AnnoSM: An Automated Annotation Tool for Determining the Substituent Modes on the Parent Skeleton Based on a Characteristic MS/MS Fragment Ion Library.

Mass spectrometry (MS) is a powerful technology for the structural elucidation of known or unknown small molecules. However, the accuracy of MS-based structure annotation is still limited due to the presence of numerous isomers in complex matrices. There are still challenges in automatically interpreting the fine structure of molecules, such as the types and positions of substituents (substituent modes, SMs) in the structure. In this study, we employed flavones, flavonols, and isoflavones as examples to develop an automated annotation method for identifying the SMs on the parent molecular skeleton based on a characteristic MS/MS fragment ion library. Importantly, user-friendly software AnnoSM was built for the convenience of researchers with limited computational backgrounds. It achieved 76.87% top-1 accuracy on the 148 authentic standards. Among them, 22 sets of flavonoid isomers were successfully differentiated. Moreover, the developed method was successfully applied to complex matrices. One such example is the extract of Ginkgo biloba L. (EGB), in which 331 possible flavonoids with SM candidates were annotated. Among them, 23 flavonoids were verified by authentic standards. The correct SMs of 13 flavonoids were ranked first on the candidate list. In the future, this software can also be extrapolated to other classes of compounds.

The Mitogen-Activated Protein Kinase Hog1 Regulates Fungal Development, Pathogenicity, and Stress Response in Botryosphaeria dothidea.

The high-osmolarity glycerol mitogen-activated protein kinase (HOG-MAPK) pathway plays a central role in environmental stress adaptation in eukaryotes. However, the biological function of the HOG-MAPK pathway varies in different fungi. In this study, we investigated the HOG-MAPK pathway by inactivation of the core element Hog1 in Botryosphaeria dothidea, the causal agent of Botryosphaeria canker and apple ring rot. Targeted deletion of BdHOG1 resulted in the loss of conidiation ability and significant reduction of virulence. In addition, the ΔBdHog1 mutant exhibited hypersensitivity to osmotic stress but resistance to phenylpyrrole and dicarboximide fungicides. Comparative transcriptome analysis revealed that inactivation of BdHog1 influenced multiple metabolic pathways in B. dothidea. Taken together, our results suggest that BdHog1 plays a crucial role in development, virulence, and stress tolerance in B. dothidea, which provides a theoretical basis for the development of target-based fungicides.

Advances in dietary proteins binding with co-existed anthocyanins in foods: Driving forces, structure-affinity relationship, and functional and nutritional properties.

Anthocyanins, which are the labile flavonoid pigments widely distributed in many fruits, vegetables, cereal grains, and flowers, are receiving intensive interest for their potential health benefits. Proteins are important food components from abundant sources and present high binding affinity for small dietary compounds, e.g., anthocyanins. Protein-anthocyanin interactions might occur during food processing, ingestion, digestion, and bioutilization, leading to significant changes in the structure and properties of proteins and anthocyanins. Current knowledge of protein-anthocyanin interactions and their contributions to functions and bioactivities of anthocyanin-containing foods were reviewed. Binding characterization of dietary protein-anthocyanins complexes is outlined. Advances in understanding the structure-affinity relationship of dietary protein-anthocyanin interaction are critically discussed. The associated properties of protein-anthocyanin complexes are considered in an evaluation of functional and nutritional values.

Economical and Sustainable Synthesis of Small-Pore Chabazite Catalysts for NOx Abatement by Recycling Organic Structure-Directing Agents.

The application of small-pore chabazite-type SSZ-13 zeolites, key materials for the reduction of nitrogen oxides (NOx) in automotive exhausts and the selective conversion of methane, is limited by the use of expensive N,N,N-trimethyl-1-ammonium adamantine hydroxide (TMAdaOH) as an organic structure-directing agent (OSDA) during hydrothermal synthesis. Here, we report an economical and sustainable route for SSZ-13 synthesis by recycling and reusing the OSDA-containing waste liquids. The TMAdaOH concentration in waste liquids, determined by a bromocresol green colorimetric method, was found to be a key factor for SSZ-13 crystallization. The SSZ-13 zeolite synthesized under optimized conditions demonstrates similar physicochemical properties (surface area, porosity, crystallinity, Si/Al ratio, etc.) as that of the conventional synthetic approach. We then used the waste liquid-derived SSZ-13 as the parent zeolite to synthesize Cu ion-exchanged SSZ-13 (i.e., Cu-SSZ-13) for ammonia-mediated selective catalytic reduction of NOx (NH3-SCR) and observed a higher activity as well as better hydrothermal stability than Cu-SSZ-13 by conventional synthesis. In situ infrared and ultraviolet-visible spectroscopy investigations revealed that the superior NH3-SCR performance of waste liquid-derived Cu-SSZ-13 results from a higher density of Cu2+ sites coordinated to paired Al centers on the zeolite framework. The technoeconomic analysis highlights that recycling OSDA-containing waste liquids could reduce the raw material cost of SSZ-13 synthesis by 49.4% (mainly because of the higher utilization efficiency of TMAdaOH) and, meanwhile, the discharging of wastewater by 45.7%.

Ammonia Abatement via Selective Oxidation over Electron-Deficient Copper Catalysts.

Selective catalytic ammonia-to-dinitrogen oxidation (NH3-SCO) is highly promising for the abatement of NH3 emissions from flue gas purification devices. However, there is still a lack of high-performance and cost-effective NH3-SCO catalysts for real applications. Here, highly dispersed, electron-deficient Cu-based catalysts were fabricated using nitrogen-doped carbon nanotubes (NCNT) as support. In NH3-SCO catalysis, the Cu/NCNT outperformed Cu supported on N-free CNTs (Cu/OCNT) and on other types of supports (i.e., activated carbon, Al2O3, and zeolite) in terms of activity, selectivity to the desired product N2, and H2O resistance. Besides, Cu/NCNT demonstrated a better structural stability against oxidation and a higher NH3 storage capacity (in the presence of H2O vapor) than Cu/OCNT. Quasi in situ X-ray photoelectron spectroscopy revealed that the surface N species facilitated electron transfer from Cu to the NCNT support, resulting in electron-deficient Cu catalysts with superior redox properties, which are essential for NH3-SCO catalysis. By temperature-programmed surface reaction studies and systematic kinetic measurements, we unveiled that the NH3-SCO reaction over Cu/NCNT proceeded via the internal selective catalytic reaction (i-SCR) route; i.e., NH3 was oxidized first to NO, which then reacted with NH3 and O2 to form N2 and H2O. This study paves a new route for the design of highly active, H2O-tolerant, and low-cost Cu catalysts for the abatement of slip NH3 from stationary emissions via selective oxidation to N2.

Inhibition Effect of Phosphorus Poisoning on the Dynamics and Redox of Cu Active Sites in a Cu-SSZ-13 NH3-SCR Catalyst for NOx Reduction.

Phosphorus (P) stemming from biodiesel and/or lubricant oil additives is unavoidable in real diesel exhausts and deactivates gradually the Cu-SSZ-13 zeolite catalyst for ammonia-assisted selective catalytic NOx reduction (NH3-SCR). Here, the deactivation mechanism of Cu-SSZ-13 by P-poisoning was investigated by ex situ examination of the structural changes and by in situ probing the dynamics and redox of Cu active sites via a combination of impedance spectroscopy, diffuse reflection infrared Fourier transform spectroscopy, and ultraviolet-visible spectroscopy. We unveiled that strong interactions between Cu and P led to not only a loss of Cu active sites for catalytic turnovers but also a restricted dynamic motion of Cu species during low-temperature NH3-SCR catalysis. Furthermore, the CuII ↔ CuI redox cycling of Cu sites, especially the CuI → CuII reoxidation half-cycle, was significantly inhibited, which can be attributed to the restricted Cu motion by P-poisoning disabling the formation of key dimeric Cu intermediates. As a result, the NH3-SCR activity at low temperatures (200 °C and below) decreased slightly for the mildly poisoned Cu-SSZ-13 and considerably for the severely poisoned Cu-SSZ-13.

Myoprotein-phytophenol interaction: Implications for muscle food structure-forming properties.

Phenolic compounds are commonly incorporated into muscle foods to inhibit lipid oxidation and modify product flavor. Those that are present in or extracted from plant sources (seeds, leaves, and stems) known as "phytophenols" are of particular importance in the current meat industry due to natural origins, diversity, and safety record. Apart from these primary roles as antioxidants and flavorings, phytophenols are now recognized to be chemically reactive with a variety of food constituents, including proteins. In processed muscle foods, where the structure-forming ability is critical to a product's texture-related quality attributes and palatability, the functional properties of proteins, especially gelation and emulsification, play an essential role. A vast amount of recent studies has been devoted to protein-phenol interactions to investigate the impact on meat product texture and flavor. Considerable efforts have been made to elucidate the specific roles of phytophenol interaction with "myoproteins" (i.e., muscle-derived proteins) probing the structure-forming process in cooked meat products. The present review provides an insight into the actions of phytophenols in modifying and interacting with muscle proteins with an emphasis on the reaction mechanisms, detection methods, protein functionality, and implications for structural characteristics and textural properties of muscle foods.

All-optical tunable microfiber knot resonator with graphene-assisted sandwich structure.

We demonstrate an all-optical tunable microfiber knot resonator (MFKR) by direct light-graphene interaction using external vertical incidence pump laser. The 1530 nm CW pump source is employed to irradiate the sample, which can achieve the performance modulation of MFKR including transmission loss, extinction ratio, and resonant wavelength by the saturable absorption, photo-thermal, and optical Kerr effects, respectively. Compared with the MFKR with only the bottom graphene film, the tunable ranges of transmission loss and extinction ratio are increased by 69 and 125 times, respectively, which can induce a remarkable amplitude tuning. The resonant wavelength of MFKR occurs a red-shift under the irradiation of the pump light, and the red-shift range can exceed one free spectral range (FSR), which means the resonant wavelength could be tuned in the full wavelength range of the transparent window of optical fiber. It is promising for the device to be applied as an all-optical modulator, tunable optical filter, etc.

Isolation and functional characterization of human erythroblasts at distinct stages: implications for understanding of normal and disordered erythropoiesis in vivo.

Terminal erythroid differentiation starts from morphologically recognizable proerythroblasts that proliferate and differentiate to generate red cells. Although this process has been extensively studied in mice, its characterization in humans is limited. By examining the dynamic changes of expression of membrane proteins during in vitro human terminal erythroid differentiation, we identified band 3 and α4 integrin as optimal surface markers for isolating 5 morphologically distinct populations at successive developmental stages. Functional analysis revealed that these purified cell populations have distinct mitotic capacity. Use of band 3 and α4 integrin enabled us to isolate erythroblasts at specific developmental stages from primary human bone marrow. The ratio of erythroblasts at successive stages followed the predicted 1:2:4:8:16 pattern. In contrast, bone marrows from myelodysplastic syndrome patients exhibited altered terminal erythroid differentiation profiles. Thus, our findings not only provide new insights into the genesis of the red cell membrane during human terminal erythroid differentiation but also offer a means of isolating and quantifying each developmental stage during terminal erythropoiesis in vivo. Our findings should facilitate a comprehensive cellular and molecular characterization of each specific developmental stage of human erythroblasts and should provide a powerful means of identifying stage-specific defects in diseases associated with pathological erythropoiesis.

Electro-optic directed XOR logic circuits based on parallel-cascaded micro-ring resonators.

We report an electro-optic photonic integrated circuit which can perform the exclusive (XOR) logic operation based on two silicon parallel-cascaded microring resonators (MRRs) fabricated on the silicon-on-insulator (SOI) platform. PIN diodes embedded around MRRs are employed to achieve the carrier injection modulation. Two electrical pulse sequences regarded as two operands of operations are applied to PIN diodes to modulate two MRRs through the free carrier dispersion effect. The final operation result of two operands is output at the Output port in the form of light. The scattering matrix method is employed to establish numerical model of the device, and numerical simulator SG-framework is used to simulate the electrical characteristics of the PIN diodes. XOR operation with the speed of 100Mbps is demonstrated successfully.

Molecular Dynamics Simulations of Supramolecular Polymers within Nanoconfinements for Enhanced Oil Recovery.

Supramolecular polymers offer promising potential for enhanced oil recovery (EOR) advancing techniques. Current instrumental analyses face limitations in capturing instantaneous intracomplex motions due to temporal and spatial constraints. The molecular mechanism of supramolecular polymer transport behavior within nanoconfinement is not yet fully understood. Therefore, the self-assembly mechanism of ß-cyclodextrin (ß-CD) and adamantane (ADA)-modified supramolecular polymers (p-AA-ß-CD-ADA) was delved into in this work. Further exploration focuses on the translocation dynamics of p-AA-ß-CD-ADA within nanoconfinement under external driving forces. Results suggest that ß-CD and ADA in p-AA-ß-CD-ADA were assembled into nodes in the form of a host and a guest, combining with a "node-rebar-cement" interaction model encapsulating the formation mechanism of these supramolecular polymers. The heightened density of the hydrate layers at the nanoscale pore throats acts as a constraining factor, resulting in restricted mobility and altered dynamics of the supramolecular polymers. During passage through nanopore throats, host-guest molecules within the supramolecular polymer experience noncovalent dissociation. Notably, these supramolecular polymers exhibit remarkable self-healing capabilities, reinstating their assembly state upon traversing pore throats. This work provides a molecular-level comprehension of the potential utility of supramolecular polymers in EOR processes, offering valuable information for the molecular design of polymers employed for EOR in low-permeability reservoirs.

A structural similarity networking assisted collision cross-section prediction interval filtering strategy for multi-compound identification of complex matrix by ion-mobility mass spectrometry.

Ion mobility coupled with mass spectrometry (IM-MS), an emerging technology for analysis of complex matrix, has been facing challenges due to the complexities of chemical structures and original data, as well as low-efficiency and error-proneness of manual operations. In this study, we developed a structural similarity networking assisted collision cross-section prediction interval filtering (SSN-CCSPIF) strategy. We first carried out a structural similarity networking (SSN) based on Tanimoto similarities among Morgan fingerprints to classify the authentic compounds potentially existing in complex matrix. By performing automatic regressive prediction statistics on mass-to-charge ratios (m/z) and collision cross-sections (CCS) with a self-built Python software, we explored the IM-MS feature trendlines, established filtering intervals and filtered potential compounds for each SSN classification. Chemical structures of all filtered compounds were further characterized by interpreting their multidimensional IM-MS data. To evaluate the applicability of SSN-CCSPIF, we selected Ginkgo biloba extract and dripping pills. The SSN-CCSPIF subtracted more background interferences (43.24%∼43.92%) than other similar strategies with conventional ClassyFire criteria (10.71%∼12.13%) or without compound classification (35.73%∼36.63%). Totally, 229 compounds, including eight potential new compounds, were characterized. Among them, seven isomeric pairs were discriminated with the integration of IM-separation. Using SSN-CCSPIF, we can achieve high-efficient analysis of complex IM-MS data and comprehensive chemical profiling of complex matrix to reveal their material basis.

Ghrelin regulates hyperactivity-like behaviors via growth hormone signaling pathway in zebrafish (Danio rerio).

Introduction: Ghrelin is originally identified as the endogenous ligand for the growth hormone secretagogue receptor (GHSR) and partially acts by stimulating growth hormone (GH) release. Our previous studies have identified GHRELIN as a novel susceptibility gene for human attention-deficit hyperactivity disorder (ADHD), and ghrelin-depleted zebrafish (Danio rerio) display ADHD-like behaviors. However, the underlying molecular mechanism how ghrelin regulates hyperactivity-like behaviors is not yet known. Results: Here, we performed RNA-sequencing analysis using adult ghrelin Δ/Δ zebrafish brains to investigate the underlying molecular mechanisms. We found that gh1 mRNA and genes related to the gh signaling pathway were significantly reduced at transcriptional expression levels. Quantitative polymerase chain reaction (qPCR) was performed and confirmed the downregulation of gh signaling pathway-related genes in ghrelin Δ/Δ zebrafish larvae and the brain of adult ghrelin Δ/Δ zebrafish. In addition, ghrelin Δ/Δ zebrafish displayed hyperactive and hyperreactive phenotypes, such as an increase in motor activity in swimming test and a hyperreactive phenotype under light/dark cycle stimulation, mimicking human ADHD symptoms. Intraperitoneal injection of recombinant human growth hormone (rhGH) partially rescued the hyperactivity and hyperreactive-like behaviors in ghrelin mutant zebrafish. Conclusion: Our results indicated that ghrelin may regulate hyperactivity-like behaviors by mediating gh signaling pathway in zebrafish. And the protective effect of rhGH on ghrelin Δ/Δ zebrafish hyperactivity behavior provides new therapeutic clues for ADHD patients.

Concentration-dependent effect of eugenol on porcine myofibrillar protein gel formation.

The effects of different concentrations of eugenol (EG = 0, 5, 10, 20, 50, and 100 mg/g protein) on the structural properties and gelling behavior of myofibrillar proteins (MPs) were investigated. The interaction of EG and MPs decreased free thiol and amine content, and reduced tryptophan fluorescence intensity and thermal stability, but enhanced surface hydrophobicity and aggregation of MPs. Compared with the control (EG free), the MPs' gels treated with 5 and 10 mg/g of EG had a higher storage modulus, compressive strength, and less cooking loss. A high microscopic density was observed in these EG-treated gels. However, EG at 100 mg/g was detrimental to the gelling properties of the MPs. The results indicate that an EG concentration of 20 mg/g is a turning point, i.e., below 20 mg/g, EG promoted MPs gelation, but above 20 mg/g, it impeded gelation by interfering with protein network formation. The EG modification of MPs could provide a novel ingredient strategy to improve the texture of comminuted meat products.

Baicalein exerts anxiolytic and antinociceptive effects in a mouse model of posttraumatic stress disorder: Involvement of the serotonergic system and spinal delta-opioid receptors.

Post-traumatic stress disorder (PTSD) is a serious mental disease featured by a stress dysfunction that occurs after an individual has faced intense mental stress, often accompanied by anxiety and chronic pain. Currently, the mainstream drug for PTSD is serotonin reuptake inhibitors (SSRIs), however, their pain management for patients is limited. Baicalein, a Chinese traditional herbal medicine, has shown promising results in treating anxiety, depression, and pain. In this study, we found that baicalein may alleviate single prolonged stress (SPS)-induced PTSD-like behaviors in mice without altering baseline nociceptive sensitivity or activity. Meanwhile, baicalein increased the noradrenaline (NE) and serotonin (5-HT) content and decreased the ratio of 5-hydroxyindoleacetic acid (5-HIAA)/5-HT by inhibiting the activity of monoamine oxidase A (MAO-A) in SPS-induce mice. The anxiolytic and antinociceptive effects induced by baicalein were totally abolished by 5-HT depleting agents. Moreover, the anxiolytic effects of baicalein could be abolished by the 5-HT1A receptor antagonist WAY-100635, and the analgesic effects could be abolished by delta-opioid receptor antagonists in the spinal. Taken together, our study provides compelling evidence that baicalein reversed anxiety-like behaviors and neuropathic pain in PTSD through serotonergic system and spinal delta-opioid receptors.

Electrical conductivity: A simple and sensitive method to determine emulsifying capacity of proteins.

Emulsifying capacity (EC) of proteins is a benchmark standard widely used to evaluate the quality of protein ingredients in emulsion foods. EC (mL of oil emulsified per g of protein) is usually measured by a sudden drop in electrical resistance (phase transition) with the continuous addition of oil to a specific protein solution. However, little is known about electrochemical mechanisms behind this process because resistance, measured with an ohmmeter, is not sensitive enough to monitor changes in the concentration of protein electrolytes. Here, pea (PPI), myofibrillar (MPI), and whey (WPI) protein isolates were vigorously homogenized with oil at a series of oil/protein ratios to prepare emulsions with different final protein concentrations. The conductivity was closely monitored using a conductivity meter. A linear relationship was discovered between conductivity and the final protein concentrations. At higher oil fractions, the migration of proteins from the aqueous phase to the oil-water interface limited protein mobility, leading to a conductivity drop. EC was calculated from the regression lines; when the starting protein concentration was raised from 0.5% to 2.0%, the EC of PPI, MPI, and WPI decreased from 717, 782, 1339 to 219, 303, and 540 mL oil/g protein, respectively. The dependence of EC on the initial protein concentration and the sensitivity of conductivity to the depleting protein electrolytes suggest that protein concentration is an important factor to consider when determining EC for a given protein or comparing EC among different proteins. PRACTICAL APPLICATION: The simple and sensitive electrical conductivity test described in this paper allows for the accurate determination of emulsifying capacity of proteins. It may be adopted by the food industry to compare the emulsifying properties of different protein ingredients.

Myofibrillar Protein Cross-Linking and Gelling Behavior Modified by Structurally Relevant Phenolic Compounds.

Protein gelation is an important phenomenon in processed meats. The present study investigated the structure-activity relationship of six phenolic compounds, that is, gallic acid (GA), chlorogenic acid (CA), propyl gallate (PG), quercetin (QT), catechin (CC), and (-)-epigallocatechin-3-gallate (EGCG) in a myofibrillar protein (MP) gelling system under controlled oxidative conditions. All phenolics induced unfolding and promoted cross-linking of MP via sulfhydryl or amine groups. At an equal molar concentration, EGCG boosted the elastic MP gel network more than other phenolics except PG. However, all three monophenols (GA, CA, and PG) and the diphenol QT increased the MP gel strength more than CC (diphenol) and EGCG (triphenol). The flavanol structure appeared to interfere with the protein gel structure development. All phenolics retarded lipid oxidation in MP-emulsion composite gels during refrigerated storage with the least polar phenolic compounds, PG and QT, showing the greatest efficacy.

Synthetic liver fibrotic niche extracts achieve in vitro hepatoblasts phenotype enhancement and expansion.

It is still a challenge for synthesizing 'cellular niche-mimics' in vitro with satisfactory reproducibility and fidelity to recreate the natural niche components (e.g., extracellular matrices and soluble factors) for stem cell cultivation. Inspired by the massive amplification of hepatic progenitor cells during liver fibrosis in vivo, here we optimized the in vitro liver fibrotic niches and subsequently harvested their bioactive ingredients as niche extracts (NEs). The fibrosis-relevant NE marginally outperformed Matrigel for phenotype maintenance of human embryonic stem cell (hESC)-derived hepatoblasts (HBs) and recapitulation of the pathological angiogenesis of hESC-derived endothelial cells both in 2D culture and 3D liver organoids. Finally, defined NE components (i.e., collagen III, IV, IL-17, IL-18 and M-CSF) were resolved by the quantitative proteomics which exhibited advantage over Matrigel for multi-passaged HB expansion. The pathology-relevant and tissue-specific NEs provide innovative and generalizable strategies for the discovery of optimal cellular niche and bioactive niche compositions.

Animal and Plant Protein Oxidation: Chemical and Functional Property Significance.

Protein oxidation, a phenomenon that was not well recognized previously but now better understood, is a complex chemical process occurring ubiquitously in food systems and can be induced by processing treatments as well. While early research concentrated on muscle protein oxidation, later investigations included plant, milk, and egg proteins. The process of protein oxidation involves both radicals and nonradicals, and amino acid side chain groups are usually the site of initial oxidant attack which generates protein carbonyls, disulfide, dityrosine, and protein radicals. The ensuing alteration of protein conformational structures and formation of protein polymers and aggregates can result in significant changes in solubility and functionality, such as gelation, emulsification, foaming, and water-holding. Oxidant dose-dependent effects have been widely reported, i.e., mild-to-moderate oxidation may enhance the functionality while strong oxidation leads to insolubilization and functionality losses. Therefore, controlling the extent of protein oxidation in both animal and plant protein foods through oxidative and antioxidative strategies has been of wide interest in model system as well in in situ studies. This review presents a historical perspective of food protein oxidation research and provides an inclusive discussion of the impact of chemical and enzymatic oxidation on functional properties of meat, legume, cereal, dairy, and egg proteins based on the literature reports published in recent decades.