Confinement Effect and 3D Design Endow Unsaturated Single Ni Atoms with Ultrahigh Stability and Selectivity toward CO2 Electroreduction.

Developing single-atomic catalysts with superior selectivity and outstanding stability for CO2 electroreduction is desperately required but still challenging. Herein, confinement strategy and three-dimensional (3D) nanoporous structure design strategy are combined to construct unsaturated single Ni sites (Ni-N3) stabilized by pyridinic N-rich interconnected carbon nanosheets. The confinement agent chitosan and its strong interaction with g-C3N4 nanosheet are effective for dispersing Ni and restraining their agglomeration during pyrolysis, resulting in ultrastable Ni single-atom catalyst. Due to the confinement effect and structure advantage, such designed catalyst exhibits a nearly 100% selectivity and remarkable stability for CO2 electroreduction to CO, exceeding most reported state-of-the-art catalysts. Specifically, the CO Faradaic efficiency (FECO) maintains above 90% over a broad potential range (-0.55 to -0.95 V vs. RHE) and reaches a maximum value of 99.6% at a relatively low potential of -0.67 V. More importantly, the FECO is kept above 95% within a long-term 100 h electrolyzing. Density functional theory (DFT) calculations explain the high selectivity for CO generation is due to the high energy barrier required for hydrogen evolution on the unsaturated Ni-N3. This work provides a new designing strategy for the construction of ultrastable and highly selective single-atom catalysts for efficient CO2 conversion.

A comprehensive investigation on the chemical changes of traditional Chinese medicine with classic processing technology: Polygonum multiflorum under nine cycles of steaming and sunning as a case study.

The processing of traditional Chinese medicine (TCM) plays an important role in the clinical application, which usually has the function of "increasing efficiency and reducing toxicity". Polygonum multiflorum (PM) has been reported to induce hepatotoxicity, while it is believed that the toxicity is reduced after processing. Studies have shown that the hepatotoxicity of PM is closely related to the changes in chemical components before and after processing. However, there is no comprehensive investigation on the chemical changes of PM during the processing progress. In this research, we established a comprehensive method to profile both small molecule compounds and polysaccharides from raw and different processed PM samples. In detail, an online two-dimensional liquid chromatography coupled with quadrupole-orbitrap mass spectrometry (2D-LC/Q-Orbitrap MS) was utilized to investigate the small molecules, and a total of 150 compounds were characterized successfully. After multivariate statistical analysis, 49 differential compounds between raw and processed products were screened out. Furthermore, an accurate and comprehensive method for quantification of differential compounds in PM samples was established based on ultra-high performance liquid chromatography/Q-Orbitrap-MS (UHPLC/Q-Orbitrap-MS) within 16 min. In addition, the changes of polysaccharides in different PM samples were analyzed, and it was found that the addition of black beans and steaming times would affect the content and composition of polysaccharides in PM significantly. Our work provided a reference basis for revealing the scientific connotation of the processing technology and increasing the quality control and safety of PM.

A Semi-Markov Approach to Study a Group of Kinesin Motors.

We propose a general mathematical and computational approach to study cellular transport driven by a group of kinesin motors. It is a framework for multi-scale modeling that integrates kinetic models of single kinesin motors, including detachment and reattachment events, to study group behaviors of several motors. By formulating the problem as a semi-Markov process and applying a central limit theorem, asymptotic velocity and diffusivity can be readily calculated, which offers considerable computational advantage over Monte Carlo simulations in tasks such as parameter sensitivity analysis and model selection. We demonstrate the method with some examples. The importance of incorporating the intrinsic microscopic-level dynamics of individual motors is illustrated by showing how changes at the microscopic level propagate to the motor-cargo complex at a mesoscopic level. Particularly, we showcase an example in which changes in the second moment of single-motor characteristics gives rise to different first moment characteristics of the motor group.

Comprehensive quality control of Qingjin Yiqi granule based on UHPLC-Q-Orbitrap-MS and UPLC-QQQ-MS.

INTRODUCTION: Qingjin Yiqi granule (QYG) is a prescription medicine of traditional Chinese medicine which is widely used clinically for the recovery of coronavirus patients. However, there is currently limited research on the quality control of QYG. OBJECTIVE: To evaluate the quality of QYG qualitatively and quantitatively by making full use of advanced chromatography-mass spectrometry techniques. METHODS: Firstly, a multicomponent characterisation of QYG was performed by ultrahigh-performance liquid chromatography coupled with a Q Exactive™ hybrid quadrupole-Orbitrap mass spectrometry (UHPLC-Q-Orbitrap-MS) system using a rapid negative/positive switching mode. Secondly, the co-condition fingerprint analysis of constituted herbal medicines of QYG was performed to unveil active ingredients as the quality markers of QYG. Thirdly, the marker compounds in 10 batches of QYG were quantified by ultrahigh-performance liquid chromatography coupled with a Waters Xevo TQ-S triple quadrupole mass spectrometry (UPLC-QQQ-MS) system. RESULTS: A comprehensive method that combined the inclusion list and data-dependent acquisition (DDA) to achieve a systematic characterisation of QYG was established by UHPLC-Q-Orbitrap-MS. After analysis based on Compound Discoverer software and Global Natural Products Social (GNPS) platform, a total of 332 compounds were detected. Eleven Q-markers were determined for the quality evaluation of QYG by comparison with the fingerprint of nine constituted herbal medicines. An adjusted multiple reaction monitoring (MRM) quantification method was further established to simultaneously determine the 11 Q-markers for holistic quality evaluation of QYG. CONCLUSION: This is the first study to report comprehensive multicomponent characterisation, identification, and quality assessment of QYG, which could be used for effective guarantee of the quality of QYG.

Comparative Analysis of Volatile Compounds in the Flower Buds of Three Panax Species Using Fast Gas Chromatography Electronic Nose, Headspace-Gas Chromatography-Ion Mobility Spectrometry, and Headspace Solid Phase Microextraction-Gas Chromatography-Mass Spectrometry Coupled with Multivariate Statistical Analysis.

The flower buds of three Panax species (PGF: P. ginseng; PQF: P. quinquefolius; PNF: P. notoginseng) widely consumed as health tea are easily confused in market circulation. We aimed to develop a green, fast, and easy analysis strategy to distinguish PGF, PQF, and PNF. In this work, fast gas chromatography electronic nose (fast GC e-nose), headspace-gas chromatography-ion mobility spectrometry (HS-GC-IMS), and headspace solid phase microextraction-gas chromatography-mass spectrometry (HS-SPME-GC-MS) were utilized to comprehensively analyze the volatile organic components (VOCs) of three flowers. Meanwhile, a principal component analysis (PCA) and heatmap were applied to distinguish the VOCs identified in PGF, PQF, and PNF. A random forest (RF) analysis was used to screen key factors affecting the discrimination. As a result, 39, 68, and 78 VOCs were identified in three flowers using fast GC e-nose, HS-GC-IMS, and HS-SPME-GC-MS. Nine VOCs were selected as potential chemical markers based on a model of RF for distinguishing these three species. Conclusively, a complete VOC analysis strategy was created to provide a methodological reference for the rapid, simple, and environmentally friendly detection and identification of food products (tea, oil, honey, etc.) and herbs with flavor characteristics and to provide a basis for further specification of their quality and base sources.

Suppressed farnesoid X receptor by iron overload in mice and humans potentiates iron-induced hepatotoxicity.

BACKGROUND AND AIMS: Iron overload (IO) is a frequent finding in the general population. As the major iron storage site, the liver is subject to iron toxicity. Farnesoid X receptor (FXR) regulates bile acid metabolism and is implicated in various liver diseases. We aimed to determine whether FXR plays a role in regulating iron hepatotoxicity. APPROACH AND RESULTS: Human and mouse hepatocytes were treated with ferric ammonium citrate or iron dextran (FeDx). Mice were orally administered ferrous sulfate or injected i.p. with FeDx. Wild-type and Fxr-/- mice were fed an iron-rich diet for 1 or 5 weeks. Mice fed an iron-rich diet were coadministered the FXR agonist, GW4064. Forced expression of FXR was carried out with recombinant adeno-associated virus 1 week before iron-rich diet feeding. Serum levels of bile acids and fibroblast growth factor 19 (FGF19) were quantified in adults with hyperferritinemia and children with ß-thalassemia. The data demonstrated that iron suppressed FXR expression and signaling in human and mouse hepatocytes as well as in mouse liver and intestine. FXR deficiency potentiated iron hepatotoxicity, accompanied with hepatic steatosis as well as dysregulated iron and bile acid homeostasis. FXR negatively regulated iron-regulatory proteins 1 and 2 and prevented hepatic iron accumulation. Forced FXR expression and ligand activation significantly suppressed iron hepatotoxicity in iron-fed mice. The FXR agonist, GW4064, almost completely restored dysregulated bile acid signaling and metabolic syndrome in iron-fed mice. Conjugated primary bile acids were increased and FGF19 was decreased in serum of adults with hyperferritinemia and children with ß-thalassemia. CONCLUSIONS: FXR plays a pivotal role in regulating iron homeostasis and protects mice against iron hepatotoxicity. Targeting FXR may represent a therapeutic strategy for IO-associated chronic liver diseases.

Comprehensive multicomponent characterization and quality assessment of Shuang-Huang-Lian powder injection using ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry and ultra-high-performance liquid chromatography-quadrupole-Orbitrap-mass spectrometry.

RATIONALE: Shuang-Huang-Lian powder injection (SHLPI) is a well-known modern traditional Chinese medicine formula preparation (TCMFP) widely used to treat acute upper respiratory infections. However, SHLPI is extracted from pure Chinese medicine and administered through an injection, and many adverse reactions have been reported clinically. Therefore, it is necessary to characterize in depth the chemical composition of SHLPI and quantitatively analyze its potential allergenic components. METHODS: In this study, the samples were analyzed using ion mobility ultra-high-performance liquid chromatography-quadrupole time-of-flight-mass spectrometry (UHPLC-QTOF-MS) combined with a self-built database. Furthermore, the parallel reaction monitoring (PRM) model of ultra-high-performance liquid chromatography-quadrupole-Orbitrap-mass spectrometry (UHPLC-Q-Orbitrap-MS) was used to successfully quantify 10 representative bioactive components. RESULTS: Using this strategy 90 compounds were identified, the fragmentation pathways of five representative compounds in the five main components of SHLPI were summarized, and 10 components (neochlorogenic acid, chlorogenic acid, sweroside, forsythiaside A, luteoloside, isochlorogenic acid B, isochlorogenic acid C, baicalin, phillyrin, and baicalein) were determine as the quality markers of SHLPI based on UPLC-Q-Orbitrap-MS. CONCLUSIONS: This work comprehensively characterized the material basis of SHLPI, summarized the cracking laws of representative substances, and quantitatively analyzed 10 potential allergenic components. Therefore, this study could provide a basis for the quality control of SHLPI and the clinical rational use of drugs to reduce its adverse reactions.

Selective Inhibition of Organic Cation Transporter 1 by Benzoylpaeoniflorin Attenuates Hepatic Lipid Accumulation through AMPK Activation.

Organic cation transporter 1 (OCT1) is a liver-specific transporter and plays an essential role in drug disposition and hepatic lipid metabolism. Therefore, inhibition of OCT1 may not only lead to drug-drug interactions but also represent a potential therapy for fatty liver diseases. In this study, we systematically investigated the inhibitory effect of 200 natural products on OCT1-mediated uptake of 4,4-dimethylaminostyryl-N-methylpyridinium (ASP+) and identified 10 potent OCT1 inhibitors. The selectivity of these inhibitors over OCT2 was evaluated using both in vitro uptake assays and in silico molecular docking analyses. Importantly, benzoylpaeoniflorin was identified as the most potent OCT1 inhibitor with the highest selectivity over OCT2. Additionally, benzoylpaeoniflorin prevented lipid accumulation in hepatocytes, with concomitant activation of AMPK and down-regulation of lipogenic genes, such as acetyl-CoA carboxylase (ACC) and fatty acid synthase (FASN). To conclude, our findings are of significant value in understanding OCT1-based natural product-drug interactions and provide a natural source of OCT1 inhibitors which may hold promise for treating fatty liver diseases.

Reaction-Diffusion Modeling of E. coli Colony Growth Based on Nutrient Distribution and Agar Dehydration.

The bacterial colony is a powerful experimental platform for broad biological research, and reaction-diffusion models are widely used to study the mechanisms of its formation process. However, there are still some crucial factors that drastically affect the colony growth but are not considered in the current models, such as the non-homogeneously distributed nutrient within the colony and the substantially decreasing expansion rate caused by agar dehydration. In our study, we propose two plausible reaction-diffusion models (the VN and MVN models) based on the above two factors and validate them against experimental data. Both models provide a plausible description of the non-homogeneously distributed nutrient within the colony and outperform the classical Fisher-Kolmogorov equation and its variation in better describing experimental data. Moreover, by accounting for agar dehydration, the MVN model captures how a colony's expansion slows down and the change of a colony's height profile over time. Furthermore, we demonstrate the existence of a traveling wave solution for the VN model.

Transporter-mediated Natural Product-Drug Interactions.

The increasing use of natural products in clinical practice has raised great concerns about the potential natural product-drug interactions (NDIs). Drug transporters mediate the transmembrane passage of a broad range of drugs, and thus are important determinants for drug pharmacokinetics and pharmacodynamics. Generally, transporters can be divided into ATP binding cassette (ABC) family and solute carrier (SLC) family. Numerous natural products have been identified as inhibitors, substrates, inducers, and/or activators of drug transporters. This review article aims to provide a comprehensive summary of the recent progress on the research of NDIs, focusing on the main drug transporters, such as P-glycoprotein (P-gp), breast cancer resistance protein (BCRP), organic anion transporter 1 and 3 (OAT1/OAT3), organic anion-transporting polypeptide 1B1 and 1B3 (OATP1B1/OATP1B3), organic cation transporter 2 (OCT2), multidrug and toxin extrusion protein 1 and 2-K (MATE1/MATE2-K). Additionally, the challenges and strategies of studying NDIs are also discussed.

Potential Involvement of Organic Anion Transporters in Drug Interactions with Shuganning Injection, a Traditional Chinese Patent Medicine.

Traditional Chinese medicine injections have been widely used in China for the treatment of various diseases. Transporter-mediated drug-drug interactions are a major contributor to adverse drug reactions. However, the research on transporter-mediated Traditional Chinese medicine injection-drug interactions is limited. Shuganning injection is a widely used Traditional Chinese medicine injection for treating various liver diseases. In this study, we investigated the inhibitory effect of Shuganning injection and its four main ingredients (baicalin, geniposide, chlorogenic acid, and oroxylin A) on 9 drug transporters. Shuganning injection strongly inhibited organic anion transporter 1 and organic anion transporter 3 with IC50 values < 0.1% (v/v), and moderately inhibited organic anion transporter 2, organic anion transporting-polypeptide 1B1, and organic anion transporting-polypeptide 1B3 with IC50 values < 1.0%. Baicalin, the most abundant bioactive ingredient in the Shuganning injection, was identified as both an inhibitor and substrate of organic anion transporter 1, organic anion transporter 3, and organic anion transporting-polypeptide 1B3. Oroxylin A had the potential to act as both an inhibitor and substrate of organic anion transporting-polypeptide 1B1 and organic anion transporting-polypeptide 1B3. In contrast, geniposide and chlorogenic acid had no significant inhibitory effect on drug transporters. Notably, Shuganning injection markedly altered the pharmacokinetics of furosemide and atorvastatin in rats. Using Shuganning injection as an example, our findings support the implementation of transporter-mediated Traditional Chinese medicine injection-drug interactions in the development of Traditional Chinese medicine injection standards.

Integrated metabolic and transcriptomic profiles reveal the germination-associated dynamic changes for the seeds of Cassia obtusifolia L.

INTRODUCTION: The seeds of Cassia obtusifolia L. (Cassiae [C.] semen) have been widely used as both food and traditional Chinese medicine in China. OBJECTIVES: We aimed to analyze the metabolic mechanisms underlying C. semen germination. MATERIALS AND METHODS: Different samples of C. semen at various germination stages were collected. These samples were subjected to 1 H-NMR and UHPLC/Q-Orbitrap-MS-based untargeted metabolomics analysis together with transcriptomics analysis. RESULTS: A total of 50 differential metabolites (mainly amino acids and sugars) and 20 key genes involved in multiple pathways were identified in two comparisons of different groups (36 h vs 12 h and 84 h vs 36 h). The metabolite-gene network for seed germination was depicted. In the germination of C. semen, fructose and mannose metabolism was activated in the testa rupture period, indicating more energy was needed (36 h). In the embryonic axis elongation period (84 h), the pentose and glucuronate interconversions pathway and the phenylpropanoid biosynthesis pathway were activated, which suggested some nutrient sources (nitrogen and sugar) were in demand. Furthermore, oxygen, energy, and nutrition should be supplied throughout the whole germination process. These global views open up an integrated perspective for understanding the complex biological regulatory mechanisms during the germination process of C. semen.

A multiple-metabolites model to predict preliminary renal injury induced by iodixanol based on UHPLC/Q-Orbitrap-MS and 1H-NMR.

BACKGROUND & AIMS: There are some problems, such as unclear pathological mechanism, delayed diagnosis, and inaccurate therapeutic target of Contrast-induced acute kidney injury (CI-AKI). It is significantly important to find biomarkers and therapeutic targets that can indicate renal injury in the early stage of CI-AKI. This study aims to establish a multiple-metabolites model to predict preliminary renal injury induced by iodixanol and explore its pathogenesis. METHODS: Both UHPLC/Q-Orbitrap-MS and 1H-NMR methods were applied for urine metabolomics studies on two independent cohorts who suffered from a preliminary renal injury caused by iodixanol, and the multivariate statistical analysis and random forest (RF) algorithm were used to process the related date. RESULTS: In the discovery cohort (n = 169), 6 metabolic markers (leucine, indole, 5-hydroxy-L-tryptophan, N-acetylvaline, hydroxyhexanoycarnine, and kynurenic acid) were obtained by the cross-validation between the RF and liquid chromatography-mass spectrometry (LC-MS). Secondly, the 6 differential metabolites were confirmed by comparison of standard substance and structural identification of 1H-NMR. Subsequently, the multiple-metabolites model composed of the 6 biomarkers was validated in a validation cohort (n = 165). CONCLUSIONS: The concentrations of leucine, indole, N-acetylvaline, 5-hydroxy-L-tryptophan, hydroxyhexanoycarnitine and kynurenic acid in urine were proven to be positively correlated with the degree of renal injury induced by iodixanol. The multiple-metabolites model based on these 6 biomarkers has a good predictive ability to predict early renal injury caused by iodixanol, provides treatment direction for injury intervention and a reference for reducing the incidence of clinical CI-AKI further.

Metabolomic Study on Iohexol-Induced Nephrotoxicity in Rats Based on NMR and LC-MS Analyses.

Iohexol, the raw material of nonionic X-ray computed tomography (X-CT) contrast medium, is usually injected into the vein before CT angiography diagnosis. It is used for angiography, urography, and lymphography. With the advantages of low contrast density and good tolerance, it is currently one of the most popular contrast media. However, the renal toxicity of iohexol seriously affects its safety use. Therefore, it is of great importance to identify new potential diagnostic biomarkers and therapeutic targets in the process of contrast medium-induced acute kidney injury (CI-AKI) in order to safely use iohexol in clinical practice. In this study, in order to understand the metabolic mechanism of CI-AKI, ultra-high-performance liquid chromatography/quadrupole-Orbitrap-mass spectrometry and 1H NMR-based metabolomic techniques were utilized to study the metabolic spectra of kidney, plasma, and urine from CI-AKI rats, and a total of 30 metabolites that were closely related to kidney injury were screened out, which were mainly related to 9 metabolic pathways. The results further indicated that iohexol might intensify kidney dysfunction in vivo by disrupting the metabolic pathways in the body, especially through blocking energy metabolism, amino acid metabolism, and promoting inflammatory reactions.

Discovery of metabolic markers for the discrimination of Helwingia species based on bioactivity evaluation, plant metabolomics, and network pharmacology.

RATIONALE: Helwingia japonica (HJ), a traditional medicinal plant, is commonly used for the treatment of dysentery, blood in the stool, and scald burns. Three major HJ species, Helwingia japonica (Thunb.) Dietr. (QJY), Helwingia himalaica Hook. f. et Thoms. ex C. B. Clarke, and Helwingia chinensis Batal., share great similarities in both morphology and chemical constituents. The discrimination of medicinal plants directly affects their pharmacological and clinical effects. Here, we solved the taxonomy uncertainty of these three HJ species and explored the discrimination and study of other traditional medicines (TMs). METHODS: First, the anti-inflammatory effects of the three HJ species were compared using lipopolysaccharide (LPS)-induced inflammatory responses in mouse leukemia cells of monocyte macrophage (RAW) 264.7 cells. Then, plant metabolomics were performed in 48 batches of samples to discover chemical markers for discriminating different HJ species. Finally, network pharmacology was applied to explore the linkages among constituents, targets, and signaling pathways. RESULTS: In vitro experiments showed that the QJY exhibited the most potential anti-inflammatory activities. Meanwhile, 172 compounds were tentatively identified and eight metabolites with higher relative content in QJY were designated as chemical markers to distinguish QJY and the other two species. According to the property of absorbed in vivo, threonic acid, arginine, and tyrosine were selected to construct a component-target-pathway network. The network pharmacology analysis confirmed that the chemotaxonomy differentiation was consistent with the bioactive assessment. CONCLUSIONS: The present study demonstrates that bioactivity evaluation integrated with plant metabolomics and network pharmacology could be used as an effective approach to discriminate different TMs and discover the active compounds.

Ultrahigh-performance liquid chromatography coupled to ion mobility quadrupole time-of-flight mass spectrometry profiling and unveiling the transformation of ginsenosides by the dual conditions of citric acid and high-pressure steaming.

RATIONALE: Many methods have been reported for the production of rare ginsenosides, including heat treatment, acid hydrolysis, alkaline hydrolysis, enzymatic hydrolysis, and microbial transformation. However, the conversion of original ginsenosides to rare ginsenosides under the dual conditions of citric acid and high-pressure steam sterilization has rarely been reported. METHODS: In this study, a method involving ultrahigh-performance liquid chromatography coupled to ion mobility quadrupole time-of-flight mass spectrometry was developed for analysis of chemical transformation of protopanaxatriol (PPT)-type ginsenosides Rg1 and Re, protopanaxadiol (PPD)-type ginsenoside Rb1 , and total ginsenosides in the dual conditions of citric acid and high-pressure steam sterilization. An internal ginsenoside database containing 126 known ginsenosides and 18 ginsenoside reference compounds was established to identify the transformation products and explore possible transformation pathways and mechanisms. RESULTS: A total of 54 ginsenosides have been preliminarily identified in the transformation products of PPD-type ginsenosides Rg1 and Re, PPD-type ginsenoside Rb1 , and total ginsenosides, and the possible transformation pathways were as follows: Rg1 , Re → 20(S)-Rh12 , 20(R)-Rh12 ; Rg1 , Re → 20(S)-Rh1 , 20(R)-Rh1 → Rk3 , Rh4 , Rh5 ; Rb1 → gypenoside LXXV; Rb1 → 20(S)-Rg3 , 20(R)-Rg3 → Rk1 , Rg5 ; Re → 20(S)-Rg2 , 20(R)-Rg2 → 20(S)-Rf2 , 20(R)-Rf2 , Rg4 , F4 . CONCLUSIONS: The results elucidated the possible transformation pathways and mechanisms of ginsenosides in the dual conditions of citric acid and high-pressure steam sterilization, which were helpful for revealing the mechanisms of ginsenosides and enhanced safety and quality control of pharmaceuticals and nutraceuticals. Meanwhile, a simple, efficient, and practical method was developed for the production of rare ginsenosides, which has the potential to produce diverse rare ginsenosides on an industrial scale.

Rapid discovery of potential ADR compounds from injection of total saponins from Panax notoginseng using data-independent acquisition untargeted metabolomics.

Injection of total saponins from Panax notoginseng (ISPN) is a modern preparation derived from traditional Chinese medicine (TCM) and is widely applied in the treatment of cardiovascular, cerebrovascular, ophthalmology, and endocrine system diseases. With the increase in the clinical application of ISPN, its adverse drug reactions (ADRs) and related safety issues have attracted much attention. In the present study, a data-independent acquisition (DIA) strategy was proposed to comprehensively characterize the saponins contained in ISPN based on the ultra-high-performance liquid chromatography/quadrupole-Orbitrap MS (UHPLC/Q-Orbitrap MS) platform. As many as 276 saponins were detected, and 250 compounds were identified or tentatively identified based on the retention times and MS/MS data. Furthermore, a metabolomic strategy was utilized to discover the discriminative saponins between normal and ADR batches. The results showed that six saponins, including ginsenoside Rh4, ginsenoside Rk3, ginsenoside Rg5, ginsenoside Rk1, ginsenoside Rg6, and 20(S)-ginsenoside Rh2, were significantly different between the two groups. According to cytotoxicity analysis and degranulation detection of RBL-2H3 cells, ginsenoside Rg5, ginsenoside Rk1, and 20(S)-ginsenoside Rh2 were considered the potential compounds responsible for clinical ADRs, ultimately. In addition, the quantitative analysis showed that the content of these three compounds in ISPN samples with ADRs was generally higher than that in samples without ADRs. This study demonstrated that it is advisable to screen out potential markers related to ADRs for developing the quality standard of ISPN by the integration of untargeted metabolomic analysis and cell biology study, and thus reduce its ADRs in the clinic.

Learning Biological Dynamics From Spatio-Temporal Data by Gaussian Processes.

Model discovery methods offer a promising way to understand biology from data. We propose a method to learn biological dynamics from spatio-temporal data by Gaussian processes. This approach is essentially "equation free" and hence avoids model derivation, which is often difficult due to high complexity of biological processes. By exploiting the local nature of biological processes, dynamics can be learned with data sparse in time. When the length scales (hyperparameters) of the squared exponential covariance function are tuned, they reveal key insights of the underlying process. The squared exponential covariance function also simplifies propagation of uncertainty in multi-step forecasting. After evaluating the performance of the method on synthetic data, we demonstrate a case study on real image data of E. coli colony.

Strategy of combining offline 2D LC-MS with LC-DIA-MS/MS to accurately identify chemical compounds and for quality control of Dioscorea septemloba Thunb.

INTRODUCTION: Dioscorea septemloba Thunb. (DST), the rhizome of Dioscorea spongiosa J. Q. Xi, M. Mizuno et W. L. Zhao or Fuzhou Dioscorea futschauensis Uline ex R. Kunth, has multiple biological activities. OBJECTIVES: We aimed to comprehensively characterize the chemical composition of DST and develop a quality control method. METHODS: Based on a UHPLC/Q-Orbitrap-MS platform, we developed an offline 2D LC-MS method (HILIC×RPLC) to characterize the chemical constituents in the 75% ethanol extract of DST at first. Secondly, a data-independent acquisition mode (DIA) was further established to conduct rapid qualitative analysis of compounds in DST from different habitats. Then, six differential compounds were screened out and selected as quantitative markers by UPLC-QQQ-MS to evaluate the content of DST from different habitats. RESULTS: In total, 137 compounds were identified in DST by combining offline 2D LC-MS with LC-DIA-MS/MS. Then, simultaneous targeted/non-targeted scanning technology was established based on the precursor ion list. Finally, six compounds, including dioscin, gracillin, pseduoprotodioscin, pseudoprotogracillin, protodioscin, and protogracillin, were accurately determined. The method validation showed a good linear relationship in the concentration range investigated (R2 > 0.999). The average recovery ranged from 86% to 107.5%, and LOD and LOQ were between 0.01 and 0.40 µg·mL-1 . CONCLUSION: Our strategy integrating offline 2D LC-MS and the DIA mode could effectively separate and identify compounds from DST, indicating it can be used in subsequent compounds characterization studies. At the same time, the quality of DST was comprehensively and systematically evaluated.

Discrimination and Characterization of the Volatile Organic Compounds in Schizonepetae Spica from Six Regions of China Using HS-GC-IMS and HS-SPME-GC-MS.

Volatile organic compounds (VOCs) are the main chemical components of Schizonepetae Spica (SS), which have positive effects on the quality evaluation of SS. In this study, HS-SPME-GC-MS (headspace solid-phase microextraction-gas chromatography-mass spectrometry) and HS-GC-IMS (headspace-gas chromatography-ion mobility spectrometry) were performed to characterize the VOCs of SS from six different regions. A total of 82 VOCs were identified. In addition, this work compared the suitability of two instruments to distinguish SS from different habitats. The regional classification using orthogonal partial least squares discriminant analysis (OPLS-DA) shows that the HS-GC-IMS method can classify samples better than the HS-SPME-GC-MS. This study provided a reference method for identification of the SS from different origins.