PubMed

J Breath Res. 2023 Jan 12. doi: 10.1088/1752-7163/acb284. Online ahead of print.ABSTRACTAssessing volatile organic compounds (VOCs) as cancer signatures is one of the most promising techniques toward developing non-invasive, simple, and affordable diagnosis. Here, we have evaluated the feasibility of employing static headspace extraction (HS) followed by gas chromatography with flame ionization detector (GC-FID) as a screening tool to discriminate between cancer patients (head and neck - HNC, n=15; and gastrointestinal cancer - GIC, n=19) and healthy controls (n=37) on the basis of a non-target (fingerprinting) analysis of oral fluid and urine. We evaluated the discrimination considering a single bodily fluid and adopting the hybrid approach, in which the oral fluid and urinary VOCs profiles were combined through data fusion. We used supervised orthogonal partial least squares discriminant analysis (OPLS-DA) for classification, and we assessed the prediction power of the models by analyzing the values of goodness of prediction (Q2Y), area under the curve (AUC), sensitivity, and specificity. The individual models HNC urine, HNC oral fluid, and GIC oral fluid successfully discriminated between healthy controls and positive samples (Q2Y = 0.560, 0.525, and 0.559; AUC = 0.814, 0.850, and 0.926; sensitivity = 84.8, 70.2, and 78.6%; and specificity = 82.3; 81.5; 87.5%, respectively), whereas GIC urine was not adequate (Q2Y = 0.292, AUC = 0.694, sensitivity = 66.1%, and specificity = 77.0%). Compared to the respective individual models, Q2Y for the hybrid models increased (0.623 for hybrid HNC and 0.562 for hybrid GIC). However, sensitivity was higher for HNC urine and GIC oral fluid than for hybrid HNC (75.6%) and hybrid GIC (69.8%), respectively. These results suggested that HS-GC-FID fingerprinting is suitable and holds great potential for cancer screening. Additionally, the hybrid approach tends to increase the predictive power if the individual models present suitable quality parameter values. Otherwise, it is more advantageous to use a single body fluid for analysis.PMID:36634358 | DOI:10.1088/1752-7163/acb284

ACS Biomater Sci Eng. 2023 Jan 12. doi: 10.1021/acsbiomaterials.2c01279. Online ahead of print.ABSTRACTRepeating l- and d-chiral configurations determine polylactide (PLA) stereochemistry, which affects its thermal and physicochemical properties, including degradation profiles. Clinically, degradation of implanted PLA biomaterials promotes prolonged inflammation and excessive fibrosis, but the role of PLA stereochemistry is unclear. Additionally, although PLA of varied stereochemistries causes differential immune responses in vivo, this observation has yet to be effectively modeled in vitro. A bioenergetic model was applied to study immune cellular responses to PLA containing >99% l-lactide (PLLA), >99% d-lactide (PDLA), and a 50/50 melt-blend of PLLA and PDLA (stereocomplex PLA). Stereocomplex PLA breakdown products increased IL-1β, TNF-α, and IL-6 protein levels but not MCP-1. Expression of these proinflammatory cytokines is mechanistically driven by increases in glycolysis in primary macrophages. In contrast, PLLA and PDLA degradation products selectively increase MCP-1 protein expression. Although both oxidative phosphorylation and glycolysis are increased with PDLA, only oxidative phosphorylation is increased with PLLA. For each biomaterial, glycolytic inhibition reduces proinflammatory cytokines and markedly increases anti-inflammatory (IL-10) protein levels; differential metabolic changes in fibroblasts were observed. These findings provide mechanistic explanations for the diverse immune responses to PLA of different stereochemistries and underscore the pivotal role of immunometabolism in the biocompatibility of biomaterials applied in medicine.PMID:36634351 | DOI:10.1021/acsbiomaterials.2c01279

Microbiol Spectr. 2023 Jan 12:e0436522. doi: 10.1128/spectrum.04365-22. Online ahead of print.ABSTRACTMen with nonobstructive azoospermia (NOA) face the dual problems of low sperm count and low sperm quality. Most men with NOA without a clear cause are classified as having idiopathic NOA (iNOA). Previous studies found that microbes exist in semen, and the semen microbes of NOA men are different from those of normal men. However, the relevant mechanism is not clear. In this study, we answered the three questions of "who is there," "what is it doing," and "who is doing it" by combining 16s rRNA, nontargeted metabolome detection and metabolite traceability analysis. We found that the composition and interaction of seminal plasma microbes in the iNOA group changed. Metabolite traceability analysis and metabolic pathway analysis revealed that microbial abnormalities in the NOA group were closely related to the decrease of microbial degradation of toluene and the increase of metabolism of fructose or mannose. In addition, the metabolic relationship between microbes and the host in male semen in iNOA revealed that such microbes can produce harmful metabolites that affect sperm quality, the microbes compete with sperm for essential nutrients, and their presence reduces sperm production of essential nutrients. IMPORTANCE Idiopathic nonobstructive azoospermia is one of the great challenges in assisted reproductive therapy. Although microdissection testicular sperm extraction technology is currently available, many men with iNOA still face the problem of poor sperm retrieval and poor sperm quality. The role of seminal plasma microbes in male disease has been continuously investigated since semen was demonstrated to harbor commensal microbes. To our knowledge, this is the first detailed description of the microbe-host relationship in iNOA semen. This study is an important complement to research on the treatment and etiology of iNOA and the rationale for our ongoing research.PMID:36633411 | DOI:10.1128/spectrum.04365-22

J Food Sci. 2023 Jan 12. doi: 10.1111/1750-3841.16453. Online ahead of print.ABSTRACTAlmond production in Portugal is of great importance for the economy of their main producing areas. However, the contamination of these nut fruits with fungi and mycotoxins poses a significant risk to food safety and security. This work intended to evaluate the influence of storage conditions on the microbial and mycotoxin stability and safety of almonds throughout long-term storage. Two almond varieties-Lauranne and Guara-were submitted to three different storage conditions, namely, 4°C with noncontrolled relative humidity (RH), 60% RH at 25°C, and 70% RH at 25°C, for a storage period of 9 months. Samples were collected after 0, 3, 6, and 9 months of storage and analyzed for microbial loads (aerobic mesophiles, yeasts, and molds), mold incidence and diversity, and mycotoxin contamination. In total, 26 species were identified belonging to 6 genera: Aspergillus, Cladosporium, Fusarium, Penicillium, Paecilomyces, and Talaromyces. For the variety Guara, mycotoxins related to Aspergillus sect. Flavi, such as aflatoxins, averufin, versicolorin C, and norsolorinic acid, were detected only after 9 months of storage at 70% and 60% RH. Penicillium mycotoxins, such as quinolactacin A and roquefortine C, were also detected. For the variety Lauranne, Penicillium mycotoxins were detected, such as citrinin, quinolactacins A and B, roquefortines C and D, cyclopenin, cyclopenol, penitrem A, viridicatin, and viridicatol. Mycotoxins related to Aspergillus, such as aspulvinone E, flavoglaucin, paspalin, asperglaucide, asperphenamate, cyclo(L-Pro-L-Tyr), and cyclo(L-Pro-L-Val), were also detected. PRACTICAL APPLICATION: (Optional, for JFS Research Articles ONLY) The quality of almonds depends on the storage period and the RH and temperature at which they are stored. Storage of almonds at 60% RH at 25°C is a good storage condition to maintain the stability and safety of nuts in terms of microbial and mycotoxin contaminations.PMID:36633227 | DOI:10.1111/1750-3841.16453

Food Funct. 2023 Jan 12. doi: 10.1039/d2fo03181g. Online ahead of print.ABSTRACTNumerous kinds of bioactive polysaccharides are identified as having intestinal immunomodulatory activity; however, the ways in which the different polysaccharides work differ. Therefore, we selected nine representative bioactive polysaccharides, including xanthan gum, inulin, guar gum, arabinogalactan, carrageenan, glucomannan, araboxylan, xylan, and fucoidan, and compared their intestinal immunomodulatory mechanisms. A cyclophosphamide (CTX)-induced immunosuppressed model was used in this experiment, and the effects of these polysaccharides on the number of T cells in the intestinal mucosa, expression of transcription factors and inflammatory factors, intestinal metabolome and gut microbiota were compared and discussed. The results revealed that the nine polysaccharides promote intestinal immunity in different ways. In detail, guar gum, inulin and glucomannan better alleviated immune suppression in intestinal mucosal T cells. Inulin improved the intestinal microenvironment by significantly upregulating the abundance of Lactobacillus and Monoglobus and promoted short chain fatty acid (SCFA) production. Fucoidan and carrageenan promoted the colonization of the beneficial bacteria Rikenella and Roseburia. In addition, fucoidan, inulin and carrageenan inhibited the colonization of harmful bacteria Helicobacter, upregulated the abundance of Clostridia_UCG-014 and alleviated the accumulation of amino acids, bile acids and indoles in the large intestine. In conclusion, our study uncovered the different intestinal immunomodulatory mechanisms of the different polysaccharides and provided a guideline for the development of superior intestinal immunomodulatory polysaccharides.PMID:36633119 | DOI:10.1039/d2fo03181g

Se Pu. 2023 Jan;41(1):47-57. doi: 10.3724/SP.J.1123.2022.04017.ABSTRACTPremature ovarian failure (POF) is a prevalent gynecological disease. In traditional Chinese medicine, it is believed that POF is directly related to abnormal function of the liver and kidneys. As such, regulation of the liver metabolism through the use of medicinal and edible substances is important for the treatment of POF. Pine pollen, a traditional Chinese medicinal and edible pollen variety, contains various active substances, such as sex hormones and phytohormones, which have been used to inhibit inflammation, regulate the immune system, and protect reproductive tissues. Using ultra-high performance liquid chromatography-triple quadrupole mass spectrometry (UHPLC-MS/MS), this study examined the influence of pine pollen on the liver metabolome of cyclophosphamide-induced POF model Sprague Dawley (SD) rats. The variations in the metabolites present in the liver tissue of control SD rats, model SD rats, and SD rats treated with various doses of pine pollen or estrogen were analyzed using principal component analysis (PCA) in combination with orthogonal partial least squares discriminant analysis (OPLS-DA) and other multivariate statistical methods to reveal the mechanism of pine pollen intervention in the livers of POF SD rats. An animal model experiment was conducted using six groups of ten-week-old rats. Cyclophosphamide was administered intraperitoneally to the model group and four intervention groups at a dosage of 60 mg/kg for 1 d followed by a dosage of 10 mg/kg for 14 d. Within the following four weeks, each of the four intervention groups received the intragastric administration of 0.1, 0.5, or 1.5 g/kg bodyweight (BW) of pine pollen, or 0.075 g/kg BW of conjugated estrogens (positive control). Equal quantities of normal saline were administered to the control and cyclophosphamide-treated model groups. Subsequently, the rat livers were subject to pseudotargeted metabolomics, and a total of 687 liver metabolites were discovered using both positive and negative ions. The metabolites differing in content were screened using the t-test (p<0.05) and the fold change (FC>2 or <0.5) in univariate analysis, and the variable importance in projection (VIP>1) in multivariate analysis. It was found that in comparison with the control group, the contents of 32 metabolites significantly increased, while those of 28 metabolites significantly decreased in the model group. The majority of these metabolites were involved α-linolenic acid metabolism, vitamin B6 metabolism, and purine metabolism, along with the lysine degradation and glycolysis/gluconeogenesis metabolic pathways. Compared with the cyclophosphamide-induced model group, the estrogen group exhibited increased levels of 47 metabolites and decreased levels of 29 metabolites, wherein 34 metabolites were restored to the levels found in the control group. These metabolites mainly involved the vitamin B6, lysine, glycolysis/gluconeogenesis, arginine and proline, and cysteine and methionine metabolic pathways. In the low/medium/high-dose pine pollen groups, the contents of 34/32/34 metabolites increased, the contents of 30/37/24 metabolites decreased, and the contents of 47/38/34 metabolites were restored to the levels found in the control group, respectively. These metabolites were mainly involved in vitamin B6 metabolism, purine metabolism, and the glycolysis/gluconeogenesis metabolic pathway. These results therefore indicate that the restoring effect of pine pollen is equivalent or superior to that of conjugated estrogen. Additionally, based on the known metabolic pathways, it appears that when estrogen interferes with the liver metabolism, the key metabolic pathways that become affected are the arginine and proline metabolism and cysteine and methionine metabolism pathways. In contrast, pine pollen intervention affected existing metabolic pathways that were known to be disordered by cyclophosphamide. The use of pine pollen may therefore restore the levels of many metabolites. It should be noted that 23 overlaps exist between the estrogen-restored metabolites and the pine pollen-restored metabolites, including a variety of acylcarnitines, such as ACar 10∶0. As a result, pine pollen extract may be able to normalize the liver metabolic abnormalities induced by POF. This study therefore establishes a theoretical reference for the development of functional applications for pine pollen and for the treatment of POF.PMID:36633076 | DOI:10.3724/SP.J.1123.2022.04017

J Agric Food Chem. 2023 Jan 12. doi: 10.1021/acs.jafc.2c07664. Online ahead of print.ABSTRACTThe use of diversified ginseng extracts in health-promoting foods is difficult to differentiate, as they share bioactive ginsenosides among different Panax species (e.g., P. ginseng, P. quinquefolius, P. notoginseng, and P. japonicus) and different parts (e.g., root, leaf, and flower). This work was designed to develop a pseudo-targeted metabolomics approach to discover ginsenoside markers facilitating the precise authentication of ginseng and its use in compound formulation products (CFPs). Versatile mass spectrometry experiments on the QTrap mass spectrometer achieved classified characterization of the neutral, malonyl, and oleanolic acid-type ginsenosides, with 567 components characterized. A pseudo-targeted metabolomics approach by multiple reaction monitoring (MRM) of 262 ion pairs could assist to establish key identification points for 12 ginseng species. The simultaneous detection of 14 markers enabled the identification of ginseng from 15 ginseng-containing CFPs. The pseudo-targeted metabolomics strategy enabled better performance in differentiating among multiple ginseng, compared with the full-scan high-resolution mass spectrometry approach.PMID:36632992 | DOI:10.1021/acs.jafc.2c07664

Environ Pollut. 2023 Jan 9:121020. doi: 10.1016/j.envpol.2023.121020. Online ahead of print.ABSTRACTMetabolomic and gut microbial responses of soil fauna to environmentally relevant concentrations of microplastics indicate the potential molecular toxicity of microplastics; however, limited data exist on these responses. In this study, earthworms (Eisenia fetida) were exposed to spherical (25-30 μm diameter) polystyrene microplastic-contaminated soil (0.02%, w:w) for 14 days. Changes in weight, survival rate, intestinal microbiota and metabolic responses of the earthworms were assessed. The results showed that polystyrene microplastics did not influence the weight, survival rate, or biodiversity of the gut microbiota, but significantly decreased the relative abundance of Bacteroidetes at the phylum level. Moreover, polystyrene microplastics disturbed the osmoregulatory metabolism of earthworms, as indicated by the significantly decreased betaine, myo-inositol and lactate, and increased 2-hexyl-5-ethyl-furan-3-sulfonic acid at the metabolic level. This study provides important insights into the molecular toxicity of environmentally relevant concentrations of polystyrene microplastics on soil fauna.PMID:36632970 | DOI:10.1016/j.envpol.2023.121020

Sci Total Environ. 2023 Jan 9:161521. doi: 10.1016/j.scitotenv.2023.161521. Online ahead of print.ABSTRACTAlternatives to Bisphenol A (BPA) such as BPF and BPAF, have found increasing industrial applications. However, toxicological research on these BPA analogues remains limited. This study aimed to investigate the effects of BPA, BPF, and BPAF exposure on hepatotoxicity in mice fed with high-fat diets (HFD). Male mice were exposed to the bisphenols at a dose of 0.05 mg per kg body weight per day (mg/kg bw/day) for eight consecutive weeks, or 5 mg/kg bw/day for the first week followed by 0.05 mg/kg bw/day for seven weeks under HFD. The low dose (0.05 mg/kg bw/day) was corresponding to the tolerable daily intake (TDI) of BPA and the high dose (5 mg/kg bw/day) was corresponding to its no observed adverse effect level (NOAEL). Biochemical analysis revealed that exposure to these bisphenols resulted in liver damage. Metabolomics analysis showed disturbances of fatty acid and lipid metabolism in bisphenol-exposed mouse livers. BPF and BPAF exposure reduced lipid accumulation in HFD mouse liver by lowering glyceride and cholesterol levels. Transcriptomics analysis demonstrated that expression levels of genes related to fatty acid synthesis and metabolism were changed, which might be related to the activation of the PPAR signaling pathway. Besides, a feedback regulation mechanism might exist to maintain hepatic metabolic homeostasis. For the first time, this study demonstrated the effects of BPF and BPAF exposure in HFD-mouse liver. Considering the reality of the high prevalence of obesity nowadays and the ubiquitous environmental distribution of bisphenols, this study provides insight and highlights the adverse effects of BPA alternatives, further contributing to the consideration of the safe use of such compounds.PMID:36632902 | DOI:10.1016/j.scitotenv.2023.161521

Theranostics. 2023 Jan 1;13(2):438-457. doi: 10.7150/thno.75973. eCollection 2023.ABSTRACTRationale: Despite growing evidence for mitochondria's involvement in cancer, the roles of specific metabolic components outside the respiratory complex have been little explored. We conducted metabolomic studies on mitochondrial DNA (mtDNA)-deficient (ρ0) cancer cells with lower proliferation rates to clarify the undefined roles of mitochondria in cancer growth. Methods and results: Despite extensive metabolic downregulation, ρ0 cells exhibited high glycerol-3-phosphate (G3P) level, due to low activity of mitochondrial glycerol-3-phosphate dehydrogenase (GPD2). Knockout (KO) of GPD2 resulted in cell growth suppression as well as inhibition of tumor progression in vivo. Surprisingly, this was unrelated to the conventional bioenergetic function of GPD2. Instead, multi-omics results suggested major changes in ether lipid metabolism, for which GPD2 provides dihydroxyacetone phosphate (DHAP) in ether lipid biosynthesis. GPD2 KO cells exhibited significantly lower ether lipid level, and their slower growth was rescued by supplementation of a DHAP precursor or ether lipids. Mechanistically, ether lipid metabolism was associated with Akt pathway, and the downregulation of Akt/mTORC1 pathway due to GPD2 KO was rescued by DHAP supplementation. Conclusion: Overall, the GPD2-ether lipid-Akt axis is newly described for the control of cancer growth. DHAP supply, a non-bioenergetic process, may constitute an important role of mitochondria in cancer.PMID:36632231 | PMC:PMC9830446 | DOI:10.7150/thno.75973

Theranostics. 2023 Jan 1;13(2):510-530. doi: 10.7150/thno.80066. eCollection 2023.ABSTRACTRationale: Sini decoction (SND) is an efficient formula against DOX-induced cardiomyopathy (DCM), but the active ingredient combination (AIC) and mechanisms of SND remain unclear. Therefore, the present study aimed to identify the AIC and elucidate the underlying mechanism of AIC on DCM. Methods: The AIC were screened by a novel comprehensive two-dimensional cardiac mitochondrial membrane chromatography (CMMC)-TOFMS analysis system and further validated by cell viability, reactive oxygen species (ROS) generation, ATP level, and mitochondrial membrane potential in DOX-induced H9c2 cell injury model. Then, an integrated model of cardiac mitochondrial metabolomics and proteomics were applied to clarify the underlying mechanism in vitro. Results: The CMMC column lifespan was significantly improved to more than 10 days. Songorine (S), neoline, talatizamine, 8-gingerol (G) and isoliquiritigenin (I), exhibiting stronger retention on the first-dimension CMMC column, were screened to have protective effects against DOX cardiotoxicity in the H9c2 cell model. S, G and I were selected as an AIC from SND according to the bioactivity evaluation and the compatibility theory of SND. The combined in vitro use of S, G and I produced more profound therapeutic effects than any component used individually on increasing ATP levels and mitochondrial membrane potential and suppressing intracellular ROS production. Moreover, SGI attenuated DCM might via regulating mitochondrial energy metabolism and mitochondrial dysfunction. Conclusions: The provided scientific evidence to support that SGI combination from SND could be used as a prebiotic agent for DCM. Importantly, the proposed two-dimensional CMMC-TOFMS analytical system provides a high-throughput screening strategy for mitochondria-targeted compounds from natural products, which could be applied to other subcellular organelle models for drug discovery.PMID:36632225 | PMC:PMC9830424 | DOI:10.7150/thno.80066

ERJ Open Res. 2023 Jan 9;9(1):00325-2022. doi: 10.1183/23120541.00325-2022. eCollection 2023 Jan.ABSTRACTBACKGROUND: The apnoea-hypopnoea index (AHI) forms the basis for severity of obstructive sleep apnoea (OSA), a condition expected to reprogramme metabolic pathways in humans. We aimed to identify the AHI breakpoint from which the majority of significant changes in the systemic metabolome of patients with sleep complaints occur.METHODS: In a prospective observational study on symptomatic individuals, who underwent polysomnography for the diagnosis of OSA, profiles of 187 metabolites including amino acids, biogenic amines, acylcarnitines, lysophosphatidylcholines, phosphatidylcholines and sphingomyelins were analysed with liquid chromatography mass spectrometry in peripheral blood drawn at three different time points overnight. Comparisons of rank-transformed data using a general linear model for repeated measures after dichotomising the study group at different AHI levels were applied to define the best cut-off based on Cohen's f.RESULTS: 65 subjects were recruited with a median AHI of 15.6 events·h-1. The mean Cohen's f over the metabolites was highest (0.161) at an AHI level of 5 events·h-1 representing the metabolomic threshold. Of the particular between-group differences, eight phosphatidylcholines, nine acylcarnitines and one amino acid (threonine) had significantly lower concentrations in the individuals with an AHI level equal to or above the metabolomic threshold. The metabolomic changes at AHI levels defining moderate and severe OSA were smaller than at an AHI of 5 events·h-1.CONCLUSIONS: The metabolomic threshold for patients with sleep complaints described in this report for the first time coincides with the AHI threshold required to confirm the diagnosis of OSA.PMID:36632170 | PMC:PMC9827367 | DOI:10.1183/23120541.00325-2022

PeerJ. 2023 Jan 6;11:e14554. doi: 10.7717/peerj.14554. eCollection 2023.ABSTRACTBACKGROUND: Hyperuricemia and gout are a group of disorders of purine metabolism. In recent years, the incidence of hyperuricemia and gout has been increasing, which is a severe threat to people's health. Several studies on hyperuricemia and gout in proteomics and metabolomics have been conducted recently. Some literature has identified biomarkers that distinguish asymptomatic hyperuricemia from acute gout or remission of gout. We summarize the physiological processes in which these biomarkers may be involved and their role in disease progression.METHODOLOGY: We used professional databases including PubMed, Web of Science to conduct the literature review. This review addresses the current landscape of hyperuricemia and gout biomarkers with a focus on proteomics and metabolomics.RESULTS: Proteomic methods are used to identify differentially expressed proteins to find specific biomarkers. These findings may be suggestive for the diagnosis and treatment of hyperuricemia and gout to explore the disease pathogenesis. The identified biomarkers may be mediators of the link between hyperuricemia, gout and kidney disease, metabolic syndrome, diabetes and hypertriglyceridemia. Metabolomics reveals the main influential pathways through small molecule metabolites, such as amino acid metabolism, lipid metabolism, or other characteristic metabolic pathways. These studies have contributed to the discovery of Chinese medicine. Some traditional Chinese medicine compounds can improve the metabolic disorders of the disease.CONCLUSIONS: We suggest some possible relationships of potential biomarkers with inflammatory episodes, complement activation, and metabolic pathways. These biomarkers are able to distinguish between different stages of disease development. However, there are relatively few proteomic as well as metabolomic studies on hyperuricemia and gout, and some experiments are only primary screening tests, which need further in-depth study.PMID:36632144 | PMC:PMC9828291 | DOI:10.7717/peerj.14554

Anal Bioanal Chem. 2023 Jan 12. doi: 10.1007/s00216-023-04516-x. Online ahead of print.ABSTRACTComprehensive two-dimensional gas chromatography with time-of-flight mass spectrometry (GC × GC-TOFMS) is one the most powerful analytical platforms for chemical investigations of complex biological samples. It produces large datasets that are rich in information, but highly complex, and its consistency may be affected by random systemic fluctuations and/or changes in the experimental parameters. This study details the optimization of a data processing strategy that compensates for severe 2D pattern misalignments and detector response fluctuations for saliva samples analyzed across 2 years. The strategy was trained on two batches: one with samples from healthy subjects who had undergone dietary intervention with high/low-Maillard reaction products (dataset A), and the second from healthy/unhealthy obese individuals (dataset B). The combined untargeted and targeted pattern recognition algorithm (i.e., UT fingerprinting) was tuned for key process parameters, the signal-to-noise ratio (S/N), and MS spectrum similarity thresholds, and then tested for the best transform function (global or local, affine or low-degree polynomial) for pattern realignment in the temporal domain. Reliable peak detection achieved its best performance, computed as % of false negative/positive matches, with a S/N threshold of 50 and spectral similarity direct match factor (DMF) of 700. Cross-alignment of bi-dimensional (2D) peaks in the temporal domain was fully effective with a supervised operation including multiple centroids (reference peaks) and a match-and-transform strategy using affine functions. Regarding the performance-derived response fluctuations, the most promising strategy for cross-comparative analysis and data fusion included the mass spectral total useful signal (MSTUS) approach followed by Z-score normalization on the resulting matrix.PMID:36631574 | DOI:10.1007/s00216-023-04516-x

Anal Bioanal Chem. 2023 Jan 11. doi: 10.1007/s00216-022-04505-6. Online ahead of print.ABSTRACTMicrobial metabolomics allows understanding and to comprehensively analyse metabolites, and their related cellular and metabolic processes, that are produced and released to the extracellular environment under specific conditions. In that regard, the main objective of this research is to understand the impact of culture media changes in the metabolic profile of Pedobacter lusitanus NL19 (NL19) and Pedobacter himalayensis MTCC 6384 (MTCC6384) and respective influence on the production of biotechnologically relevant compounds. Solid-phase microextraction combined with comprehensive two-dimensional gas chromatography coupled to time-of-flight mass spectrometry with time-of-flight analyser (GC × GC-ToFMS) was applied to comprehensively study the metabolites produced by NL19 and MTCC6384 both in tryptic soy broth 100% (TSB100) and tryptic soy broth with 25% casein peptone (PC25). A total of 320 metabolites were putatively identified, which belong to different chemical families: alcohols, aldehydes, esters, ethers, hydrocarbons, ketones, nitrogen compounds, sulphur compounds, monoterpenes, and sesquiterpenes. Metabolites that were statistically different from the control (sterile medium) were selected allowing for the construction of the metabolic profile of both strains. A set of 80 metabolites was tentatively associated to the metabolic pathways such as the metabolism of fatty acids, branched-chain aminoacids, phenylalanine, methionine, aromatic compounds, and monoterpene and sesquiterpene biosynthesis. This study allowed to better understand how slight changes of the culture media and thus the composition of nutrients impair the metabolic profile of bacteria, which may be further explored for metabolomics pipeline construction or biotechnological applications.PMID:36631573 | DOI:10.1007/s00216-022-04505-6

J Chem Ecol. 2023 Jan 12. doi: 10.1007/s10886-022-01402-1. Online ahead of print.ABSTRACTAnthracnose caused by Colletotrichum gloeosporioides affects the leaves, inflorescences, nuts, and peduncles of cashew trees (Anacardium occidentale). The use of genetically improved plants and the insertion of dwarf cashew clones that are more resistant to phytopathogens are strategies to minimize the impact of anthracnose on cashew production. However, resistance mechanisms related to the biosynthesis of secondary metabolites remain unknown. Thus, this study promoted the investigation of the profile of volatile organic compounds of resistant cashew clone leaves ('CCP 76', 'BRS 226' and 'BRS 189') and susceptible ('BRS 265') to C. gloeosporioides, in the periods of non-infection and infection of the pathogen in the field (July-December 2019 - Brazil). Seventy-eight compounds were provisionally identified. Chemometric analyses, such as Principal Component Analysis (PCA), Discriminating Partial Least Squares Analysis (PLS-DA), Discriminating Analysis of Orthogonal Partial Least Squares (OPLS-DA), and Hierarchical Cluster Analysis (HCA), separated the samples into different groups, highlighting hexanal, (E)-hex-2-enal, (Z)-hex-2-en-1-ol, (E)-hex-3-en-1-ol, in addition to α-pinene, α-terpinene, γ-terpinene, β-pinene, and δ-3-carene, in the samples of the resistant clones in comparison to the susceptible clone. According to the literature, these metabolites have antimicrobial activity and are therefore chemical marker candidates for resistance to C. gloeosporioides in cashew trees.PMID:36631524 | DOI:10.1007/s10886-022-01402-1

Sci Rep. 2023 Jan 11;13(1):585. doi: 10.1038/s41598-022-24878-z.ABSTRACTThe purpose of our study was to explore potential characteristic biomarkers in patients with sepsis. Peripheral blood specimens from sepsis patients and normal human volunteers were processed by liquid chromatography-mass spectrometry-based analysis. Outlier data were excluded by principal component analysis and orthogonal partial least squares-discriminant analysis using the metabolomics R software package metaX and MetaboAnalyst 5.0 ( https://www.metaboanalyst.ca/home.xhtml ) online analysis software, and differential metabolite counts were identified by using volcano and heatmaps. The obtained differential metabolites were combined with KEGG (Kyoto Gene and Kyoto Encyclopedia) analysis to screen out potential core differential metabolites, and ROC curves were drawn to analyze the changes in serum metabolites in sepsis patients and to explore the potential value of the metabolites in the diagnosis of sepsis patients. By metabolomic analysis, nine differential metabolites were screened for their significance in guiding the diagnosis and differential diagnosis of sepsis namely: 3-phenyl lactic acid, N-phenylacetylglutamine, phenylethylamine, traumatin, xanthine, methyl jasmonate, indole, l-tryptophan and 1107116. In this study, nine metabolites were finally screened based on metabolomic analysis and used as potential characteristic biomarkers for the diagnosis of sepsis.PMID:36631483 | DOI:10.1038/s41598-022-24878-z

Cell Death Dis. 2023 Jan 11;14(1):14. doi: 10.1038/s41419-022-05529-7.ABSTRACTTP73 is expressed as multiple N- and C-terminal isoforms through two separate promoters or alternative splicing. While N-terminal p73 isoforms have been well studied, very little is known about p73 C-terminal isoforms. Thus, CRISPR was used to delete TP73 Exon13 (E13-KO) to induce p73α to p73β isoform switch. We showed that E13-KO led to decreased cell proliferation and migration and sensitized cells to ferroptosis, which can be reverted by knockdown of TAp73β in E13-KO cells. To understand the biological function of p73β in vivo, we generated a mouse model in that the Trp73 E13 was deleted by CRISPR. We showed that p73α to p73β isoform switch led to increased cellular senescence in mouse embryonic fibroblasts. We also showed that E13-deficient mice exhibited shorter life span and were prone to spontaneous tumors, chronic inflammation and liver steatosis as compared to WT mice. Additionally, we found that the incidence of chronic inflammation and liver steatosis was higher in E13-deficient mice than that in Trp73-deficient mice, suggesting that p73β is a strong inducer of inflammatory response. Mechanistically, we showed that TAp73β was able to induce cysteine dioxygenase 1 (CDO-1), leading to cysteine depletion and subsequently, enhanced ferroptosis and growth suppression. Conversely, knockdown of CDO-1 was able to alleviate the growth suppression and ferroptosis in E13-KO cells. Together, our data suggest that at a physiologically relevant level, TAp73β is a strong inducer of growth suppression but insufficient to compensate for loss of TAp73α in tumor suppression due to aberrant induction of inflammatory response and liver steatosis.PMID:36631448 | DOI:10.1038/s41419-022-05529-7

Physiol Plant. 2023 Jan 11:e13851. doi: 10.1111/ppl.13851. Online ahead of print.ABSTRACTAnthocyanins widely exist in plants and they are important pigments for color of petals and fruits. They are produced through a multi-step pathway controlled by transcription factor complexes. The anthocyanin skeleton modification is the last reaction in the anthocyanin synthesis pathway, which improves the stability of anthocyanins. Acylation modification is an important modification of anthocyanins. However, the identification and function of anthocyanin acyltransferase genes and their expression regulation are rarely reported. In this study, we identified the petunia anthocyanin acyltransferase gene, PhAAT1. PhAAT1 is located in the cytoplasm and PhAAT1 silencing changed flower color and reduced the stability of anthocyanin. Metabolomics analysis showed that PhAAT1 silencing led to the reduction of p-coumaroylated and caffeoylated anthocyanins. In addition, PhAAT1 was positively regulated by the MYB transcription factor, PhAN2, which directly interacts with the promoter of PhAAT1.PMID:36631431 | DOI:10.1111/ppl.13851

Redox Biol. 2023 Jan 2;59:102600. doi: 10.1016/j.redox.2023.102600. Online ahead of print.ABSTRACTCurrent treatments for acute ischemic stroke aim to reinstate a normal perfusion in the ischemic territory but can also cause significant ischemia-reperfusion (IR) injury. Previous data in experimental models of stroke show that ischemia leads to the accumulation of succinate, and, upon reperfusion, the accumulated succinate is rapidly oxidized by succinate dehydrogenase (SDH) to drive superoxide production at mitochondrial complex I. Despite this process initiating IR injury and causing further tissue damage, the potential of targeting succinate metabolism to minimize IR injury remains unexplored. Using both quantitative and untargeted high-resolution metabolomics, we show a time-dependent accumulation of succinate in both human and mouse brain exposed to ischemia ex vivo. In a mouse model of ischemic stroke/mechanical thrombectomy mass spectrometry imaging (MSI) shows that succinate accumulation is confined to the ischemic region, and that the accumulated succinate is rapidly oxidized upon reperfusion. Targeting succinate oxidation by systemic infusion of the SDH inhibitor malonate upon reperfusion leads to a dose-dependent decrease in acute brain injury. Together these findings support targeting succinate metabolism upon reperfusion to decrease IR injury as a valuable adjunct to mechanical thrombectomy in ischemic stroke.PMID:36630820 | DOI:10.1016/j.redox.2023.102600