PubMed

Food Funct. 2024 Oct 17. doi: 10.1039/d4fo03633f. Online ahead of print.ABSTRACTInsufficient selenium intake can lead to serious health problems. However, most research on the functional properties of selenium-enriched probiotics has focused on sub-health conditions or disease models, with limited studies involving healthy subjects. Additionally, previous research has primarily explored the direct effects of selenium itself, neglecting its influence on gut microbiota and metabolism. This study aimed to explore whether long-term intake of Pichia kudriavzevii enriched with selenium affected gut microbiota and host metabolism in mice and to identify microbiota and metabolites related to beneficial outcomes. Results demonstrated that selenium-enriched P. kudriavzevii (SeY) exhibited non-toxic properties, did not cause colon or liver damage, enhanced antioxidant capacity, and reduced inflammation in a selenium dose-dependent manner. Additionally, SeY supplementation significantly altered the gut microbiota. High-dose SeY (HSeY) elevated the abundance of beneficial bacteria such as Lactobacillus and suppressed harmful bacteria such as Eubacterium nodatum group, Prevotellaceae_NK3B31_group, and unclassified_f__Lachnospiraceae. Low-dose SeY (LSeY) increased the abundance of Faecalibaculum. The strain without enriched selenium exhibited higher levels of Akkermansia compared to selenium-enriched strains. Both strains, with or without enriched selenium, stimulated the production of short-chain fatty acids. Non-targeted metabolomics analysis revealed that HSeY treatment regulated various metabolic pathways, such as tryptophan metabolism, tyrosine metabolism, and arginine biosynthesis. LSeY treatment modulated tyrosine metabolism, secondary bile acid metabolism, bile secretion, and primary bile acid metabolism. P. kudriavzevii regulated the metabolism of purine, arginine, proline, and tryptophan. Our study highlights the promise of SeY supplementation in regulating host metabolism and the gut microbiota, offering insights into its implications for promoting health.PMID:39417221 | DOI:10.1039/d4fo03633f

Front Microbiol. 2024 Oct 2;15:1463911. doi: 10.3389/fmicb.2024.1463911. eCollection 2024.ABSTRACTStreptomyces sp. VB1, an actinomycete isolated from marine sediments in Valparaíso Bay, Chile, synthesizes antimicrobial and antiproliferative compounds. This study presents comprehensive metabolomics and comparative genomics analyses of strain VB1. LC-HRMS dereplication and Molecular Networking analysis of crude extracts identified antibiotics such as globomycin and daunorubicin, along with known and potentially novel members of the arylomycin family. These compounds exhibit activity against a range of clinically relevant bacterial and cancer cell lines. Phylogenomic analysis underscores the uniqueness of strain VB1, suggesting it represents a novel taxon. Such uniqueness is further supported by its Biosynthetic Novelty Index (BiNI) and BiG-SCAPE analysis of Gene Cluster Families (GCFs). Notably, two Biosynthetic Gene Clusters (BGCs) were found to be unique to VB1 compared to closely related strains: BGC #15, which encodes potentially novel anthracycline compounds with cancer cell growth inhibition properties, and BGC #28, which features a non-canonical configuration combining arylomycin, globomycin, and siamycin BGCs. This supercluster, the first described to consist of more than two adjacent and functional BGCs, co-produces at least three antimicrobial compounds from different antibiotic families. These findings highlight Streptomyces sp. VB1's potential for discovering new bioactive molecules, positioning it as a promising candidate for further research.PMID:39417076 | PMC:PMC11479970 | DOI:10.3389/fmicb.2024.1463911

Toxicol Res (Camb). 2024 Oct 15;13(5):tfae169. doi: 10.1093/toxres/tfae169. eCollection 2024 Oct.ABSTRACTHuman exposure to mycotoxins through food involve a mixture of compounds, which can be harmful to human health. The Fusarium fungal species are known to produce zearalenone (ZEN), a non-steroidal estrogenic mycotoxin, and its metabolite alpha-zearalenol (α-ZEL), both of which possess endocrine-disruptive properties. Given their potential harm to human health through food exposure, investigating the combined effects of ZEN and α-ZEL becomes crucial. Hence, the combined impact of ZEN and α-ZEL study hold significant importance. This in vitro study delves into the critical area, examining their combined impact on the proliferation and metabolic profile of endometrial cancer Ishikawa cells via sulforhodamine, clonogenic, proliferating cell nuclear antigen (PCNA) and liquid chromatography-high resolution mass spectrometry (LC-HRMS) based untargeted metabolomics. Low concentrations of ZEN (25 nm), α-ZEL (10 nm), or a combination of both were observed to significantly enhance cell proliferation of Ishikawa cells, as evidenced by PCNA immunostaining, immunoblotting as well and clonogenic assays. The metabolomics revealed the perturbations in glycerophospholipid metabolism, nicotinate and nicotinamide metabolism and phenylalanine, tyrosine, tryptophan biosynthesis provides valuable insights into potential mechanism by which these mycotoxins may facilitate cell proliferation. However, further investigations are warranted to comprehensively understand the implications of these findings and their possible implications for human health.PMID:39417035 | PMC:PMC11474235 | DOI:10.1093/toxres/tfae169

Biotechnol Notes. 2023 Dec 31;5:1-7. doi: 10.1016/j.biotno.2023.12.006. eCollection 2024.ABSTRACTFungal endophytes are valuable sources of bioactive compounds with diverse applications. The exploration of these compounds not only contributes to our understanding of ecological interactions but also holds promise for the development of novel products with agricultural, medicinal, and industrial significance. Continued exploration of fungal endophyte diversity and understanding the ecological roles of bioactive compounds present opportunities for new discoveries and applications. Omics techniques, which include genomics, transcriptomics, proteomics, and metabolomics, contribute to the discovery of novel bioactive compounds produced by fungal endophytes with their potential applications. The omics techniques play a critical role in unraveling the complex interactions between fungal endophytes and their host plants, providing valuable insights into the molecular mechanisms and potential applications of these relationships. This review provides an overview of how omics techniques contribute to the study of fungal endophytes.PMID:39416692 | PMC:PMC11446381 | DOI:10.1016/j.biotno.2023.12.006

bioRxiv [Preprint]. 2024 Oct 11:2024.10.07.617124. doi: 10.1101/2024.10.07.617124.ABSTRACTChronic infections drive a CD8 T cell program termed T cell exhaustion, characterized by reduced effector functions. While cell-intrinsic mechanisms underlying CD8 T cell exhaustion have been extensively studied, the impact of the metabolic environment in which exhausted CD8 T cells (Tex) operate remains less clear. Using untargeted metabolomics and the murine lymphocytic choriomeningitis virus infection model we investigated systemic metabolite changes early and late following acute versus chronic viral infections. We identified distinct short-term and persistent metabolite shifts, with the most significant differences occurring transiently during the acute phase of the sustained infection. This included nutrient changes that were independent of viral loads and partially associated with CD8 T cell-induced anorexia and lipolysis. One remarkable observation was the elevation of medium- and long-chain fatty acid (FA) and acylcarnitines during the early phase after chronic infection. During this time, virus-specific CD8 T cells from chronically infected mice exhibited increased lipid accumulation and uptake compared to their counterparts from acute infection, particularly stem-like Tex (Tex STEM ), a subset that generates effector-like Tex INT which directly limit viral replication. Notably, only Tex STEM increased oxidative metabolism and ATP production upon FA exposure. Consistently, short-term reintroduction of FA during late chronic infection exclusively improved Tex STEM mitochondrial fitness, percentages and numbers. This treatment, however, also reduced Tex INT , resulting in compromised viral control. Our study offers a valuable resource for investigating the role of specific metabolites in regulating immune responses during acute and chronic viral infections and highlights the potential of long-chain FA to influence Tex STEM and viral control during a protracted infection.SIGNIFICANCE: This study examines systemic metabolite changes during acute and chronic viral infections. Notably, we identified an early, transient nutrient shift in chronic infection, marked by an increase in medium- and long-chain fatty acid related species. Concomitantly, a virus-specific stem-like T cell population, essential for maintaining other T cells, displayed high lipid avidity and was capable of metabolizing exogenous fatty acids. Administering fatty acids late in chronic infection, when endogenous lipid levels had normalized, expanded this stem-like T cell population and enhanced their mitochondrial fitness. These findings highlight the potential role of fatty acids in regulating stem-like T cells in chronic settings and offer a valuable resource for studying other metabolic signatures in both acute and persistent infections.PMID:39416134 | PMC:PMC11483027 | DOI:10.1101/2024.10.07.617124

bioRxiv [Preprint]. 2024 Oct 10:2024.10.07.617109. doi: 10.1101/2024.10.07.617109.ABSTRACTDespite extensive efforts, extracting information on medication exposure from clinical records remains challenging. To complement this approach, we developed the tandem mass spectrometry (MS/MS) based GNPS Drug Library. This resource integrates MS/MS data for drugs and their metabolites/analogs with controlled vocabularies on exposure sources, pharmacologic classes, therapeutic indications, and mechanisms of action. It enables direct analysis of drug exposure and metabolism from untargeted metabolomics data independent of clinical records. Our library facilitates stratification of individuals in clinical studies based on the empirically detected medications, exemplified by drug-dependent microbiota-derived N -acyl lipid changes in a human immunodeficiency virus cohort. The GNPS Drug Library holds potential for broader applications in drug discovery and precision medicine.PMID:39416075 | PMC:PMC11482764 | DOI:10.1101/2024.10.07.617109

Comput Struct Biotechnol J. 2024 Sep 17;23:3454-3466. doi: 10.1016/j.csbj.2024.09.010. eCollection 2024 Dec.ABSTRACTThe advent of the genomics era enabled the generation of high-throughput data and computational methods that serve as powerful hypothesis-generating tools to understand the genomic and gene functional basis of plant stress resilience. The proliferation of experimental and analytical methods used in biology has resulted in a situation where plentiful data exists, but the volume and heterogeneity of this data has made analysis a significant challenge. Current advanced deep-learning models have displayed an unprecedented level of comprehension and problem-solving ability, and have been used to predict gene structure, function and expression based on DNA or protein sequence, and prominently also their use in high-throughput phenomics in agriculture. However, the application of deep-learning models to understand gene regulatory and signalling behaviour is still in its infancy. We discuss in this review the availability of data resources and bioinformatic tools, and several applications of these advanced ML/AI models in the context of plant stress response, and demonstrate the use of a publicly available LLM (ChatGPT) to derive a knowledge graph of various experimental and computational methods used in the study of plant stress. We hope this will stimulate further interest in collaboration between computer scientists, computational biologists and plant scientists to distil the deluge of genomic, transcriptomic, proteomic, metabolomic and phenomic data into meaningful knowledge that can be used for the benefit of humanity.PMID:39415960 | PMC:PMC11480249 | DOI:10.1016/j.csbj.2024.09.010

Front Pharmacol. 2024 Oct 2;15:1452921. doi: 10.3389/fphar.2024.1452921. eCollection 2024.ABSTRACTThe gut microbiota may help mitigate bone loss linked to postmenopausal osteoporosis by affecting the immune and inflammatory responses and the gut-bone axis. Dihydromyricetin (DMY), a natural flavonoid, has some anti-inflammatory and antioxidant properties. This study aimed to investigate the mechanisms underlying the amelioration of bone loss in ovariectomized (OVX) mice treated with various doses of DMY. Eight-week-old C57/BL6 mice underwent ovariectomy and received varying DMY doses over 8 weeks. Thereafter, femoral bone microarchitecture, serum biomarker levels, and colon samples were analyzed to assess bone metabolism and inflammatory and hormonal responses. Fecal samples were subjected to 16S rDNA sequencing, and short-chain fatty acids were quantified. An untargeted metabolomics approach was applied to both serum and fecal samples to investigate alterations in the intestinal microbiota and metabolic profiles following DMY treatment in the OVX mice. The results show high-dose DMY has anti-osteoporotic effects. Compared to the OVX group, the DMY-treated group showed enhanced bone mineral density and reduced inflammation and colonic damage levels. The DMY treatment altered the gut microbiota composition, including the relative abundances at both the phylum and genus levels. In addition, DMY treatment increased the production of acetate and propionate. Metabolomic analysis revealed differential regulation of 37 and 70 metabolites in the serum and feces samples, respectively, in the DMY-treated group compared to those in the OVX group, affecting the serotonergic signaling, arachidonic acid metabolism, and unsaturated fatty acid biosynthesis pathways. In conclusion, these findings indicate that DMY can ameliorate bone loss in OVX mice via the gut-bone axis.PMID:39415843 | PMC:PMC11479887 | DOI:10.3389/fphar.2024.1452921

Microb Biotechnol. 2024 Oct;17(10):e70026. doi: 10.1111/1751-7915.70026.ABSTRACTFusarium wilt is one of the major constraints on global watermelon production, and Fusarium oxysporum f. sp. niveum (Fon) is the causative agent of Fusarium wilt in watermelon and results in severe yield and quality losses worldwide. The enhancement of antifungal activity from antagonistic bacteria against Fon is highly practical for managing Fusarium wilt in watermelon. The aim of this study was to maximize the antifungal activity of Bacillus velezensis LZN01 by optimizing fermentation conditions and analysing its regulatory mechanism via transcriptome sequencing. The culture and fermentation conditions for strain LZN01 were optimized by single-factor and response surface experiments. The optimum culture conditions for this strain were as follows: the addition of D-fructose at 35 g/L and NH4Cl at 5 g/L in LB medium, pH 7, and incubation at 30°C for 72 h. The fungal inhibition rate for strain LZN01 reached 71.1%. The improvement of inhibition rate for strain LZN01 in optimization fermentation was supported by transcriptomic analysis; a total of 491 genes were upregulated, while 736 genes were downregulated. Transcriptome analysis revealed that some differentially expressed genes involved in carbon and nitrogen metabolism, oxidation-reduction, fatty acid and secondary metabolism; This optimization process could potentially lead to significant alterations in the production levels and types of antimicrobial compounds by the strain. Metabolomics and UPLC/Q-Exactive Orbitrap MS analysis revealed that the production yields of antimicrobial compounds, such as surfactin, fengycin, shikimic acid, and myriocin, increased or were detected in the cell-free supernatant (CFS) after the fermentation optimization process. Our results indicate that fermentation optimization enhances the antifungal activity of the LZN01 strain by influencing the expression of genes responsible for the synthesis of antimicrobial compounds.PMID:39415743 | DOI:10.1111/1751-7915.70026

Curr Pharm Des. 2024 Oct 16. doi: 10.2174/0113816128333694240928161703. Online ahead of print.ABSTRACTDiabetic nephropathy (DN) is increasing worldwide in parallel with type 2 diabetes mellitus. Identifying diagnostic biomarkers for DN at an early stage is crucial due to the considerable societal and economic burden associated with diabetes mellitus (DM) and its risk factors. In the past, early indicators of microvascular problems, such as microalbuminuria (MA), have been used to predict the possibility of developing advanced chronic kidney disease (CKD). However, because of the incapacity of MA to appropriately estimate DN, particularly, non-albuminuric DN, additional markers have been suggested for recognizing the early renal abnormalities and structural lesions, even before MA. This study aims to assess the existing and future biomarkers used to diagnose or predict early DN. This review provides comprehensive insight into diagnostic approaches for early detection of CKD, addressing the following areas: (i) markers of glomerular damage, (ii) markers of tubular damage, (iii) oxidative stress biomarkers, (iv) inflammatory biomarkers and (v) futuristic biomarkers such as micro-ribonucleic acids (miRNAs), proteomics, metabolomics and genomics and gut microbiota. Early detection of DN may lead to improvement in clinical management and quality of life, emphasizing the importance of identifying a specific and reliable predictive biomarker. Emerging serum and urinary biomarkers offer promise for early DN diagnosis, potentially reducing prevalence and preventing progression to end-stage renal disease (ESRD). Further advancements in miRNAs, proteomics, metabolomics genomics and gut microbiota offer prospects for even earlier and more precise DN diagnosis.PMID:39415582 | DOI:10.2174/0113816128333694240928161703

Magn Reson Chem. 2024 Oct 16. doi: 10.1002/mrc.5488. Online ahead of print.ABSTRACTDiffusion-ordered NMR spectroscopy (DOSY) is a powerful tool to analyse mixtures. Spatially encoded (SPEN) DOSY enables recording a full DOSY dataset in just one scan by performing spatial parallelisation of the gradient dimension. The simplest and most widely used approach to processing DOSY data is to fit each peak in the spectrum with a single or multiple exponential decay. However, when there is peak overlap, and/or when the diffusion decays of the contributing components are too similar, this method has limitations. Multivariate analysis of DOSY data, which is an attractive alternative, consists of decomposing the experimental data, into compound-specific diffusion decays and 1D NMR spectra. Multivariate analysis has been very successfully used for conventional DOSY data, but its use for SPEN DOSY data has only recently been reported. Here, we present a comparison, for SPEN DOSY data, of two widely used algorithms, SCORE and OUTSCORE, that aim at unmixing the spectra of overlapped species through a least square fit or a cross-talk minimisation, respectively. Data processing was performed with the General NMR Analysis Toolbox (GNAT), with custom-written code elements that now expands the capabilities, and makes it possible to import and process SPEN DOSY data. This comparison is demonstrated on three different two-component mixtures, each with different characteristics in terms of signal overlap, diffusion coefficient similarity, and component concentration.PMID:39415466 | DOI:10.1002/mrc.5488

Am J Epidemiol. 2024 Oct 16:kwae400. doi: 10.1093/aje/kwae400. Online ahead of print.ABSTRACTOur study aimed to investigate the impact of tea and coffee consumption and related metabolomic signatures on dynamic transitions from diabetes-free status to incident type 2 diabetes (T2D), and subsequently to T2D-related complications and death. We included 438,970 participants in the UK Biobank who were free of diabetes and diabetes complications at baseline. Of these, 212,146 individuals had information on all metabolic biomarkers. We identified tea- and coffee-related metabolomic signatures using elastic net regression models. We examined associations of tea and coffee intake and related metabolomic signatures with the onset and progression of T2D using multi-state regression models. We observed that tea and coffee consumption and related metabolomic signatures were inversely associated with the risk of five T2D transitions. For example, HRs (95% CIs) per SD increase of the tea-related metabolomic signature were 0.87 (0.85, 0.89), 0.97 (0.95, 0.99), 0.91 (0.90, 0.92), 0.92 (0.91, 0.94), and 0.91 (0.90, 0.92) for transitions from diabetes-free state to incident T2D, from diabetes-free state to total death, from incident T2D to T2D complications, from incident T2D to death, and from T2D complications to death. These findings highlight the benefit of tea and coffee intake in reducing the risk of occurrence and progression of T2D.PMID:39415441 | DOI:10.1093/aje/kwae400

Biofactors. 2024 Oct 16. doi: 10.1002/biof.2132. Online ahead of print.ABSTRACTMitochondrial dysfunction may precipitate intestinal dysfunction, while inflammatory bowel disease manifests as a chronic inflammatory ailment affecting the gastrointestinal tract. This condition disrupts the barrier function of the intestinal epithelium and alters metabolic products. Increasing mitochondrial adenosine triphosphate (ATP) synthesis in intestinal epithelial cells presents a promising avenue for colitis treatments. Nevertheless, the impact of cedrol on ATP and the intestinal barrier remains unexplored. Hence, this study is dedicated to examining the cedrol's protective effect on an inflammatory cocktail (IC)-induced intestinal epithelial barrier dysfunction in Caco-2 cells. The finding reveals that cedrol enhances ATP content and the transepithelial electrical resistance value in the intestinal epithelial barrier. Moreover, cedrol mitigates the IC-induced decrease in the messenger ribonucleic acid (mRNA) expression of tight junction proteins (ZO-1, Occludin, and Claudin-1), thereby ameliorating intestinal epithelial barrier dysfunction. Furthermore, nuclear magnetic resonance (NMR)-based metabolomic analysis indicated that IC-exposed Caco-2 cells are restored by cedrol treatments. Notably, cedrol elevates metabolites such as amino acids, thereby enhancing the intestinal barrier. In conclusion, cedrol alleviates IC-induced intestinal epithelial barrier dysfunction by promoting ATP-dependent proliferation of Caco-2 cells and bolstering amino acid levels to sustain tight junction messenger ribonucleic acid expression.PMID:39415440 | DOI:10.1002/biof.2132

Am J Epidemiol. 2024 Oct 16:kwae402. doi: 10.1093/aje/kwae402. Online ahead of print.ABSTRACTBiliary tract cancer (BTC) is potentially influenced by metabolic dysregulation yet previous metabolomic evaluations are limited. To address this gap, we prospectively investigated associations of blood metabolites and BTC risk in the UK biobank cohort study. We used Cox proportional hazards models to estimate hazard ratios (HR) and 95% confidence intervals (95% CI) between 249 plasma metabolites per standard deviation and BTC risk in 232,781 participants. We implemented exploratory factor analyses and evaluated associations between factors and BTC risk. Associations at p-value<0.001 were considered statistically significant after multiple comparison adjustments. In a median follow-up of 11.8 years, we identified 268 first primary incident BTC cases. Of 49 biomarkers significantly associated with BTC risk, 12% were fatty acids, and 49%, 31%, and 8% were cholesterol, triglyceride, and phospholipid to total lipids ratios, respectively. Multiple cholesterol ratios were inversely associated with BTC with HRs (95% CIs) of 0.74 (0.65-0.84), p<6.0x10-6. Conversely, a triglyceride ratio was positively associated with BTC with an HR (95% CI) of 1.40 (1.22-1.61), p=2.5x10-6. Congruently, a factor high in cholesterol measures and low in triglyceride measures was inversely associated with BTC. Multiple metabolite biomarkers were associated with BTC risk, suggesting metabolism has a substantial role in BTC etiology.PMID:39415432 | DOI:10.1093/aje/kwae402

Anim Microbiome. 2024 Oct 16;6(1):57. doi: 10.1186/s42523-024-00344-1.ABSTRACTBACKGROUND: Recirculating aquaculture systems can cause chronic stress in fish when stocking density is too high. However, this study tested whether low stocking density can cause fish stress. Adult rainbow trout, with an average weight of 1.517 kg (± 0.39), were subjected to low (12 kg/m3 ± 0.94) and moderate (43 kg/m3 ± 2.03) stocking densities for 24 days in a recirculating system maintained at 15 °C. At the end of the experiment, fecal microbiome analysis was carried out using a 16S rRNA amplicon sequencing. Additionally, an untargeted plasma metabolomics analysis was conducted.RESULTS: The moderate stocking density group harboured greater numbers of commensals, such as C. somerae, R. lituseburensis, and L. plantarum. In contrast, detrimental species such as S. putrifacens and P. putida were abundant in the low-stocking density fish. Functional microbiome profiling revealed vitamin B12 salvage and synthesis in moderate stocking densities, which may support intestinal tight junction function. Additionally, vitamin B1 biosynthesis pathways were more abundant in the moderate stocking density group, which may function towards oxidative energy metabolism and protect against oxidative stress. A complementary plasma metabolomics study, although done at slightly different stocking densities and duration, confirmed the presence of blood metabolic stress markers. Elevated levels of L-lactic acid and L-Norvaline, L-Valine, and L-glutamine, indicate low stocking density fish were under stress. Furthermore, a P4HA2 stress gene biomarker confirmed the occurrence of stress in low-density fish. This study suggests that low stocking density can induce stress in fish. Moreover, moderate stocking density leads to a distinct and beneficial fecal microbiome profile.CONCLUSION: Our study highlights the potential benefits of optimizing the stocking density of fish in recirculating aquaculture systems. This can improve fish health and welfare, promoting a more resilient fecal microbiome.PMID:39415222 | DOI:10.1186/s42523-024-00344-1

Transl Psychiatry. 2024 Oct 17;14(1):439. doi: 10.1038/s41398-024-03157-7.ABSTRACTThere is increasing interest in the pathophysiological role of arginine metabolism in schizophrenia, particularly in relation to the modulation of the endogenous messenger nitric oxide (NO). The assessment of specific arginine metabolites that, unlike NO, are stable can provide useful insights into NO regulatory enzymes such as isoform 1 of dimethylarginine dimethylaminohydrolase (DDAH1) and arginase. We investigated the role of arginine metabolomics in schizophrenia by conducting a systematic review and meta-analysis of the circulating concentrations of arginine metabolites associated with DDAH1, arginase, and NO synthesis [arginine, citrulline, asymmetric dimethylarginine (ADMA), symmetric dimethylarginine (SDMA), dimethylamine, and ornithine] in this patient group. We searched PubMed, Scopus, and Web of Science from inception to the 31st of May 2023 for studies investigating arginine metabolites in patients with schizophrenia and healthy controls. The JBI Critical Appraisal Checklist for analytical studies and GRADE were used to assess the risk of bias and the certainty of evidence, respectively (PROSPERO registration number: CRD42023433000). Twenty-one studies were identified for analysis. There were no significant between-group differences in arginine, citrulline, and SDMA. By contrast, patients with schizophrenia had significantly higher ADMA (DDAH1 substrate, standard mean difference, SMD = 1.23, 95% CI 0.86-1.61, p < 0.001; moderate certainty of evidence), dimethylamine (DDAH1 product, SMD = 0.47, 95% CI 0.24-0.70, p < 0.001; very low certainty of evidence), and ornithine concentrations (arginase product, SMD = 0.32, 95% CI 0.16-0.49, p < 0.001; low certainty of evidence). In subgroup analysis, the pooled SMD for ornithine was significantly different in studies of untreated, but not treated, patients. Our study suggests that DDAH1 and arginase are dysregulated in schizophrenia. Further studies are warranted to investigate the expression/activity of these enzymes in the brain of patients with schizophrenia and the effects of targeted treatments.PMID:39414767 | DOI:10.1038/s41398-024-03157-7

Plant Cell Rep. 2024 Oct 16;43(11):264. doi: 10.1007/s00299-024-03356-y.ABSTRACTCellulose synthase-like OsCSLD4 plays a pivotal role in regulating diverse agronomic traits, enhancing resistance against bacterial leaf blight, and modulating metabolite indices based on the multi-omics analysis in rice. To delve deeper into this complex network between agronomic traits and metabolites in rice, we have compiled a dataset encompassing genome, phenome, and metabolome, including 524 diverse accessions, 11 agronomic traits, and 841 metabolites, enabling us to pinpoint eight hotspots through GWAS. We later discovered four distinct metabolite categories, encompassing 15 metabolites that are concurrently present on the QTL qC12.1, associated with leaf angle of flag and spikelet length, and finally focused the cellulose synthase-like OsCSLD4, which was pinpointed through a rigorous process encompassing sequence variation, haplotype, ATAC, and differential expression across diverse tissues. Compared to the wild type, csld4 exhibited significant reductions in the plant height, flag leaf length, leaf width, spikelet length, 1000-grain weight, grain width, grain thickness, fertility, yield per plant, and bacterial blight resistance. However, there were significant increase in tiller numbers, degree of leaf rolling, flowering period, growth period, grain length, and empty kernel rate. Furthermore, the content of four polyphenol metabolites, excluding metabolite N-feruloyltyramine (mr1268), notably rose, whereas the levels of the other three polyphenol metabolites, smiglaside C (mr1498), 4-coumaric acid (mr1622), and smiglaside A (mr1925) decreased significantly in mutant csld4. The content of amino acid L-tyramine (mr1446) exhibited a notable increase, whereas the alkaloid trigonelline (mr1188) displayed a substantial decrease among the mutants. This study offered a comprehensive multi-omics perspective to analyze the genetic mechanism of OsCSLD4, and breeders can potentially enhance rice's yield, bacterial leaf blight resistance, and metabolite content, leading to more sustainable and profitable rice production.PMID:39414689 | DOI:10.1007/s00299-024-03356-y

Int J Biol Macromol. 2024 Oct 1:135992. doi: 10.1016/j.ijbiomac.2024.135992. Online ahead of print.ABSTRACTEmerging evidence suggests that gut microbiota and its metabolites significantly influence the effectiveness of EGFR-TKIs (e.g., gefitinib, erlotinib) in lung cancer treatment. Plant polysaccharides can interact with gut microbiota, leading to changes in the host-microbe metabolome that may affect drug metabolism and therapeutic outcomes. Our previous research demonstrated the efficacy of basil polysaccharide (BPS) in treating various cancers by regulating hypoxic microenvironment and inhibiting epithelial-mesenchymal transition process. However, the potential impact of BPS on gut microbiota has not been thoroughly explored. In this study, we employed an immunodeficient gefitinib-resistant xenograft mouse model to explore whether BPS enhances the antitumor effects of gefitinib. A multi-omics approach, including 16S rDNA amplicon sequencing and LC-MS, was used to elucidate these synergistic effects. Our findings indicate that BPS can enhance tumor responsiveness to gefitinib by modulating the gut microbiota and its metabolites through multiple metabolic pathways. These changes in gut microbiota and metabolites could potentially affect cancer related signaling pathway and lung resistance-related protein, which are pivotal in determining the efficacy of EGFR-TKIs in cancer treatment.PMID:39414535 | DOI:10.1016/j.ijbiomac.2024.135992

Mol Cell Proteomics. 2024 Oct 14:100862. doi: 10.1016/j.mcpro.2024.100862. Online ahead of print.ABSTRACTWell-controlled metabolism is associated with high quality of oocytes and optimal development of a healthy embryo. However, the metabolic framework that controls mammalian oocyte growth remains unknown. In the present study, we comprehensively depict the temporal metabolic dynamics of mouse oocytes during in vivo growth through the integrated analysis of metabolomics and proteomics. A number of novel metabolic features are discovered during this process. Of note, glycolysis is enhanced and oxidative phosphorylation capacity is reduced in the growing oocytes, presenting a Warburg-like metabolic program. For the nucleotide biosynthesis, the salvage pathway is markedly activated during oocyte growth, whereas the de novo pathway is evidently suppressed. Fatty acid synthesis and channeling into phosphoinositides are specifically elevated in oocytes accompanying primordial follicle activation; nevertheless, fatty acid oxidation is reduced in these oocytes simultaneously. Our data establish the metabolic landscape during in vivo oocyte growth and serve as a broad resource for probing mammalian oocyte metabolism.PMID:39414232 | DOI:10.1016/j.mcpro.2024.100862

J Adv Res. 2024 Oct 14:S2090-1232(24)00461-2. doi: 10.1016/j.jare.2024.10.007. Online ahead of print.ABSTRACTINTRODUCTION: Climate change poses various threats to marine life, particularly in shallow tropical waters.OBJECTIVE: The impact of increased temperature and ultraviolet (UV) exposure on two photosymbiotic Cnidarians, a common bubble-tip anemone and an upside-down jellyfish, was investigated.METHODS: To illustrate the response of aquatic organisms, the metabolomes of unstressed Entacmaea quadricolor and Cassiopea andromeda were compared for detailed metabolite profiling. UHPLC-MS coupled with chemometrics and GNPS molecular networking was employed for sample classification and identification of markers unique to stress responses in each organism.RESULTS: Several compounds with bioactive functions, including peptides and terpenoids, were reported for the first time in both organisms, viz. cyclic tetraglutamate, campestriene, and ceramide aminoethyl phosphonate (CEAP d18:2/16:0). Both anemone and jellyfish were subjected to either elevated UV-B light intensity up to 6.6 KJ m-2 or increased temperatures (28 °C, 30 °C, 32 °C, and 34 °C) over 4 days. Phospholipids, steroids, and ceramides emerged as chief markers of both types of stress, as revealed by the multivariate data analysis. Lysophosphatidylcholine (LPC 16:0), LPC (18:0/0:0), and echinoclasterol sulfate appeared as markers in both UV and thermal stress models of the anemone, whereas methyl/propyl cholestane-hexa-ol were discriminatory in the UV stress model only. In the case of jellyfish, nonpolar glycosyl ceramide GlcCer (d14:1/28:6) served as a marker for UV stress, whereas polar peptides were elevated in the thermal stress model. Interestingly, both models of jellyfish share a phospholipid, lysophosphatidylethanolamine (LPE 20:4), as a distinctive marker for stress, reported to be associated indirectly with the activity of innate immune response within other photosymbiotic Cnidaria such as corals and appears to be a fundamental stress response in marine organisms.CONCLUSION: This study presents several bioinformatic tools for the first time in two cnidarian organisms to provide not only a broader coverage of their metabolome but also broader insights into cnidarian bleaching in response to different stressors, i.e., heat and UV light, by comparing their effects in anemone versus jellyfish.PMID:39414229 | DOI:10.1016/j.jare.2024.10.007