evaluated. The results indicated that incorporation of either CTS or ATS significantly enhanced the gel properties of kung-wan in a dose-dependent manner (P < 0.05), as well as the rheological properties of meat batter. Moreover, hydrogen bonds and electrostatic interaction were the major intermolecular forces in kung-wan when incorporated with CTS or ATS. Meanwhile, CTS and ATS acted as fillers in the meat protein gel matrix, which was further verified by the microstructure of kung-wan. However, CTS produced a more uniform and dense meat protein gel network than ATS, which was mainly due to its limited swelling characteristics. In addition, the incorporation of CTS or ATS significantly increased the in vitro digestibility of protein in kung-wan with increasing level of addition (P < 0.05). However, no significant differences in protein digestibility were detected between the CTS and ATS groups at the same addition level (P > 0.05). Our results provided some critical points for the actual application of modified tapioca starch to promote the quality profiles of kung-wan.

Amorphous carbon thin films: Mechanisms of hydrogen incorporation during magnetron sputtering and consequences for the secondary electron emission

Amorphous carbon (a-C) films, having low secondary electron yield (SEY), are used at CERN to suppress electron multipacting in the beam pipes of particle accelerators. It was already demonstrated that hydrogen impurities increase the SEY of a-C films. In this work, a systematic characterization of a set of a-C coatings, deliberately contaminated by deuterium during the magnetron sputtering deposition, by scanning electron microscopy, ion beam analysis, secondary ion mass spectrometry, and optical absorption spectroscopy was performed to establish a correlation between the hydrogen content and the secondary electron emission properties. In parallel, the mechanisms of contamination were also investigated. Adding deuterium allows resolving the contributions of intentional and natural contamination. The results enabled us to quantify the relative deuterium/hydrogen (D/H) amounts and relate them with the maximum SEY (SEYmax). The first step of incorporation appears to be formation of D/H atoms in the discharge. An increase in both the flux of deposited carbon atoms and the discharge current with a D2 fraction in the gas discharge can be explained by target poisoning with deuterium species followed by etching of CxDy clusters, mainly by physical sputtering. For overall relative D/H amounts between 11% and 47% in the discharge gas, the SEYmax increases almost linearly from 0.99 to 1.38. An abrupt growth of SEYmax from 1.38 to 2.12 takes place in the narrow range of D/H relative content of 47%–54%, for which the nature of the deposited films changes to a polymer-like layer.

The A12.2 Subunit Plays an Integral Role in Pyrophosphate Release of RNA Polymerase I

RNA polymerase I (Pol I) synthesizes ribosomal RNA (rRNA), which is the first and rate-limiting step in ribosome biosynthesis. A12.2 (A12) is a critical subunit of Pol I that is responsible for activating Pol I’s exonuclease activity. We previously reported a kinetic mechanism for single-nucleotide incorporation catalyzed by Pol I lacking the A12 subunit (ΔA12 Pol I) purified from S. cerevisae and revealed that ΔA12 Pol I exhibited much slower incorporation compared to Pol I. However, it is unknown if A12 influences each nucleotide incorporation in the context of transcription elongation. Here, we show that A12 contributes to every repeating cycle of nucleotide addition and that deletion of A12 results in an entirely different kinetic mechanism compared to WT Pol I. We found that instead of one irreversible step between each nucleotide addition cycle, as reported for wild type (WT) Pol I, the ΔA12 variant requires one reversible step to describe each nucleotide addition. Reversibility fundamentally requires slow PPi release. Consistently, we show that Pol I is more pyrophosphate (PPi) concentration dependent than ΔA12 Pol I. This observation supports the model that PPi is retained in the active site of ΔA12 Pol I longer than WT Pol I. These results suggest that A12 promotes PPi release, revealing a larger role for the A12.2 subunit in the nucleotide addition cycle beyond merely activating exonuclease activity.

Hide and Seek—Trace Element Incorporation and Diffusion in Olivine

Olivine, once overlooked as a host of trace elements, is becoming increasingly important for our understanding of the kinetic and equilibrium behaviour of these elements. Much of our understanding of trace element substitution and diffusion in geological materials comes as a result of experimental and petrological studies of olivine. Here, we consider trace element concentrations and incorporation mechanisms, and how these relate to diffusive behaviour. If we understand trace element behaviour in olivine, we have a powerful tool kit that can be directly applied to address many problems in petrology and volcanology. Perhaps more importantly, what we have learned from olivine can be applied to other minerals and aid us in addressing other far-reaching questions from across the Earth sciences.

Mechanism of Anion Incorporation into NaCl Particles During Crystallization Processes

日本において塩は海水を濃縮して製造されるため，製品中には海水由来のBrイオンなどの不純物が含まれる．結晶成長速度や種結晶の純度などが不純物濃度へ影響を及ぼすことが報告されているが，不純物取込の詳細なメカニズムは明らかではない．そこで本研究では，分子シミュレーションによる取込メカニズムの解析を行い，結晶成長過程の初期における結晶－溶液界面での不純物イオン効果を明らかにした．

Computer simulation of phosphate-silicate and calcium phosphate-silicate systems

The structure of P2O5-SiO2 and CaO-P2O5-SiO2 systems have been systematically investigated by molecular dynamics simulation. The structural characteristics were clarified with intuitive figures and images at atomic scale. Specially, we have applied the recognition and visualization methods to clarify short range order, intermediate range order, and network structure. The structural and compositional heterogeneities and mechanism of alkaline Earth metals incorporation into -O-P-O-Si-O- network have been discussed in detail. This is useful information for designing bioactive systems with many potential applications.

An Overview of Modeling Approaches for Compositional Control in III-V Ternary Nanowires.

Modeling of the growth process is required for the synthesis of III-V ternary nanowires with controllable composition. Consequently, new theoretical approaches for the description of epitaxial growth and the related chemical composition of III-V ternary nanowires based on group III or group V intermix were recently developed. In this review, we present and discuss existing modeling strategies for the stationary compositions of III-V ternary nanowires and try to systematize and link them in a general perspective. In particular, we divide the existing approaches into models that focus on the liquid-solid incorporation mechanisms in vapor-liquid-solid nanowires (equilibrium, nucleation-limited, and kinetic models treating the growth of solid from liquid) and models that provide the vapor-solid distributions (empirical, transport-limited, reaction-limited, and kinetic models treating the growth of solid from vapor). We describe the basic ideas underlying the existing models and analyze the similarities and differences between them, as well as the limitations and key factors influencing the stationary compositions of III-V nanowires versus the growth method. Overall, this review provides a basis for choosing a modeling approach that is most appropriate for a particular material system and epitaxy technique and that underlines the achieved level of the compositional modeling of III-V ternary nanowires and the remaining gaps that require further studies.

Mechanism of 5S RNP recruitment and helicase-surveilled rRNA maturation during pre-60S biogenesis.

Ribosome biogenesis proceeds along a multifaceted pathway from the nucleolus to the cytoplasm that is extensively coupled to several quality control mechanisms. However, the mode by which 5S ribosomal RNA is incorporated into the developing pre-60S ribosome, which in humans links ribosome biogenesis to cell proliferation by surveillance by factors such as p53-MDM2, is poorly understood. Here, we report nine nucleolar pre-60S cryo-EM structures from Chaetomium thermophilum, one of which clarifies the mechanism of 5S RNP incorporation into the early pre-60S. Successive assembly states then represent how helicases Dbp10 and Spb4, and the Pumilio domain factor Puf6 act in series to surveil the gradual folding of the nearby 25S rRNA domain IV. Finally, the methyltransferase Spb1 methylates a universally conserved guanine nucleotide in the A-loop of the peptidyl transferase center, thereby licensing further maturation. Our findings provide insight into the hierarchical action of helicases in safeguarding rRNA tertiary structure folding and coupling to surveillance mechanisms that culminate in local RNA modification.

Diffusion of Hydroxylated Si Vacancies in Olivine, and Its Relevance to Si Diffusion

AbstractThe diffusion coefficient associated with the 3,612 cm−1 infrared absorbance band in H‐bearing olivine, attributed to a defect involving a vacant Si site balanced by four H+ (i.e., ), was determined in H in‐diffusion experiments at 1200°C–1400°C and 1.5–3.0 GPa in piston‐cylinder and multi‐anvil apparatuses. The retrieved values are in good agreement with experimentally determined diffusion coefficients ascribed to the same process from previous experiments, despite those being conducted at atmospheric pressure and representing out‐diffusion rather than in‐diffusion. Overall, the diffusivity of the Si vacancy is several orders of magnitude lower than that of the M‐site vacancy (∼4 orders of magnitude at 1000°C), with a higher activation energy (∼450–500 vs. 200–250 kJ mol−1), when both are charge‐compensated solely by H+. From these data, the diffusion coefficient of Si in H‐bearing olivine can be estimated using the relationship between vacancy concentration, vacancy diffusivity, and diffusivity of an ion moving by a vacancy mechanism. However, these diffusivities are inconsistent with published results for Si diffusivity, with a considerable discrepancy of around two orders of magnitude. This suggests that simple relationships between diffusion coefficients of vacancies and species moving by vacancy diffusion mechanisms may be inappropriate, highlighting again the complexity of H incorporation and diffusion mechanisms in olivine.

Sphalerite as a non-traditional critical metal source: Correlative microscopy (EPMA, EBSD, and APT) of cobalt-enriched sulfides from the sediment-hosted copper-cobalt Dolostone Ore Formation deposit, Namibia

Sphalerite from the sediment-hosted Dolostone Ore Formation (DOF) Cu-Co-Zn deposit, in northwestern Namibia, has previously been shown to contain extremely high concentrations of the critical metal Co (up to 1 wt%). These concentrations are the highest reported in sphalerite to date, and the how and why of sphalerite being able to incorporate such high concentrations of Co are poorly understood. We use correlative electron probe microanalysis, electron backscattered diffraction, and atom probe to reconstruct the likely incorporation mechanisms and modes of occurrence of such high Co concentrations in natural sphalerite. While over twenty samples were studied, the comprehensive analytical workflow was executed on one representative sample to gain a detailed understanding of Co enrichment. The sulfides of the studied sample are Co-rich pyrite, chalcopyrite, Co-rich sphalerite, linnaeite, cobaltpentlandite, and cobaltite, mentioned in order of abundance. Detailed petrography of these sulfides indicates that they formed through three stages during the main Cu-Co-Zn ore stage of the DOF. Cobalt was initially contained in pyrite that grew during Ore Stage 1 and was later affected by oxidizing fluids (Ore Stage two). This led to remobilization and growth of linnaeite (Co2+Co3+2S4). A later change in fO2 (Ore Stage three) led to the breakdown of linnaeite and the further growth of accessory cobaltite along with the Co-rich sphalerite and chalcopyrite. The hyper-enriched Co-sphalerite then is the last major sink for Co in the DOF deposit. A low Fe and Co and high Zn sub-grain boundary network within the Co-rich sphalerite was identified by EPMA and EBSD. This sub-grain network is believed to have formed during a later, secondary metamorphic stage (Cu-Zn (-Pb) Ore Stage 4), which developed during ductile deformational mineralization styles such as pressure shadows and veins. Our APT data reconstructions show no evidence for Co-inclusions within the Co-sphalerite, and spatial ion correlation analyses of the data suggest that Co occurs in the sphalerite through simple substitution of Zn. This study demonstrates that sphalerite may contain significant concentrations of the Co through simple substitution, potentially representing an important non-traditional Co source in future critical metal exploration.

Deconvoluting Cr states in Cr-doped UO2 nuclear fuels via bulk and single crystal spectroscopic studies

Cr-doped UO2 is a leading accident tolerant nuclear fuel where the complexity of Cr chemical states in the bulk material has prevented acquisition of an unequivocal understanding of the redox chemistry and mechanism for incorporation of Cr in the UO2 matrix. To resolve this, we have used electron paramagnetic resonance, high energy resolution fluorescence detection X-ray absorption near energy structure and extended X-ray absorption fine structure spectroscopic measurements to examine Cr-doped UO2 single crystal grains and bulk material. Ambient condition measurements of the single crystal grains, which have been mechanically extracted from bulk material, indicated Cr is incorporated substitutionally for U+4 in the fluorite lattice as Cr+3 with formation of additional oxygen vacancies. Bulk material measurements reveal the complexity of Cr states, where metallic Cr (Cr0) and oxide related Cr+2 and Cr+32O3 were identified and attributed to grain boundary species and precipitates, with concurrent (Cr+3xU+41-x)O2-0.5x lattice matrix incorporation. The deconvolution of chemical states via crystal vs. powder measurements enables the understanding of discrepancies in literature whilst providing valuable direction for safe continued use of Cr-doped UO2 fuels for nuclear energy generation.

Incorporation and corrosion protection mechanism of TiO2 nano-particles in SnAgCu composite alloys: Experimental and density functional theory study

This work studied the incorporation mechanism of TiO2 nano-particles into SnAgCu solders and their effect on the corrosion behavior of the composite alloy. Composite solder alloys have been made from 99Sn0.3Ag0.7Cu solder alloy and TiO2 nano-particles between 0.25 and 1 wt%. The alloys in solder joints were exposed to 4000 h long 85 °C/85RH% thermal-humidity test, and their surface was observed by SEM and FIB techniques. Large localized corrosion spots and numerous Sn whiskers have been found on the samples, except for the samples with 0.25 wt% TiO2 content. The corrosion of the Sn grains resulted in a volumetric increase and mechanical stress, which was relaxed via whisker growth. TiO2 nano-particles in 0.25 wt% incorporated layer-like at the boundaries of the Sn grain. Density functional theory calculations proved that at soldering conditions, the Sn atoms of the solder alloy could bond to the TiO2 NPs through the O atoms of TiO2. The TiO2–Sn oxide layer at the grain boundaries could suppress the corrosion of the composite solder alloys and whisker growth. In the case of higher weight fractions TiO2, the nano-particles were agglomerated and could not perform corrosion protection effect.

Crystal Chemistry of the Copper Oxalate Biomineral Moolooite: The First Single-Crystal X-ray Diffraction Studies and Thermal Behavior.

Moolooite, Cu(C2O4)·nH2O, is a typical biomineral which forms due to Cu-bearing minerals coming into contact with oxalic acid sources such as bird guano deposits or lichens, and no single crystals of moolooite of either natural or synthetic origin have been found yet. This paper reports, for the first time, on the preparation of single crystals of a synthetic analog of the copper-oxalate biomineral moolooite, and on the refinement of its crystal structure from the single-crystal X-ray diffraction (SCXRD) data. Along with the structural model, the SCXRD experiment showed the significant contribution of diffuse scattering to the overall diffraction data, which comes from the nanostructural disorder caused by stacking faults of Cu oxalate chains as they lengthen. This type of disorder should result in the chains breaking, at which point the H2O molecules may be arranged. The amount of water in the studied samples did not exceed 0.15 H2O molecules per formula unit. Apparently, the mechanism of incorporation of H2O molecules governs the absence of good-quality single crystals in nature and a lack of them in synthetic experiments: the more H2O content in the structure, the stronger the disorder will be. A description of the crystal structure indicates that the ideal structure of the Cu oxalate biomineral moolooite should not contain H2O molecules and should be described by the Cu(C2O4) formula. However, it was shown that natural and synthetic moolooite crystals contain a significant portion of "structural" water, which cannot be ignored. Considering the substantially variable amount of water, which can be incorporated into the crystal structure, the formula Cu(C2O4)·nH2O for moolooite is justified.

Incorporation and solidification mechanism of manganese doped cement clinker.

Using municipal and industrial solid waste as a substitute raw material and fuel in cement rotary kiln co-processing is considered an economic and environmentally friendly alternative to the use of traditional fuels. However, the presence of heavy metals in solid waste is a growing concern in the cement rotary kiln co-processing technique. The solidification mechanism of heavy metals in cement clinker is directly related to their stabilization. Cement clinkers doped with manganese oxide (MnO2: 0.0%-5.0% wt%) were prepared in a laboratory to investigate the impacts of extrinsic Mn on cement clinker calcination. The insignificant changes in X-ray diffractometer patterns indicated that the fixed Mn had little influence on the mineral lattice structure. Raman spectra and X-ray photoelectron spectroscopy revealed the transformation of the silicate phase when the Mn dose was increased. Moreover, the satisfactory solidification ratio confirmed the incorporation of Mn in the cement clinker. These results provided evidence of the influence rule of Mn in the cement clinker calcination process. Furthermore, Raman spectroscopy showed great potential for the qualitative and semi-quantitative analysis of the cementitious materials derived from cement rotary kiln co-processing. These results will be important for the further development of green cement manufacturing technology.

In-Depth Insight into the Mechanism of Incorporation of Abelmoschus manihot Gum on the Enhancement of Gel Properties and In Vitro Digestibility of Frankfurters.

This study aimed to investigate the effects of different concentrations (0.1, 0.2, 0.3, 0.4, and 0.5% w/w) of Abelmoschus manihot gum (AMG) on the gel properties and in vitro digestibility of frankfurters. The results indicated that AMG incorporation significantly enhanced the emulsion stability and texture of frankfurters, as well as the dynamic rheological characteristics of raw meat batter, with the optimal concentration being 0.3% (p < 0.05). Furthermore, hydrogen bonds and disulphide bonds were the main molecular forces of the frankfurters in the presence of AMG. Microstructural images showed that more uniform and dense microstructures of frankfurters were formed due to AMG supplementation. In addition, AMG incorporation significantly increased the in vitro protein digestibility of frankfurters as the level of addition increased (p < 0.05). In conclusion, our results provided critical information for the practical application of AMG in the production of emulsified meat products.

Azide-Masked Fluorescence Turn-On Probe for Imaging Mycobacteria.

A fluorescence turn-on probe, an azide-masked and trehalose-derivatized carbazole (Tre-Cz), was developed to image mycobacteria. The fluorescence turn-on is achieved by photoactivation of the azide, which generates a fluorescent product through an efficient intramolecular C-H insertion reaction. The probe is highly specific for mycobacteria and could image mycobacteria in the presence of other Gram-positive and Gram-negative bacteria. Both the photoactivation and detection can be accomplished using a handheld UV lamp, giving a limit of detection of 103 CFU/mL, which can be visualized by the naked eye. The probe was also able to image mycobacteria spiked in sputum samples, although the detection sensitivity was lower. Studies using heat-killed, stationary-phase, and isoniazid-treated mycobacteria showed that metabolically active bacteria are required for the uptake of Tre-Cz. The uptake decreased in the presence of trehalose in a concentration-dependent manner, indicating that Tre-Cz hijacked the trehalose uptake pathway. Mechanistic studies demonstrated that the trehalose transporter LpqY-SugABC was the primary pathway for the uptake of Tre-Cz. The uptake decreased in the LpqY-SugABC deletion mutants ΔlpqY, ΔsugA, ΔsugB, and ΔsugC and fully recovered in the complemented strain of ΔsugC. For the mycolyl transferase antigen 85 complex (Ag85), however, only a slight reduction of uptake was observed in the Ag85 deletion mutant ΔAg85C, and no incorporation of Tre-Cz into the outer membrane was observed. The unique intracellular incorporation mechanism of Tre-Cz through the LpqY-SugABC transporter, which differs from other trehalose-based fluorescence probes, unlocks potential opportunities to bring molecular cargoes to mycobacteria for both fundamental studies and theranostic applications.

Case Studies in the Application of a Workflow-Based Crystallization Design for Optimized Impurity Rejection in Pharmaceutical Development

Crystallization is an important unit operation in pharmaceutical drug substance manufacturing for the isolation of organic products. Impurity control is a recurring critical quality attribute in most commercial pharmaceutical crystallization processes. A systematic workflow that can reveal the incorporation mechanism of various impurities during crystallization and guide us to understand impurity rejection is useful for crystallization process design. Such a workflow was recently published by Urwin et al. Herein, we present three case studies implementing this workflow, covering surface deposition, conglomerate formation, and agglomeration as principal routes for impurity incorporation during crystallization of a drug substance’s active pharmaceutical ingredient and its intermediates. We demonstrate the experimental steps to identify various impurity incorporation mechanisms and discuss the strategy for impurity rejection in each case. We built upon the previous approach to demonstrate a material sparing approach through our case studies. We highlight the value of stepwise dissolution and show the importance of doing it early in the impurity incorporation identification stage. At this stage, we introduce a missing incorporation mechanism in prior work, namely, conglomerate systems. We show how to identify and resolve this mode of incorporation mechanism through stepwise dissolution and solubility-limited rejection maps.

Structure, Properties, and Reactivity of Polyoxocationic Zirconium and Hafnium Clusters: A Computational Investigation

Tetravalent zirconium and hafnium molecular metal oxides clusters are key building blocks of many metal-organic frameworks; however, the chemical space to form all possible MOF nodes is vast, containing many potential new clusters. Our computational study provides a complete picture of the structure, properties, and reactivity of two tetrameric zirconium and hafnium [M4(μ2-η2:η2-O2)x(μ2-OH)8-2x(H2O)16]8+ polycationic clusters. The electronic structure of the studied species has characteristic polyoxometalate oxygen-based and metal-based bands in the valence region. The energetics for the evolution of pure metal clusters into mixed-metal clusters revealed that only the incorporation of zirconium into hafnium clusters is thermodynamically favorable. We confirmed that the incorporation of up to four peroxide ligands is thermodynamically favorable; however, the experimental absence of rich peroxide species with three or more peroxides is attributed to their thermal degradation. The mechanism for peroxide incorporation involves the partial dissociation of the cluster rather than complete dissociation.

Lithium ion transport in water-containing Li(SCN) over a wide compositional range: From water doping to hydration

This work explores the Li+ cation transport mechanisms in the system Li(SCN) · x H2O, complementary to our previous studies on crystal structures and hydration properties of lithium thiocyanate Li(SCN). Anhydrous Li(SCN) is a Schottky defective material with lithium vacancies VLi' being the dominant mobile defect. Two water incorporation mechanisms are identified: (i) At very low concentrations H2O acts as a dopant and forms H2OSCN• defects, constituting a substitutive incorporation mechanism. Doping with water not only increases the concentration of VLi' in Li(SCN), but also the vacancy mobility, making H2O-doping a special case. A complete quantitative defect chemical model is derived, including enthalpies and entropies of defect formation, association, and migration. (ii) Higher water activities induce chemical and structural changes in Li(SCN) · x H2O, i.e. hydration by reactive incorporation occurs. Single-phases as well as composites are investigated for their Li+ ion transport mechanisms. In case of x ≤ 1, defect associates determine the conductivity resulting in exceptionally high activation enthalpies. Further hydration to 1 < x < 2 creates composites of solid mono- and dihydrates, in which the low-melting diyhdrate can form percolating pathways and increase the conductivity to values as high as 7 × 10−4 S/cm at room temperature. Further increase of x leads to complete liquefaction. The entire range of x in the Li(SCN) – H2O system was studied regarding ion transport properties, identifying the individual mechanisms and temperature dependences. The results of this work deepen the understanding of hydration effects on solid ion conductors in solid state ionics, and help to elucidate transport phenomena in salt – solvent systems.

First-principles simulations of liquid iron-heavy element alloys at high pressure

Iron-rich metallic liquid in the Earth's outer core is thought to contain many elements. While the incorporation of light elements in liquid iron has been widely studied, liquid iron-heavy element mixtures, particularly considering Co, Mo, and W which are relevant in constraining core-forming conditions need more studies. Here we investigate the thermodynamic and structural behavior of these siderophile elements and Ni dissolved in liquid iron in the amount of 2.67 atom% using first-principles molecular dynamics over the pressure range of the entire Earth's interior at temperatures 4000 to 7000 K. The calculated pressure-volume-temperature results of these iron-rich alloys are accurately described by adding the appropriative terms to the equation of state of pure iron liquid to account for the effects of temperature and impurity. The calculated mean iron coordination number of Mo and W is somewhat larger than that of Ni and Co and host iron atoms thus implying substitutional incorporation mechanism. The lack of clustering activity among the impurity atoms means that each of these impurity elements is soluble in liquid iron. Our analysis also shows that Mo and W increase the liquid density much more than Ni and Co mainly for mass reason while the bulk modulus remains essentially unaffected in all cases. The presence of heavy elements widens the apparent density gap between iron-rich liquid and the outer core so additional amounts of lighter impurity elements should be considered when constraining the core composition.