Liquid Chromatography-high Resolution Mass Spectrometry Research Articles

Deciphering Transcriptomic and Metabolomic Wood Responses to Grapevine Trunk Disease-Associated Fungi

Esca is one of the main grapevine trunk diseases affecting vineyards worldwide. Phaeoacremonium minimum and Phaeomoniella chlamydospora are thought to be two of the main causal agents of this disease. However, the molecular mechanisms underlying plant defense responses in the grapevine trunk against esca-associated pathogens are poorly understood. To provide a first glimpse at the trunk responses to P. minimum and P. chlamydospora, transcriptomic and metabolomic analyses were performed to compare and contrast host responses to these pathogens. Transcriptomic analysis revealed different gene expression reprogramming in the trunk in response to each fungus. The main significant differences were found among genes associated with secondary metabolism, signaling, and hormone signaling. An untargeted liquid chromatography–high resolution mass spectrometry metabolomic approach performed 3 weeks after inoculation was used, and dereplication mainly highlighted flavonoids and stilbenes as plant defense metabolites in the infected trunk. Some metabolites were overproduced with both fungi, but specific responses were also observed. Particularly, a lipophilic flavonoid cluster was emphasized after P. minimum inoculation. The assessment of fungal infection 6 weeks postinfection showed more copies of P. minimum than P. chlamydospora. This dissimilarity in the level of colonization could be linked to the metabolomic responses observed. Our results reveal both different gene expression reprogramming and metabolomic-specific signatures depending on the wood pathogen. Altogether, these observations suggest that grapevine trunks can differently perceive and respond to P. minimum and P. chlamydospora. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Enhancing Molecular Characterization of Dissolved Organic Matter by Integrative Direct Infusion and Liquid Chromatography Nontargeted Workflows.

Dissolved organic matter (DOM) in aquatic systems is a highly heterogeneous mixture of water-soluble organic compounds, acting as a major carbon reservoir driving biogeochemical cycles. Understanding DOM molecular composition is thus of vital interest for the health assessment of aquatic ecosystems, yet its characterization poses challenges due to its complex and dynamic chemical profile. Here, we performed a comprehensive chemical analysis of DOM from highly urbanized river and seawater sources and compared it to drinking water. Extensive analyses by nontargeted direct infusion (DI) and liquid chromatography (LC) high-resolution mass spectrometry (HRMS) through Orbitrap were integrated with novel computational workflows to allow molecular- and structural-level characterization of DOM. Across all water samples, over 7000 molecular formulas were calculated using both methods (∼4200 in DI and ∼3600 in LC). While the DI approach was limited to molecular formula calculation, the downstream data processing of MS2 spectral information combining library matching and in silico predictions enabled a comprehensive structural-level characterization of 16% of the molecular space detected by LC-HRMS across all water samples. Both analytical methods proved complementary, covering a broad chemical space that includes more highly polar compounds with DI and more less polar ones with LC. The innovative integration of diverse analytical techniques and computational workflow introduces a robust and largely available framework in the field, providing a widely applicable approach that significantly contributes to understanding the complex molecular composition of DOM.

Plasma metabolomic and lipidomic profiles accurately classify mothers of children with congenital heart disease: an observational study

IntroductionCongenital heart disease (CHD) is the most common congenital anomaly, representing a significant global disease burden. Limitations exist in our understanding of aetiology, diagnostic methodology and screening, with metabolomics offering promise in addressing these.ObjectiveTo evaluate maternal metabolomics and lipidomics in prediction and risk factor identification for childhood CHD.MethodsWe performed an observational study in mothers of children with CHD following pregnancy, using untargeted plasma metabolomics and lipidomics by ultrahigh performance liquid chromatography-high resolution mass spectrometry (UHPLC-HRMS). 190 cases (157 mothers of children with structural CHD (sCHD); 33 mothers of children with genetic CHD (gCHD)) from the children OMACp cohort and 162 controls from the ALSPAC cohort were analysed. CHD diagnoses were stratified by severity and clinical classifications. Univariate, exploratory and supervised chemometric methods were used to identify metabolites and lipids distinguishing cases and controls, alongside predictive modelling.Results499 metabolites and lipids were annotated and used to build PLS-DA and SO-CovSel-LDA predictive models to accurately distinguish sCHD and control groups. The best performing model had an sCHD test set mean accuracy of 94.74% (sCHD test group sensitivity 93.33%; specificity 96.00%) utilising only 11 analytes. Similar test performances were seen for gCHD. Across best performing models, 37 analytes contributed to performance including amino acids, lipids, and nucleotides.ConclusionsHere, maternal metabolomic and lipidomic analysis has facilitated the development of sensitive risk prediction models classifying mothers of children with CHD. Metabolites and lipids identified offer promise for maternal risk factor profiling, and understanding of CHD pathogenesis in the future.

Non-target liquid chromatography high-resolution mass spectrometry screening to prioritize unregulated micropollutants that persist through domestic wastewater treatment

Efforts to regulate and monitor emerging contaminants are insufficient because new chemicals are continually brought to market, and many are unregulated and potentially harmful. Domestic wastewater treatment plants are not designed to remove micropollutants and are important sources of emerging contaminants in the aquatic environment. In this study, non-target screening, an unbiased method for analyzing compounds without prior information, was used to identify compounds that may be emitted in wastewater treatment plant effluent and should be monitored. Nine wastewater treatment plants using different treatment methods were studied, and a non-target screening data-processing method was used. The frequencies at which the contaminants were detected and contaminant persistence through the treatment processes were considered, and then the contaminants were prioritized. The predicted no-effect concentration of each prioritized contaminant was used to determine whether further analysis and monitoring of the contaminant was necessary. Quantitative analyses of five compounds (amantadine, atenolol, benzotriazole, diphenhydramine, and sulpiride) were performed using reference standards. Probable molecular formulae and structures were proposed for 17 contaminants, and the risks posed by the contaminants were estimated using predicted no-effect concentrations. The results provide valuable insights into how unregulated micropollutants can be identified and prioritized for monitoring in future studies.

Acacia saligna Extract Might Alleviate Quetiapine-Induced Sexual Toxicity in Male Albino Rats: Insights from UPLC-MS/MS Metabolite Profiling, Structural and PI3K/NF-κB Pathway Assessments

BackgroundQuetiapine (QET) abuse has increased due to its anxiolytic and hedonic effects, necessitating protective adjunct treatments. Acacia saligna (A. saligna) flowers, used in traditional medicine, have potential health benefits. AimTo investigate the protective role of A. saligna flower extract against QET-induced sexual toxicity, and to elucidate the possible underlying mechanisms through metabolomic and physiological studies. MethodsA. saligna extract was subjected to metabolite profiling via High-Resolution Ultra-Performance Liquid Chromatography-Mass Spectrometry (UPLC-ESI–qTOF-MS). Forty-eight adult male albino rats were assigned into six groups for 30 days. The intracavernosal pressure (ICP), semen, biochemical, hormonal, histological, genetic and western blot (WB) analyses were determined. ResultsA. saligna extract is rich in phenolic compounds, flavonoids, tannins, and unsaturated fatty acids. QET significantly decreased ICP and negatively affected semen parameters. A. saligna mitigated decreased sperm motility and ameliorated overexpressed proinflammatory genes in QET-55 group. A. saligna ameliorated the reduction of the antioxidant biomarkers, testosterone, luteinizing hormone (LH), and follicle-stimulating hormone (FSH), concurrent with downregulation of the nuclear factor kappa B (NF-κB) protein. A. saligna counteracted the disrupted testicular and prostatic structures revealed by histological examination. ConclusionThe extract from A. saligna, which contains a high concentration of antioxidants and anti-inflammatory chemicals, effectively mitigates sexual toxicity caused by QET. This study provided the first known explanation of the hypothesized processes behind the protective properties of A. saligna through biological, biochemical, and histological parameters. The results emphasize the potential of A. saligna as a safeguarding agent against drug-induced sexual toxicity.

Multiple androgen pathways contribute to the steroid signature of adrenarche

ContextAdrenarche is a normal developmental event in mid-childhood characterized by increasing adrenal androgen secretion. The role of the classic androgen pathway has been well described in adrenarche, but the role of newer active androgens and additional androgen pathways is less clear. ObjectiveTo study the contribution of novel androgens and related steroid biosynthesis pathways to the development of adrenarche, and to identify additional steroid biomarkers of adrenarche. DesignA longitudinal study of children aged 6–8 years at baseline, followed up at ages 8–10 and 14–16 years. A total of 34 children (20 girls) with clinical and/or biochemical signs of adrenarche (cases) and 24 children (11 girls) without these signs (controls) at age 8–10 years were included. Serum steroid profiling was performed by liquid chromatography high-resolution mass spectrometry. Main outcome measuresThirty-two steroids compartmentalized in progestagens, gluco- and mineralocorticoid pathways, and four androgen related pathways, including the classic, backdoor, 11-oxy, and 11-oxy backdoor pathways. ResultsThe classic and 11-oxy androgen pathways were more active, and serum concentrations of main androgens in the classic (dehydroepiandrosterone, dehydroepiandrosterone sulfate, androstenedione and androsterone) and 11-oxy (11β-hydroxyandrostenedione, 11β-hydroxytestosterone, 11-ketoandrostenedione, and 11-ketotestosterone) pathways were higher in cases at ages 6–8 and 8–10 years. Pregnenolone concentrations at adrenarchal age (8–10 years) and cortisol concentrations at adolescence (14–16 years) were higher in cases. 11β-hydroxyandrosterone and 11-ketoandrosterone tended to be higher in cases with clinical signs compared to cases who had only biochemical evidence of adrenarche, albeit they were detected at low levels. In biomarker analyses, calculated steroid ratios with cortisol, cortisone, or 11-deoxycortisone as dividers were better classifiers for adrenarche than single steroids. Among these ratios, androstenedione/cortisone was the best. ConclusionsThe classic and 11-oxy androgen pathways are active in adrenarche. Children with earlier timing of adrenarche have higher serum cortisol levels at late pubertal age, suggesting that early adrenarche might have long-term effects on adrenal steroidogenesis by increasing the activity of the glucocorticoid pathway. Future studies should employ comprehensive steroid profiling to define novel classifiers and biomarkers for adrenarche and premature adrenarche.

Metabolomics analysis reveals characteristic metabolites in different levels of oxaliplatin-induced neurotoxicity.

Oxaliplatin (L-OHP), a third-generation platinum-based anti-tumor drug, finds widespread application in the first-line treatment of metastatic colorectal cancer. Despite its efficacy, the drug's usage is curtailed by a litany of side effects, with L-OHP-induced peripheral neuropathy (OIPN) being the most debilitating. This condition can be classified into varying degrees of severity. Employing serum metabolomics, a high-sensitivity, high-throughput technique, holds promise as a method to identify biomarkers for clinical assessment and monitoring of OIPN patients across different severity levels. In our study, we analyzed serum metabolites in patients with different OIPN levels using ultra-performance liquid chromatography-high resolution mass spectrometry. By employing statistical analyses and pathway enrichment studies, we aimed to identify potential biomarkers and metabolic pathways. Our findings characterized the serum metabolic profiles of patients with varying OIPN levels. Notably, pathway analysis revealed a significant correlation with lipid metabolism, amino acid metabolism, and energy metabolism. Multivariate statistical analysis and receiver operator characteristic curve evaluation pointed to anhalamine and glycochenodeoxycholic acid as potential biomarkers for OIPN C and A, which suggest that serum metabolomics may serve as a potent tool for exploring the metabolic status of patients suffering from diverse diseases and for discovering novel biomarkers.

Nontarget Discovery of Per- and Polyfluoroalkyl Sulfonyl Halides in Soils by Integration of Derivatization and Specific Fragment-Based Liquid Chromatography-High Resolution Mass Spectrometry Screening.

Though long recognized as synthetic precursors to other poly- and perfluoroalkyl substances (PFASs), most poly- and perfluoroalkyl sulfonyl halides (PASXs) cannot be directly measured and have generally received minimal attention. Inspired by the redox reaction between sulfonyl halide groups and p-toluenethiol in organic chemistry, we developed a novel nontarget analysis strategy for PASXs by intergrating derivatization and specific fragment-based liquid chromatography-high resolution mass spectrometry screening for m/z 82.961 [SO2F-] and m/z 95.934 [S2O2-]. By using this strategy, we discovered 11 PASXs, namely, perfluoroalkyl sulfonyl fluorides (5), polyfluoroalkyl sulfonyl fluorides (2), unsaturated perfluoroalkyl sulfonyl fluoride (1), and perfluoroalkyl sulfonyl chlorides (3) in soil samples collected from an abandoned fluorochemical manufacturing park. These average ∑PASXs concentrations were 1120 μg kg-1 (range: 9.7-9860 μg kg-1), which were very likely to be the key intermediates and undesired byproducts of electrochemical fluorination processes. Spatial variation in the mass ratio of ∑PASXs to ∑PFSAs (range: 0.7-795%) also indicates their different transportation pathways. More importantly, the decline of PASXs and increase of perfluoroalkyl sulfonates (when compared to a prior study at this site) suggest the continued hydrolysis of PASXs and the relatively fast environmental transformation rates in the abandoned fluorochemical park soils. Overall, these findings demonstrated the utility of a novel nontarget analysis strategy, which may change most PASXs from inferred precursors to measured intermediates and further could be adapted for structures, distribution, and transformation studies of PFASXs in other matrices.

Enzyme-Driven LC-HRMS Approach for Specific Recognition of 12α-Hydroxy Bile Acids.

The synthesis of 12α-hydroxylated bile acids (12HBAs) and non-12α-hydroxylated bile acids (non-12HBAs) occurs via classical and alternative pathways, respectively. The composition of these BAs is a crucial index for pathophysiologic assessment. However, accurately differentiating 12HBAs and non-12HBAs is highly challenging due to the limited standard substances. Here, we innovatively introduce 12α-hydroxysteroid dehydrogenase (12α-HSDH) as an enzymatic probe synthesized by heterologous expression in Escherichia coli, which can specifically and efficiently convert 12HBAs in vitro under mild conditions. Coupled to the conversion rate determined by liquid chromatography-high resolution mass spectrometry (LC-HRMS), this enzymatic probe allows for the straightforward distinguishing of 210 12HBAs and 312 non-12HBAs from complex biological matrices, resulting in a BAs profile with a well-defined hydroxyl feature at the C12 site. Notably, this enzyme-driven LC-HRMS approach can be extended to any molecule with explicit knowledge of enzymatic transformation. We demonstrate the practicality of this BAs profile in terms of both revealing cross-species BAs heterogeneity and monitoring the alterations of 12HBAs and non-12HBAs under asthma disease. We envisage that this work will provide a novel pattern to recognize the shift of BA metabolism from classical to alternative synthesis pathways in different pathophysiological states, thereby offering valuable insights into the management of related diseases.

The potential of Sonneratia caseolaris mangrove leaves extract as a bioactive food ingredient using various water extract

Background Sonneratia caseolaris, known as the red pidada, has been widely utilized by the Indonesian. S. caseolaris leaves contain various active compounds, contributing to their popularity in the treatment of various diseases. Mangrove leaves are also known to exhibit very high antioxidant activity. This study aims to assess the antioxidant activity of S . caseolaris leaves extracted using different solvents. The resulting extract was evaluated for antioxidant activity by the 2,2-diphenyl-1-picrylhydrazyl radical scavenging activity (DPPH) techniques. Methods Analysis of total flavonoids, total phenols, identification of active compounds with Liquid Chromatography High Resolution Mass Spectrometry (LC-HRMS), and bioinformatics were also carried out to obtain temporary conclusions about the antioxidant activity of S. caseolaris leaf extract. Results The results indicated that S. caseolaris leaves extracted with methanol and distilled water exhibited the highest antioxidant activity compared to other extracts. The analysis of total flavonoids and total phenols yielded results consistent with the antioxidant activity tests. LC-HRMS results identified three compounds in all S. caseolaris leaf extracts with antioxidant activity, namely Tempo, Choline, and Betaine. Tempo demonstrated a higher antioxidant activity than Choline and Betaine, as indicated by the binding affinity values in the bioinformatics analysis. Conclusions It is evident that S. caseolaris leaf extract has the potential to serve as an effective an antioxidant agent. Further research is needed to elucidate confirm the potential compounds in Sonneratia caseolaris leaves water extract interact with the target protein Keap1. S. caseolaris, in order to utilize them as active components in food and enhance antioxidant consumption among consumers.

Non-Targeted Detection of Synthetic Oligonucleotides in Equine Serum Using Liquid Chromatography-High-Resolution Mass Spectrometry.

There is great concern in equine sport over the potential use of pharmaceutical agents capable of editing the genome or modifying the expression of gene products. Synthetic oligonucleotides are short, single-stranded polynucleotides that represent a class of agents capable of modifying gene expression products with a high potential for abuse in horseracing. As these substances are not covered by most routine anti-doping analytical approaches, they represent an entire class of compounds that are not readily detectable. The nucleotide sequence for each oligonucleotide is highly specific, which makes targeted analysis for these agents problematic. Accordingly, we have developed a non-targeted approach to detect the presence of specific product ions that are not naturally present in ribonucleic acids. Briefly, serum samples were extracted using solid-phase extraction with a mixed-mode cartridge following the disruption of protein interactions to isolate the oligonucleotides. Following the elution and concentration steps, chromatographic separation was achieved utilizing reversed-phase liquid chromatography. Following an introduction to a Thermo Q Exactive HF mass spectrometer using electrospray ionization, analytes were detected utilizing a combination of full-scan, parallel reaction monitoring and all ion fragmentation scan modes. The limits of detection were determined along with the accuracy, precision, stability, recovery, and matrix effects using a representative 13mer oligonucleotide. Following method optimization using the 13mer oligonucleotide, the method was applied to successfully detect the presence of specific product ions in three unique oligonucleotide sequences targeting equine-specific transcripts.

N-ethylhexedrone: a very long and bad trip! A Case series.

N-ethylhexedrone (NEH) is a new cathinone derivative with, currently, low toxicocokinetic, and toxicocodynamic knowledge. We present 3 documented clinical cases of NEH intoxication with plasma, and urine concentrations. A thorough search for metabolites was performed. The 3 patients were admitted to the emergency department, and 2 out of the 3 were hospitalized for an extended period. While recovering from the drug effects, 12 to 24 hours after nasal intake of New Psychoactive Substance (NPS), the patients described the following disorders: anxiety, feelings of persecution, asthenia, anhedonia, abulia, psychomotor slowing, and loss of consciousness. NEH was identified in all samples by liquid chromatography-high resolution mass spectrometry (LC-HRMS), and quantified by liquid chromatography coupled to tandem mass spectrometry (LC-MS-MS). Quantitative analysis showed decreasing concentrations over time: for case 1, from 97.2 (Day 1, D1) to 0.7 (Day 7, D7) µg/L for plasma, and from 724 (D1) to 0.5 (D7) µg/L for urine. NEH concentration of 7.9 µg/L was found in the plasma collected at admission for case 2. For case 3: concentrations ranging from 49 (D1) to 1.8 (D7) µg/L in plasma, and from 327.3 (Day 5, D5) to 116.8 (D7) µg/L in urine were found. NEH was no longer detected in the urine sample at Day 10. Elimination half-life was estimated at 19, and 28 hours in patients 1 and 3, respectively. Four metabolites were identified in blood and urine: reduced NEH, dealkyl-NEH, reduced dealkyl-NEH, and hydroxy-NEH. The cases presented highlight the long detectable lifetime of NEH. Characterization of the metabolites will allow better identification of the consumption of this drug. Serious adverse events can be observed after NEH consumption, as 2 out of 3 patients required intubation and ventilation. A syndrome of inappropriate antidiuretic hormone secretion (SIADH) was also diagnosed. Two out of the three cases are notable because of the number of samples collected and because NEH was the only drug of abuse detected.

Glutathione conjugation of sesquimustard: in vitro investigation of potential biomarkers.

Sesquimustard (Q) is a powerful blistering agent that contains additional sulfur atoms. Sulfur mustard causes covalent bonding by alkylating nucleophilic groups of biologically important macromolecules such as lipids, proteins, DNA, or RNA. Most cells maintain relatively high amounts of a unique tripeptide called glutathione (GSH) (γ-glutamyl-cysteinyl glycine), which possesses a free thiol group, to prevent unwanted reactions caused by reactive chemical entities. Moreover, these thiol groups on cysteines (Cys) are the main target for alkylation. Although Q is the most potent vesicant among sulfur mustards, research studies identifying biomarkers of Q are very limited. Therefore, here in this study, we aimed to identify the GSH and Cys conjugates of Q using mass spectrometric methods and to observe the formation of these conjugates in HaCat cell culture following exposure to different doses. We identified four different conjugates of Q, which are bis-glutathionyl ethylthioethylthioethyl conjugate (GSH-ETETE-GSH), hydroxyethylthioethylthioethyl glutathione conjugate (HETETE-GSH), bis-cysteinyl ethylthioethylthioethyl conjugate (Cys-ETETE-Cys), and hydroxyethylthioethylthioethyl cysteine conjugate (HETETE-Cys). The identity of the conjugates was elucidated using liquid chromatography-high-resolution mass spectrometry (LC-HRMS). We also investigated changes in conjugate formation with exposure concentration and time elapsed after exposure in the cell culture. After exposure, GSH conjugates decreased until 1st hour, while Cys conjugates increased until 6th hour. We also observed that conjugate formation depended on the concentration of Q. This is the first study to elucidate the conjugates of Q dependent on GSH conjugation. As biomarkers are essential tools for evaluating exposure to Q, this study contributes to the limited number of studies identifying biomarkers for Q.

Components analysis of San-Bai decoction, and its pharmacodynamics and mechanism on preventing and treating melasma

Ethnopharmacological relevanceSan-Bai Decoction (SBD) is a classic whitening prescription originally recorded in the ‘Introduction to Medicine’ of the Ming Dynasty. SBD has been known for invigorating Qi and blood, promoting spleen and stomach, whitening skin, and fading melasma. However, its pharmacodynamic material basis and specific mechanism remain unclear. Aim of the studyThe aim of this study is to clarify the pharmacodynamic material basis of SBD and its mechanism of removing melasma. Materials and methodsThe positive and negative ion mass spectrum data of SBD extract were collected by UHPLC-Q-Exactive Orbitrap MS/MS, imported into Compound Discoverer (CD) 3.1 software, matched through the online database, and manually checked. Finally, the in vitro chemical components of SBD were classified. Similarly, the mass spectrum data of SBD in the serum of normal rats and melasma model rats were also analyzed by CD 3.1 software. The in vitro identified Compound file of SBD was imported into the Expected Compounds and the Generate Expected Compounds project was selected. The SBD compounds were then chosen under the Compound Section. All phase I and II reaction types related to SBD components were selected, and the metabolic platform of CD 3.1 software was utilized to process the results and obtain possible metabolites. The metabolites were scored and products with high scores were subsequently screened. According to literature comparison, the final metabolites of SBD in both normal rats and melasma model rats were determined and comprehensively analyzed. The Melasma model rats were constructed through intramuscular injection of progesterone and ultraviolet radiation B (UVB) irradiation. The preventing and treating effect of SBD on melasma were evaluated by regulating inflammation, epidermal collagen content, and oxidative stress. Additionally, the effect of SBD on the Phosphatidylinositol 3-kinase (PI3K)/Protein kinase B (Akt)/Glycogen synthase kinase 3β (GSK3β) pathway was investigated through Western blot (WB) to explore its underlying mechanism on whitening and removing melasma efficacy. ResultsUltimately, 94 components were identified in SBD, including 41 flavonoids, 27 organic acids, and 9 glycosides, 3 terpenoids, 2 amides, 2 aldehydes, 1 phenylpropanoid and 9 other compounds. In the blood of normal rat group, a total of 24 prototype components and 61 metabolites were identified. Similarly, there were19 prototype components and 44 metabolites identified from the blood of melasma model rats. Pharmacodynamic experiment results indicated that SBD effectively reduced the incidence of melasma, prevent the loss of epidermal collagen, and elevate the activity of superoxide dismutase and decrease the malondialdehyde content in both liver and skin. Interestingly, the WB results demonstrated that SBD effectively activated PI3K/Akt/GSK3β pathway, and down-regulated the expression of melanin-related proteins. ConclusionsFor the first time, the components of SBD extracts, and its prototype components and metabolites in the blood of normal rats and melasma model rats were successfully identified by high-resolution liquid chromatography-mass spectrometry with CD software. Additionally, the differences of in vivo components of SBD between normal rats and melasma model rats were analyzed. The preventive and therapeutic effect of SBD on melasma was verified in the melasma model rats induced by progesterone and UVB irradiation, and its mechanism was related to activating PI3K/Akt/GSK3β pathway and downregulating the expression of melanin-related proteins. These results provide an experimental foundation for further research on the pharmacodynamic substance basis and pharmacodynamic mechanism of SBD, as well as developing new anti-melasma formula with SBD.

Exploring the antimicrobial activity of Origanum majorana L. against the highly virulent multidrug-resistant Acinetobacter baumannii AB5075: UPLC-HRMS profiling with in vitro and in silico studies

BackgroundThe infamous multidrug-resistant (MDR) bacterium Acinetobacter baumannii is becoming a nightmare in intensive care units across the globe. Since there are now very few effective antimicrobial agents, it is necessary to explore unconventional resources for novel antimicrobials. This study investigated the potential antimicrobial activity of Origanum majorana L. against A. baumannii employing multiple approaches including antimicrobial susceptibility, fractionation, ultra-performance liquid chromatography–high-resolution mass spectrometry (UPLC-HRMS) dereplication, and in silico analysis for target/ligand identification.ResultsOn the extremely pathogenic MDR strain A. baumannii AB5075, O. majorana L. has shown a significant growth inhibitory effect (MIC = 0.675 mg/mL). The polar 50% methanol fraction was the most active (MIC = 0.5 mg/mL). The UPLC-HRMS dereplication of the bioactive fraction detected 29 metabolites belonging to different chemical classes. Justicidin B, one of the identified metabolites, was projected by preliminary in silico analysis to be the most highly scoring metabolite for binding with molecular targets in A. baumannii with a Fit score = 8.56 for enoyl-ACP reductase (FabI) (PDB ID: 6AHE), suggesting it to be its potential target. Additionally, docking, molecular dynamics simulation, and bioinformatics analysis suggested that this interaction is similar to a well-known FabI inhibitor. The amino acids involved in the interaction are conserved among different MDR A. baumannii strains and the effectiveness could extend to Gram-negative pathogens within the ESKAPE group.ConclusionsOriganum majorana L. extract exhibits antimicrobial activity against A. baumannii using one or more metabolites in its 50% methanol fraction. The characterized active metabolite is hypothesized to be justicidin B which inhibits the growth of A. baumannii AB5075 via targeting its fatty acid synthesis.

Sensitivity and quantitativeness of large-volume injection combined with liquid chromatography/high-resolution mass spectrometry for target screening analysis of emerging contaminants

Solid phase extraction (SPE) has been widely used for pretreatment in target screening (TS) analysis. However, some compounds are difficult to recover by SPE or their recovery is unstable for environmental samples. In this study, we tested large-volume injection (LVI) without SPE for TS analysis of 103 compounds listed by the Ministry of the Environment (Japan)—so-called ‘items to be surveyed’—using liquid chromatography high-resolution mass spectrometry. We evaluated the limit of quantification (LOQ) by LVI and compared this LOQ with the LOQ by SPE pretreatment using a hydrophilic-lipophilic balance (HLB) combined with activated carbon, which was found previously to afford the best SPE cartridges for target compounds recovery. The LOQ generally decreased as the injection volume increased, and the LOQ was at least 250 times lower for a 500-μL injection than for a 2-μL injection for half of the compounds. LVI provided LOQs lower than the predicted no effect concentration for more compounds than the SPE method. The average matrix effect (ME) by LVI was in the range 70%–130% for 69 out of 97 compounds. The ME was higher or lower for some of the remaining compounds, but the ME was in the range 10%–1000% for all 18 water samples for 84 of the 97 compounds. Comparing the ME by LVI and the recovery ratio by the SPE method showed that LVI achieved more accurate quantitation than the SPE method for a larger number of compounds. Therefore, LVI provides better sensitivity and quantitativeness than the SPE method using HLB and activated carbon for TS analysis of as many ‘items to be surveyed’ as possible.

Revealing mechanism of phenol-amine reaction to form humus in compost based on high-resolution liquid chromatography mass spectrometry and spectroscopy

Humus is the stable form of carbon storage in straw compost. The phenol-amine reaction is a pathway for humus formation in straw compost. In this study, two reaction systems, GP group (pyrogallol and glycine) and GCP group (catechol, pyrogallol, and glycine), were constructed in a simulated composting environment and revealed the molecular binding mechanism of the phenol-amine reaction through spectroscopy and mass spectrometry. The results showed that phenolic self-polymerization was faster than phenol-amine reaction. Therefore, the aromatization degree of GP was 27.14 % higher than that of GCP. The phenol-amine reaction first produced fulvic acid, and then formed humus units rich in active functional group structures (i.e., phenolic hydroxyl and carboxyl groups). These units further captured small molecule compounds to form humic acid eventually. This study would provide theoretical support for exploring the humus formation process and the promotion of straw humification by adding phenol or amino acids to compost.

Metabolite profiling of chemically modified oligonucleotides in rat liver homogenates using hydrophilic interaction liquid chromatography-high resolution mass spectrometry

Chemically modified oligonucleotide is a rapidly emerging field of biotherapeutics. The evaluation of the metabolic stability of therapeutic oligonucleotides is critical. The current methods are limited to the ion-pairing reversed phase chromatographic techniques. Due to complex chemical modifications of therapeutic oligonucleotides and diverse structural changes in their metabolites, comprehensive metabolite profiling is still challenging. Therefore, an alternative analytical method for the metabolism study of oligonucleotides is urgently needed. In this study, a novel hydrophilic interaction liquid chromatography-high resolution mass spectrometry (HILIC-HRMS) method was developed and applied to the metabolism study of two chemically modified oligonucleotides, i.e., N11-GalNAc (phosphorothioate, 2′-F, 2′-OMe, and 3′-GalNAc) and N9 (phosphorothioate, 2′-F), in rat liver homogenates. Highly broad retention of metabolites on the HILIC column was achieved, with truncated metabolite having a single nucleotide being detected. A stepped normalized collisional energy (NCE) in HRMS led to characteristic c/y, d/y, and b/y fragment ion series, and diagnostic fragment ions for linker and GalNAc, which covered the whole sequence of oligonucleotides. A total number of twenty-seven and twenty-nine metabolites were identified in rat liver homogenates for N11-GalNAc and N9, respectively, by using the isotopic envelope of the precursor ion and stepped NCE-based sequence mapping data. The time-dependent production of metabolites was observed. The UCU sequence with the uniform 2′-F modification on ribose was identified as the major metabolic site for N11-GalNAc, and the phosphodiester bonds between nucleosides involving unmodified uracil were identified as the metabolic soft sites for N9. The developed HILIC-HRMS method provided a high coverage of various oligonucleotide metabolites. Characteristic fragment ions enable sequence mapping and therefore unambiguous metabolite identifications. This approach can be broadly applicable to the metabolism study of chemically modified oligonucleotides and the identification of their metabolic soft sites.

CNKSR2 interactome analysis indicates its association with the centrosome/microtubule system

Abstract The protein connector enhancer of kinase suppressor of Ras 2 (CNKSR2), present in both the postsynaptic density and cytoplasm of neurons, is a scaffolding protein with several protein-binding domains. Variants of the CNKSR2 gene have been implicated in neurodevelopmental disorders, particularly intellectual disability, although the precise mechanism involved has not yet been fully understood. Research has demonstrated that CNKSR2 plays a role in facilitating the localization of postsynaptic density protein complexes to the membrane, thereby influencing synaptic signaling and the morphogenesis of dendritic spines. However, the function of CNKSR2 in the cytoplasm remains to be elucidated. In this study, we used immunoprecipitation and high-resolution liquid chromatography-mass spectrometry to identify the interactors of CNKSR2. Through a combination of bioinformatic analysis and cytological experiments, we found that the CNKSR2 interactors were significantly enriched in the proteome of the centrosome. We also showed that CNKSR2 interacted with the microtubule protein DYNC1H1 and with the centrosome marker CEP290. Subsequent colocalization analysis confirmed the centrosomal localization of CNKSR2. When we downregulated CNKSR2 expression in mouse neuroblastoma cells (Neuro 2A), we observed significant changes in the expression of numerous centrosomal genes. This manipulation also affected centrosome-related functions, including cell size and shape, cell proliferation, and motility. Furthermore, we found that CNKSR2 interactors were highly enriched in de novo variants associated with intellectual disability and autism spectrum disorder. Our findings establish a connection between CNKSR2 and the centrosome, and offer new insights into the underlying mechanisms of neurodevelopmental disorders.

Comparative metabolite analysis of Piper sarmentosum organs approached by LC–MS-based metabolic profiling

Piper sarmentosum Roxb. (Piperaceae) is a traditional medicinal and food plant widely distributed in the tropical and subtropical regions of Asia, offering both health and culinary benefits. In this study the secondary metabolites in different organs of P. sarmentosum were identified and their relative abundances were characterized. The metabolic profiles of leaves, roots, stems and fruits were comprehensively investigated by liquid chromatography high-resolution mass spectrometry (LC-HR-MS) and the data subsequently analyzed using multivariate statistical methods. Manual interpretation of the tandem mass spectrometric (MS/MS) fragmentation patterns revealed the presence of 154 tentatively identified metabolites, mostly represented by alkaloids and flavonoids. Principle component analysis and hierarchical clustering indicated the predominant occurrence of flavonoids, lignans and phenyl propanoids in leaves, aporphines in stems, piperamides in fruits and lignan-amides in roots. Overall, this study provides extensive data on the metabolite composition of P. sarmentosum, supplying useful information for bioactive compounds discovery and patterns of their preferential biosynthesis or storage in specific organs. This can be used to optimize production and harvesting as well as to maximize the plant’s economic value as herbal medicine or in food applications.Graphical