MetaboAnalyst 4.0: towards more transparent and integrative metabolomics analysis

Integrated cartilage metabolomics and proteomics analysis reveals the therapeutic effect of Wenjing Tongluo Decoction on Knee osteoarthritis rats

Knee osteoarthritis (KOA)is an age-related degenerative whole-joint disease characterized by poor outcomes. Wenjing Tongluo Decoction (WJTLD), a Chinese herbal remedy, has demonstrated favorable clinical effects on KOA. However, the precise mechanisms therein remain poorly defined. In this study, we employed the method of anterior cruciate ligament transection (ACLT) method to establish a rat model of KOA. Following 8 weeks of oral administration of WJTLD, the morphology of knee joint cartilage was evaluated using Safranin-O/Fast green staining, H&E staining, and micro-CT imaging. Utilizing GC-MS based untargeted metabolomics and nano-LC-QE-MS based proteomics, we identified altered metabolites and proteins associated with knee cartilage in different rat groups, which were further validated through western blotting and real-time PCR. Our findings indicate that WJTLD alleviates damage to knee joint cartilage and inhibits cartilage degradation. Proteomics data revealed that the altered proteins in OA and WJTLD treated group were related to the biological process including amoebiasis, platelet activation, ECM-receptor interaction, protein digestion and absorption, and ribosome function. Western blotting results confirmed that the expression levels of MMP8 and LDHA were significantly upregulated in the KOA group but were rescued by WJTLD treatment. According to untargeted metabolomics, the intensities of lactic acid, isoleucine, lysine, glutamate, myo-inositol, adenosine, and β-alanine were significantly elevated in the KOA group, however, these metabolites experienced a dramatic following WJTLD treatment. These results suggest that WJTLD exerts a therapeutic effect on KOA by suppressing inflammation and cartilage degradation, as well as regulating multiple pathways related to ECM degradation, amino acid metabolism, and energy metabolism, including glycolysis.

Carbon metabolism and partitioning in citrus leaves is determined by hybrid, cultivar and leaf type

The partitioning and metabolism of carbohydrates and lignin in leaves are essential for numerous physiological functions, growth and development of plants. This study was aimed to characterize these processes in four leaf types (i.e., autumn-, summer-, spring- and current-year spring shoots) of two citrus hybrids (loose-skin mandarin cultivars OP (i.e., cultivars 'Orah' (OR) Citrus reticulata Blanco and 'Ponkan' (PO) Citrus reticulata Blanco and the sweet orange cultivars NT 'Newhall navel orange' (NO) Citrus sinensis (L.) Osbeck and 'Tarocco' (TA) Citrus sinensis (L.) Osbeck) differing in fruit maturation under field conditions. For this purpose, we analyzed the levels of foliar structural, non-structural carbohydrates and lignin and the expression of related genes. Our results showed that the contents of structural, non-structural carbohydrates and lignin measured in the two hybrids and its partitioning were mostly determined by differences in gene expression recorded in hybrids, cultivars and leaf type. Particularly, differences between leaf types were largely attributed to up- and down-regulation of the expression of genes of cellulose synthesis, lignin precursor synthesis, the Calvin cycle, glycolysis, the tricarbonic acid and starch synthesis and degradation pathways. These differences between leaf types required more complex transcriptional regulation than differences between hybrids and cultivars. The present results indicated that the two citrus hybrids studied differed in the expression of structural, non-structural carbohydrates and lignin-related genes. Future studies have to show if the differences observed in foliar partitioning and metabolism of carbohydrates and lignin are translated into partitioning and metabolism of carbohydrates and lignin in the roots.

Lipid pro-oxidative reactions mediated by heat, light and microwave and the structural characteristics of their products: Revealed via multi-omics approaches

Heat, light, and microwave treatments differentially modulate food flavor profiles through lipid oxidation, but the mechanistic distinctions remain unclear. This study monitored and compared lipid molecular species and flavor compounds in salmon oil processed by these methods via multi-omics technology. Thermal treatment yielded the highest concentrations of alkanes, alkenals, enols, and aldehydes (50.09 % of total volatiles), predominantly C5-C10 compounds. Light treatment generated alkenes, enols, alcohols, and alkanes (74.85 % of total volatiles), primarily C4-C5 and C8 compounds. Microwave processing enriched enols, benzenes, alkenals, and alkenes (72.28 % of total volatiles), predominantly C4-C10 compounds. Volatiles were primarily derived from polyunsaturated triglycerides, with even‑carbon fatty acids undergoing chain shortening to odd‑carbon species during reaction. Microwave-induced lipid oxidation mechanism was linked to both thermal and photo oxidation, attributing to its electromagnetic wave properties and thermal effects. These findings provide a theoretical basis for precise flavor modulation through combining several processing methods.

Effects of fasting and inflammatory challenges on the swine hepatic metabolome

The liver is simultaneously impacted by environmental challenges and modulates the response to these insults. Efforts to understand the effects of stressors on the activity of the liver typically consider one type of challenge (e.g., nutrition, toxin, disease), profile targeted molecules, or study the hepatic disruptions in one sex. The present study characterized hepatic changes in the metabolome of females and males exposed to the nutritional challenge of fasting and inflammatory signals elicited by the viral mimetic Poly(I:C). The hepatic metabolome of pigs was profiled using untargeted liquid chromatography-mass spectrometry analysis enabling the quantification of metabolites. The analysis of pathways enriched among metabolites showing sex-by-distress interactions revealed molecular processes affected by fasting and immune stresses in a sex-specific manner, including SLC-mediated transmembrane transport, the urea cycle, and G-protein coupled receptor signaling. Metabolites differentially abundant across sex-distress groups in the previous pathways included creatine, taurine, and glycine derivatives. Pathways over-represented among metabolites significantly affected by distress included glucose homeostasis, the Krebs cycle, and the metabolism of water-soluble vitamins, with key metabolites including S-adenosylmethionine, histidine, glycerophosphocholine, and lactic acid. These results indicate that 24-h fasting, and low-grade systemic inflammation modulate the liver metabolism. The detection of metabolic disruption that varies with sex enforces the need to develop therapies that can restore hepatic homeostasis in females and males.

1H NMR metabolomic profiling of resistant and susceptible oil palm root tissues in response to Ganoderma boninense at the nursery stage

Oil palm plantations face serious challenges from Ganoderma boninense, a pathogen that causes basal stem rot (BSR), leading to significant productivity losses, with an estimated economic impact of 68.73%. Ganoderma spreads through direct root contact and airborne spores, affecting plantations across Indonesia, Malaysia, and other countries. Understanding the mechanisms of oil palm resistance to Ganoderma is crucial for developing effective strategies. Metabolomic profiling, ¹H NMR spectroscopy, offers a promising tool for identifying and quantifying metabolic changes associated with Ganoderma resistance. This study, ¹H NMR was employed to analyze root tissues of resistant, susceptible, and control oil palm seedlings exposed to Ganoderma. The results indicated that PCA effectively differentiated resistant palms from susceptible ones, while PLS-DA identified 14 significant metabolites. Further analysis using OPLS-DA and ROC revealed that ascorbic acid, D-gluconic acid, D-fructose, and 2-oxoisovalerate could serve as potential biomarkers for screening resistant palms. The metabolites identified in this study hold considerable promise for supporting breeding programs to develop oil palm varieties with enhanced resistance to BSR.

Elevated butyric acid and histamine in feces and serum as an indicator of onset of necrotic enteritis in broiler chickens

Background

Clostridium perfringens (CP) induced necrotic enteritis (NE) is an economically significant intestinal disease of broiler chickens. Identifying potential biological markers during the development of NE might facilitate early disease control measures. Therefore, the current study aimed to identify the metabolites and metabolic pathways changes associated with the onset of NE in serum and feces of CP-infected broiler chickens.

Methodology

The protein content of the feed was abruptly altered from 20% to 28% using a well-established NE model before challenging the birds with CP. Then, we performed a targeted, fully quantitative liquid chromatography-tandem mass spectrometry (LC-MS/MS) -based assay for analyzing the metabolomics profile of serum, feces, and jejunal contents in NE birds. The data were analyzed to understand the trend of metabolite distribution, relationships between metabolites and pathway impacts.

Results

Birds with NE showed metabolic variations including lipids, amino acids, and organic acids, across all the biological samples analyzed. This variation was higher in serum samples (310/597 metabolites, 51.92%), compared to fecal (182/608 metabolites, 29.93%), and jejunal samples (125/607 metabolites, 20.59%). A robust statistical analysis of these metabolites identified 19 common metabolites, including butyric acid and histamine. Pathway analysis identified that six of them were enriched in key pathways, like tricarboxylic acid cycle (TCA cycle) (citric acid and cis-aconitic acid), glyoxylate and dicarboxylate metabolism (citric acid and cis-aconitic acid), arginine-proline metabolism (spermine and creatinine), butanoate metabolism (butyric acid), and histidine metabolism (histamine). These pathways were related to energy synthesis, nitrogen metabolism, and immune response in NE birds.

Conclusion

This study highlights metabolic differences in birds with NE and underscores butyric acid and histamine as potential early biomarkers for NE diagnosis. The upregulation of these metabolites across serum, jejunal and fecal samples reflects their local and systemic impacts on the disease. These biomarkers play key roles in several NE hallmark features, including gut barrier disruption, dysbiosis of microbes and tissue injury through immune system activation, and systemic inflammation. Future studies need to validate our findings across field conditions and different predisposing factors.

Mass Spectrometry Imaging of Lipid and Metabolite Distributions in Cysts of Besnoitia besnoiti-Infected Bovine Skin

Bovine besnoitiosis is a disease caused by the obligate intracellular parasite Besnoitia besnoiti. During its chronic stage, the parasite forms large, thick-walled cysts of up to 600 μm in diameter in the skin and other tissues. To assess an overview of parasite-induced metabolic changes during chronic infection, B. besnoiti-infected skin samples were analyzed by high-resolution atmospheric-pressure scanning microprobe matrix-assisted laser desorption/ionization mass spectrometry imaging (AP-SMALDI MSI). Overall, infection-driven, significant changes of 467 lipids and metabolites were found in comparison to noninfected control samples. Most of them belong to the group of phosphatidic acids (PAs), phosphatidylserines (PSs), phosphatidylcholines (PCs)/phosphatidylethanolamines (PEs), triacylglycerides (TGs), phosphatidylinositols (PIs) and phosphatidylglycerols (PGs). When these quantitative data were combined with analyses on the lateral distribution of respective infection markers, MS images of significantly changed ion signals with specific lateral distributions were generated, matching with typical biological structures as observed in Hematoxylin and eosin (H&E)-stained tissue sections. Ultrahigh-resolution MALDI MSI with a pixel size of 2 μm and 3-dimensional reconstruction gave further insights into cyst construction.

Microfluidics-based label-free SERS profiling of exosomes with machine learning for osteosarcoma diagnosis

Osteosarcoma (OS) calls for early diagnosis to significantly improve patient survival rates. Exosomes hold significant potential as noninvasive biomarkers for the early diagnosis of cancer. Here, we design a microfluidic device to purify and analyze plasma-derived exosomes by label-free surface-enhanced Raman spectroscopy (SERS) profiling for OS diagnosis. Exosomes were isolated, purified, and enriched using a size-dependent microfluidic chip with tangential flow filtration, achieving a high recovery rate of 82 %. The isolated exosomes were then analyzed by label-free SERS using a nanoarray chip with self-assembly monolayers of gold nanoparticles (GNPs). Exosomes originating from different OS cell types were differentiated based on the intrinsic SERS signals. Our approach was further employed to analyze the plasma-derived exosomes from healthy donors and OS patients without the need for specific biomarker labeling. A machine learning-based diagnostic model for OS was constructed, achieving an accuracy of 93 %. The findings indicate that our method is valuable for noninvasive and precise diagnosis of OS and could be generalized to other diseases in the future.

MSIght: A Modular Platform for Improved Confidence in Global, Untargeted Mass Spectrometry Imaging Annotation

Mass spectrometry imaging (MSI) has gained popularity in clinical analyses due to its high sensitivity, specificity, and throughput. However, global profiling experiments are often still restricted to LC-MS/MS analyses that lack spatial localization due to low-throughput methods for on-tissue peptide identification and confirmation. Additionally, the integration of parallel LC-MS/MS peptide confirmation, as well as histological stains for accurate mapping of identifications, presents a large bottleneck for data analysis, limiting throughput for untargeted profiling experiments. Here, we present a novel platform, termed MSIght, which automates the integration of these multiple modalities into an accessible and modular platform. Histological stains of tissue sections are coregistered to their respective MSI data sets to improve spatial localization and resolution of identified peptides. MS/MS peptide identifications via untargeted LC-MS/MS are used to confirm putative MSI identifications, thus generating MS images with greater confidence in a high-throughput, global manner. This platform has the potential to enable large-scale clinical cohorts to utilize MSI in the future for global proteomic profiling that uncovers novel biomarkers in a spatially resolved manner, thus widely expanding the utility of MSI in clinical discovery.

Metabolomics identified distinct molecular-level responses in Daphnia magna after exposure to phenanthrene and its oxygen and nitrogen containing analogs

The prevalence of polycyclic aromatic hydrocarbons and their oxygenated and nitrogen containing analogs in freshwater ecosystems are of concern due to their reported toxicity to several aquatic species including Daphnia magna. This study explored the molecular-level responses of phenanthrene (PHEN), 9,10-phenanthrenequinone (PHQ), and phenanthridine (PN) as little is known about the impacts of these pollutants on the metabolic profile of D. magna. For this purpose, D. magna was exposed to three sub-lethal concentrations of these pollutants for 24 h. To assess molecular-level responses, 52 polar metabolites were extracted from individual adult daphnids, and analyzed using a mass spectrometry-based targeted metabolomics approach. Exposure to PN resulted in the most statistically significant changes to the metabolic profile of D. magna followed by PHQ, and then PHEN exposures. After PN exposure, the biochemical pathway analysis showed that all exposure concentrations shared 21 perturbed metabolic pathways. However, the number of disrupted metabolic pathways increased with increasing exposure concentrations for PHEN and PHQ. The results suggest that PN and PHQ exposures are more disruptive due to the presence of reactive functional groups when compared to PHEN exposure. For the tested concentration ranges, the findings indicate that exposure to PN resulted in non-monotonic disruptions across exposure concentrations. In contrast, exposure to PHEN and PHQ elicited perturbations that were concentration-dependent. Although the reported median effective concentration (EC50) for PN is higher than PHEN and PHQ, our data shows that metabolomics captures molecular-level changes that may not be detected by traditional toxicity metrics.

Omics technologies as powerful approaches to unravel colorectal cancer complexity and improve its management

Colorectal cancer (CRC) continues to rank among the deadliest and most prevalent cancers worldwide, necessitating an innovative and comprehensive approach that addresses this serious health challenge at various stages, from screening and diagnosis to treatment and prognosis. As CRC research progresses, the adoption of an omics-centered approach holds transformative potential to revolutionize the management of this disease. Advances in omics technologies encompassing genomics, transcriptomics, proteomics, metabolomics, and epigenomics allow to unravel the oncogenic alterations at these levels, elucidating the intricacies and the heterogeneous nature of CRC. By providing a comprehensive molecular landscape of CRC, omics technologies enable the discovery of potential biomarkers for early non-invasive detection of CRC, definition of CRC subtypes, prediction of its staging, prognosis, and overall survival of CRC patients. They also allow the identification of potential therapeutic targets, prediction of drug response, tracking treatment efficacy, detection of residual disease and cancer relapse, and deciphering the mechanisms of drug resistance. Moreover, they allow the distinction of non-metastatic CRC patients from metastatic ones as well as the stratification of metastatic risk. Importantly, omics technologies open up new opportunities to establish molecular-based criteria to guide the selection of effective treatment paving the way for the personalization of therapy for CRC patients. This review consolidates current knowledge on the omics-based preclinical discoveries in CRC research emphasizing the significant potential of these technologies to improve CRC screening, diagnosis, and prognosis and promote the implementation of personalized medicine to ultimately reduce CRC prevalence and mortality.

Proteomics and lipidomics of human umbilical cord mesenchymal stem cells exposed to ionizing radiation

OBJECTIVES

Mesenchymal stem cell (MSC)-based therapies exhibit beneficial effects on various forms of tissue damage, including ionizing radiation-induced lesions. However, whether ionizing radiation affects the functions of human umbilical cord mesenchymal stem cells (hucMSCs) remains unclear. This study aimed to investigate the effect and possible mechanisms of ionizing radiation on the proliferation and differentiation of hucMSCs.

METHODS

The hucMSCs were divided into the 1 Gy group (exposure to a single dose (1 Gy) of X-ray radiation (1 Gy/min) for 14 days) and control (without radiation treatment) group. The proliferation, apoptosis, and adipogenic and osteogenic differentiation abilities of hucMSCs in the two groups were evaluated. Moreover, the lipidomics and proteomics analyses were conducted to explore crucial lipids and proteins by which ionizing radiation affected the functions of hucMSCs. In addition, the effects of BYSL on radiation-treated hucMSCs were explore, as well as the involved potential mechanisms.

RESULTS

X-ray radiation treatment inhibited proliferation, promoted apoptosis, and decreased adipogenic and osteogenic differentiation abilities of hucMSCs. Key lipids, such as triglyceride (TG) and phosphatidylcholine (PC), and hub proteins (BYSL, MRTO4, and RRP9) exhibited significant differences between the 1 Gy group and control group. Moreover, BYSL, MRTO4, and RRP9 were significantly correlated with TG and PC. BYSL overexpression evidently promoted the cell proliferation, adipogenic and osteogenic differentiation abilities of radiation-treated hucMSCs, as well as the protein expression levels of p-GSK-3β/GSK-3β and β-catenin, while suppressed cell apoptosis. However, the GSK-3β inhibitor (1-Az) treatment reversed the protein expression levels of p-GSK-3β/GSK-3β, β-catenin and BYSL, as well as the cell proliferation, apoptosis, adipogenic and osteogenic differentiation abilities of radiation-treated hucMSCs.

CONCLUSIONS

Our findings reveal that the proliferation and differentiation of hucMSCs are suppressed by radiation, which may be associated with the changes of key lipids (TG and PC) and proteins (BYSL, MRTO4, and RRP9). Furthermore, BYSL promotes adipogenic and osteogenic differentiation abilities of radiation-treated hucMSCs via GSK-3β/β-catenin pathway. These findings help explain the response of hucMSCs to radiation and have clinical implications for improving the outcomes of MSC-based therapies after radiotherapy.

Investigative needle core biopsies support multimodal deep-data generation in glioblastoma

Glioblastoma (GBM) is an aggressive primary brain cancer with few effective therapies. Stereotactic needle biopsies are routinely used for diagnosis; however, the feasibility and utility of investigative biopsies to monitor treatment response remains ill-defined. Here, we demonstrate the depth of data generation possible from routine stereotactic needle core biopsies and perform highly resolved multi-omics analyses, including single-cell RNA sequencing, spatial transcriptomics, metabolomics, proteomics, phosphoproteomics, T-cell clonotype analysis, and MHC Class I immunopeptidomics on standard biopsy tissue obtained intra-operatively. We also examine biopsies taken from different locations and provide a framework for measuring spatial and genomic heterogeneity. Finally, we investigate the utility of stereotactic biopsies as a method for generating patient-derived xenograft (PDX) models. Multimodal dataset integration highlights spatially mapped immune cell-associated metabolic pathways and validates inferred cell-cell ligand-receptor interactions. In conclusion, investigative biopsies provide data-rich insight into disease processes and may be useful in evaluating treatment responses.

Associations of blood RNA biomarkers and circulating tumour cells in patients with previously untreated metastatic colorectal cancer

BACKGROUND

In patients with metastatic colorectal cancer, analysis of the number of basal circulating tumour cells (bCTCs) has been shown to be a strong prognostic indicator. In this study, we aim to explore the potential associations between whole blood mRNA and microRNA expression profiles and bCTC counts, tumour mutations and prognosis in untreated metastatic colorectal cancer patients.

METHODS

A total of 151 patients previously screened for inclusion in two clinical trials (VISNÚ1 and VISNÚ2) were enrolled in this study. Real-time quantitative PCR (qPCR) analyses were performed to determine the whole blood expression of selected RNAs (mRNAs and microRNAs) involved in the metastatic process. The CellSearch system was used to enumerate circulating tumour cells. The primary objective was to correlate RNA expression with the number of bCTCs, while the secondary objectives were to investigate the relationship between the levels of circulating RNA biomarkers in whole blood and the clinical, pathological, and molecular characteristics and prognosis of patients with metastatic colorectal cancer.

RESULTS

bCTC count was significantly associated with AGR2 mRNA in the entire cohort of 151 patients. AGR2, ADAR1 and LGR5 were associated with the number of bCTC, both in the subgroup with bCTC ≥ 3 and in the subgroup with native RAS/BRAF/PIK3 CA tumours. In patients with RAS/BRAF/PIK3 CA mutations no correlations with bCTC were detected, but an upregulation of miR-224-5p and the stemness marker LGR5 and a downregulation of immune regulatory CD274 were found. Lower levels of miR-106a-5p/miR-26a-5p were associated with shorter overall survival, with independent statistical significance in the multivariate analysis.

CONCLUSIONS

A correlation was identified between the levels of a subset of whole blood RNAs, including AGR2, ADAR1, and LGR5, and the number of bCTC and RAS/BRAF/PIK3 CA mutational status. Furthermore, another set of whole blood RNAs, specifically miR-106a-5p and miR-26a-5p, was found to be associated with poor prognosis. This may be helpful for risk stratification.

TRIAL REGISTRATION

Clinical Trials Gov. NCT01640405 and NCT01640444. Registered on 13 June 2012. https://clinicaltrials.gov/ .

Physiological and Metabolic Responses of Wheat (Triticum aestivum L.) after One-Generation Exposure to Perfluorooctanesulfonic Acid (PFOS)

The pattern of plant responses, particularly on the seeds/grains metabolite profile, after generational exposure to contaminants is not well documented. Seeds from wheat cultivated in soil amended with PFOS at 0 and 25 mg/kg in the first generation were grown in clean soil to produce daughter plants and seeds in the second generation and assigned treatment combinations of 0-0 mg/kg PFOS and 25-0 mg/kg PFOS. Plant stress and responses including growth and biomass production, chlorophyll content, lipid peroxidation, and enzyme activity were measured over a short exposure period (21 days growth period). Biomass yields, elemental concentration, and grain metabolites were also measured after a long exposure period (92 days growth period). The daughter plants exhibited decreased chlorophyll content and lipid peroxidation in a short exposure period. The elemental concentrations were mostly not affected except for changes in microelements, except B, in the grains. In the metabolomics analysis, grains harvested from plants previously exposed to PFOS (i.e., 25-0 mg/kg PFOS) showed increased abundances of sucrose, linolenic acid, tryptophan, inositol-4-monophosphate, and ferulic acid, perhaps in response to adaptation to former stress. The current findings seem to suggest that one-generation exposure to PFOS does not cause detrimental effects on the next generation after the cessation of exposure. The results provide insights into the effects of generational exposure of plants to PFOS.

Edible Flowers in Modern Gastronomy: A Study of Their Volatilomic Fingerprint and Potential Health Benefits

Given the transformation that gastronomy has undergone in recent years, there is a need to characterize some new foods that are being incorporated into the modern diet. Among them, edible flowers stand out, which are used today not only to enhance the organoleptic properties of gourmet dishes but also for some of the beneficial properties they provide to human health. In this study, the volatilomic fingerprint of seven edible flowers that are used daily in Michelin-starred restaurants on Madeira Island was established. For this purpose, the extraction of volatile organic metabolites (VOMs) was carried out using the headspace solid-phase microextraction (HS-SPME) technique followed by gas chromatography coupled to mass spectrometry (GC-MS). The results showed a wide variability among the analyzed flowers. While fewer VOMs were detected in some flowers, other flowers, such as Viola tricolor and Rosa spp., exhibited a greater number of these compounds. Acmella oleracea had the highest number of detected VOMs. Each of these VOMs contributes to the characteristic aroma representative of the respective flower, highlighting their potential health benefits, as some are known for their anti-inflammatory, antimicrobial, and even anticancer properties.

Do co-solvents used in exposure studies equally perturb the metabolic profile of Daphnia magna?

Dissolution methods such as co-solvents are used to solubilize insoluble compounds in exposure experiments. Several exposure studies have followed the guidelines from the Organization for Economic Co-operation and Development where co-solvents are applied at 0.01% v/v of the total exposure volume. Although no observable apical endpoint abnormalities were reported following these guidelines, little is known about the molecular-level impacts of co-solvents used in exposure studies. A targeted metabolomics approach using liquid chromatography coupled with triple quadrupole mass spectrometry was used to assess Daphnia magna responses to four commonly used co-solvents, including acetone (ACT), acetonitrile (ACN), methanol (MeOH), and dimethyl sulfoxide (DMSO), at three different levels (0.01%, 0.05%, and 0.1% v/v) over 48 hr. Based on the observed metabolic disruptions, exposure to MeOH and DMSO induced higher metabolic perturbations in amino acid levels and associated biochemical pathways in comparison to ACT and ACN exposures. However, as with mixtures, when co-solvents are combined with the pollutants under investigation, there is a possibility for additive, synergistic, or antagonistic interactions. Hence, to examine the possible impairments in co-solvent and pollutant mixtures, ACT and ACN applied at 0.01% v/v were chosen to be tested with phenanthridine (PN). Daphnia magna exposure to PN dissolved in ACT had less disruptions; in contrast to PN prepared in ACN, which triggered a higher degree of antagonism in the D. magna metabolic profile. Consequently, exposing D. magna to ACT applied at 0.01% v/v resulted in the lowest metabolic perturbation in both parts of this study, suggesting that it is the least disruptive co-solvent for molecular-level exposure studies involving D. magna.

Artificial intelligence in traditional Chinese medicine: advances in multi-metabolite multi-target interaction modeling

Traditional Chinese Medicine (TCM) utilizes multi-metabolite and multi-target interventions to address complex diseases, providing advantages over single-target therapies. However, the active metabolites, therapeutic targets, and especially the combination mechanisms remain unclear. The integration of advanced data analysis and nonlinear modeling capabilities of artificial intelligence (AI) is driving the transformation of TCM into precision medicine. This review concentrates on the application of AI in TCM target prediction, including multi-omics techniques, TCM-specialized databases, machine learning (ML), deep learning (DL), and cross-modal fusion strategies. It also critically analyzes persistent challenges such as data heterogeneity, limited model interpretability, causal confounding, and insufficient robustness validation in practical applications. To enhance the reliability and scalability of AI in TCM target prediction, future research should prioritize continuous optimization of the AI algorithms using zero-shot learning, end-to-end architectures, and self-supervised contrastive learning.

Mendelian randomization analysis of blood metabolites and immune cell mediators in relation to GVHD and relapse

BACKGROUND

Graft-versus-host disease (GVHD) and relapse are major complications following allogeneic hematopoietic stem cell transplantation (allo-HSCT). Metabolites play crucial roles in immune regulation, but their causal relationships with GVHD and relapse remain unclear.

METHODS

We utilized genetic variants from genome-wide association studies (GWAS) of 309 known metabolites as instrumental variables to evaluate their causal effects on acute GVHD (aGVHD), gut GVHD, chronic GVHD (cGVHD), and relapse in different populations. Multiple causal inference methods, heterogeneity assessments, and pleiotropy tests were conducted to ensure result robustness. Multivariable MR analysis was performed to adjust for potential confounders, and validation MR analysis further confirmed key findings. Mediation MR analysis was employed to explore indirect causal pathways.

RESULTS

After correction for multiple testing, we identified elevated pyridoxate and proline levels as protective factors against grade 3-4 aGVHD (aGVHD3) and relapse, respectively. Conversely, glycochenodeoxycholate increased the risk of aGVHD3, whereas 1-stearoylglycerophosphoethanolamine had a protective effect. The robustness and stability of these findings were confirmed by multiple causal inference approaches, heterogeneity, and horizontal pleiotropy analyses. Multivariable MR analysis further excluded potential confounding pleiotropic effects. Validation MR analyses supported the causal roles of pyridoxate and 1-stearoylglycerophosphoethanolamine, while mediation MR revealed that pyridoxate influences GVHD directly and indirectly via CD39 + Tregs. Pathway analyses highlighted critical biochemical alterations, including disruptions in bile acid metabolism and the regulatory roles of vitamin B6 derivatives. Finally, clinical metabolic analyses, including direct fecal metabolite measurements, confirmed the protective role of pyridoxate against aGVHD.

CONCLUSIONS

Our findings provide novel insights into the metabolic mechanisms underlying GVHD and relapse after allo-HSCT. Identified metabolites, particularly pyridoxate, may serve as potential therapeutic targets for GVHD prevention and management.

Comprehensive characterization of volatile terpenoids and terpene synthases in Lanxangia tsaoko

Lanxangia tsaoko is widely utilized in human cuisine as a popular flavoring agent due to its distinctive aroma. It also has a long history of use in traditional Chinese medicine. The edible and medicinal properties of L. tsaoko are primarily attributed to its diverse array of volatile metabolites. Previous research has mainly focused on classifying the constituents and their pharmacological activities in L. tsaoko, leaving gaps in comprehensive identification and elucidation of the biosynthetic mechanisms of these metabolites. In this study, we employed a multi-omics approach and functional characterization to investigate the biosynthesis of volatile terpenoids in L. tsaoko. The results demonstrated that terpenoids constituted the highest proportion of volatile compounds in L. tsaoko. Additionally, 42 terpene synthase (TPS) coding genes were identified through genome-wide analysis. Functional characterization revealed that eight LtTPSs effectively catalyzed geranyl pyrophosphate to produce monoterpenoids, while four LtTPSs converted farnesyl pyrophosphate to generate sesquiterpenoids. Genome-wide and single-gene duplication events contributed to functional diversification among LtTPSs with high identity, promoting the diversity of terpenoids. These findings provide a foundation for understanding the biosynthesis of volatile terpenoids in L. tsaoko, enhance the current knowledge of TPS, and contribute to the broader understanding of the biochemical diversity of terpenoids in plants.

Integration of untargeted lipidomics and targeted metabolomics revealed the mechanism of flavor formation in lightly cured sea bass driven via salt

Salt enhances flavor and salinity in Chinese curing; however, excessive use can pose health risks, while reducing NaCl may harm taste. This study utilized targeted and untargeted metabolomics to investigate the intrinsic molecular mechanisms that drive flavor formation in cured sea bass subjected to salt. Glycine, succinic acid, lactic acid and uridine significantly contributed to the taste profile of the cured sea bass. A total of 668 lipid molecules were annotated in the samples, of which 60 were classified as differential lipids. Non-targeted lipidomic analysis identified phosphatidylcholine and phosphatidylethanolamine as the major flavor precursors, constituting 40.12 % of the total. Elevated salt concentrations significantly enhanced the production and accumulation of key differential volatile flavor components, including 1-octen-3-ol, 2-undecanone and 2-pentylfuran. Thus, salt facilitated the degradation and oxidation of lipids, leading to the formation of key flavor compounds that contribute to the enhancement of the flavor profile of cured sea bass.

Ecotoxicological mechanism of glyphosate on Moerella iridescens: Evidence from enzyme, histology and metabolome

This study aimed to elucidate the regulatory mechanisms underlying the toxic effects of glyphosate (GLY) on rainbow clam (M. iridescens), with implications for their culture and conservation. GLY residues in aquatic systems raise significant environmental and public health concerns, yet the underlying mechanisms remain largely elusive. In this study, M. iridescens were acutely exposed to GLY at various concentrations (0, 2.34, 5.45, 12.74, 29.74, and 69.46 mg/L) for 7 days. Gill and hepatopancreas samples were collected to assess oxidative stress status and histopathological examination. Additionally, three concentration groups low concentration (LC) group at 2.34 mg/L, medium concentration (MC) group at 12.74 mg/L, and high concentration (HC) group at 69.46 mg/L were selected for metabolomic analysis. The findings indicated that GLY exposure led to oxidative stress and structural changes in tissues. The metabolomic analysis suggested that GLY exposure exacerbates inflammatory responses and disrupts endocrine function, and sex hormones.

Characterising Sex-Specific Metabolite Differences in New Zealand Geoduck (Panopea zelandica) Using LC-MS/MS Metabolomics

Geoduck aquaculture is becoming a key component in meeting international market demand, given the natural and regulatory restrictions on wild geoduck supply. Geoduck clams are not sexually dimorphic, making it practically unfeasible to distinguish between males and females prior to a spawning event. To facilitate increased production of geoduck, a better understanding of reproductive biology and associated targeted bio-markers is required. In this study, metabolomics was utilised as a research tool to distinguish between metabolites related to male and female New Zealand geoduck (Panopea zelandica), gill and muscle samples collected from broodstock individuals housed in an experimental hatchery. A total of 17 metabolites were detected, showing significant differences between sexes. The findings indicate that metabolites associated with lipid biosynthesis were increased in female clams to support reproductive functions. An increase in carbohydrate-linked metabolic pathways was detected in male geoduck, arguably to sustain sperm production. Taurine has been reported as a biomarker to distinguish between male and female bivalves in other studies and is confirmed within this study, with significant elevation in male adductor muscle tissue. Moreover, male geoduck had increased purine and pyrimidine biosynthesis, supporting energy needs. This study provides useful sex biomarkers for future breeding strategies of P. zelandica.

Remodeling of Cellular Respiration and Insulin Signaling Are Part of a Shared Stress Response in Divergent Bee Species

The honey bee (Apis mellifera) is of paramount importance to human activities through the pollination services they provide in agricultural settings. Honey bee colonies in the United States have suffered from an increased rate of annual die-off in recent years, stemming from a complex set of interacting stressors that remain poorly described. Defining the cellular responses that are perturbed by divergent stressors represents a key step in understanding these synergies. We found that multiple model stressors induce upregulated expression of the lactate dehydrogenase (Ldh) gene in the midgut of the eusocial honey bee and that the Ldh gene family is expanded in diverse bee species. Alterations in Ldh expression were concomitant with changes in the expression of other genes involved in cellular respiration and genes encoding insulin/insulin-like growth factor signaling (IIS) pathway components. Additionally, changes in metabolites in the midgut after stress, including increased levels of lactate, linked metabolic changes with the observed changes in gene expression. Select transcriptional changes in response to stress were similarly observed in the solitary alfalfa leafcutting bee (Megachile rotundata). Thus, increased Ldh expression may be part of a core stress response remodeling cellular respiration and insulin signaling. These findings suggest that a conserved cellular response that regulates metabolic demands under diverse stressful conditions may play a protective role in bees regardless of life history.

Contribution of metabolomics to the taxonomy and systematics of octocorals from the Tropical Eastern Pacific

Octocorals are sessile invertebrates that play a key role in marine habitats, with significant diversity in the Tropical Eastern Pacific, especially in Ecuador's shallow waters. This study focuses on the most representative octocorals within the Marine Protected Area El Pelado, Santa Elena, Ecuador, as a part of a marine biodiscovery project employing an integrative approach. While molecular techniques have advanced, challenges persist in distinguishing closely related species. Octocorals produce a wide range of compounds, characterized by unique chemical structures and diverse biological properties. Therefore, the main objective of this study was to assess the potential of metabolomics and advanced analytical techniques to analyze the metabolome of these organisms, aiming to refine species classification and improve understanding of octocoral systematics in this region. Untargeted metabolomics effectively discriminates 12 octocoral species across five genera: Muricea, Leptogorgia, Pacifigorgia, Psammogorgia, and Heterogorgia, with notable differentiation between species within the genus Muricea, reinforcing its utility as an additional data set for species characterization. Secondary metabolites such as sterols, steroids, and terpenes (furanocembranolides and sesquiterpenes), were identified in Leptogorgia and Muricea. Overall, this method enabled the identification of 11 known species and a potentially new one, Leptogorgia cf. alba, confirming the extreme diversity of this group in the Tropical Eastern Pacific and within the Ecuadorian marine ecosystem. The study highlights the value of metabolomics in octocoral systematics and encourages for its broader application in marine biodiversity research.

Metabolic Profiles of Encapsulated Chondrocytes Exposed to Short-Term Simulated Microgravity

The mechanism by which chondrocytes respond to reduced mechanical loading environments and the subsequent risk of developing osteoarthritis remains unclear. This is of particular concern for astronauts. In space the reduced joint loading forces during prolonged microgravity (10-6 g) exposure could lead to osteoarthritis (OA), compromising quality of life post-spaceflight. In this study, we encapsulated human chondrocytes in an agarose gel of similar stiffness to the pericellular matrix to mimic the cartilage microenvironment. We then exposed agarose-chondrocyte constructs to simulated microgravity (SM) for four days using a rotating wall vessel (RWV) bioreactor to better assess the cartilage health risks associated with spaceflight. Metabolites extracted from media and agarose gel constructs were analyzed on liquid chromatography-mass spectrometry. Global metabolomic profiling detected a total of 1205 metabolite features, with 497 significant metabolite features identified by ANOVA (FDR-corrected p-value < 0.05). Specific metabolic shifts detected in response to SM exposure resulted in clusters of co-regulated metabolites, with glutathione, nitrogen, histidine, vitamin B3, and aminosugars metabolism identified by variable importance in projection scores. Microgravity-induced metabolic shifts in gel constructs and media were indicative of protein synthesis, energy and nucleotide metabolism, and oxidative catabolism. Microgravity associated-metabolic shifts were consistent with our previously published early osteoarthritic metabolomic profiles in human synovial fluid, suggesting that even short-term exposure to microgravity (or other reduced mechanical loading environments) may lead to the development of OA. This work further suggests the potential to detect these metabolic perturbations in synovial fluid in vivo to ascertain osteoarthritis risk in astronauts.

Genetic regulation and variation of fetal plasma metabolome in the context of sex, paternal breeds and variable fetal weight

Metabolic processes in fetuses can significantly influence piglet weight at birth. Understanding the genetic determinants of systemic metabolism is crucial for uncovering how genetic and molecular pathways impact biological mechanisms, particularly during the fetal phase. We present data on 1112 plasma metabolites using untargeted ultra-high performance liquid chromatography-tandem mass spectrometry methods, of 260 backcross (BC) fetuses from two sires' breeds at 63 days post-conception. Eight chemical superclasses have been identified, with lipids accounting for the majority of metabolites. Genomic heritability (h²) was estimated for each metabolite, revealing that 50% had h² values below 0.2, with a higher average in the amino acid class compared with the lipid. We annotated 448 significant metabolite quantitative trait loci associated with 10 metabolites, primarily lipids, indicating strong genetic regulation. Additionally, metabolite associations with sex, fetal weight and sire's breed were explored, revealing significant associations for 354 metabolites. Fetal weight influenced the largest number of metabolites, particularly glycerophospholipids and sphingolipids, emphasizing the genetic and metabolic complexity underlying fetal development. These findings enhance our understanding of the genetic regulation of metabolite levels and their associations with key phenotypic traits in fetuses, providing insights into metabolic pathways, potential biomarkers and serving as a baseline dataset for metabolomics studies of fetuses.

Utilization of Bone Alkaline Phosphatase (BAP) and Tartrate Resistant Acid Phosphatase (TRAP) as Biomarkers of Eggshell Quality and Bone Metabolism in Broiler Breeders and Progeny

Eggshell breakage and broiler bone disorders are major problems for the breeder and broiler industries which are linked to mineral metabolism and animal genetics. The purpose of this work was to discover the link between individual animal phenotypic differences in mineral metabolism against concentrations of novel plasma biomarkers including tartrate resistant acid phosphatase (TRAP) and bone alkaline phosphatase (BAP). A subset of hens were selected from a flock of Cobb 500 breeders with the best or worst eggshell quality based upon dual energy x-ray absorptiometry (DEXA) and specific gravity (SG). Breeders were defined as having good eggshell quality (SG ≥ 1.080), or poor eggshell quality (SG < 1.080). Progeny hatched from breeders with good or poor eggshell quality were reared to 2 week of age and blood and bone samples were obtained after euthanasia. In both breeders and progeny, plasma concentrations of BAP and TRAP were measured, and bone mineral density was evaluated by DEXA. Results showed that breeders selected for eggshell quality had significantly different plasma concentrations of BAP (Good = 326.5 pg/mL, Poor = 253.2 pg/mL), and TRAP activity (Good = 2203 U, Poor = 4985 U). Breeders selected for eggshell quality produced progeny with different bone breaking strength (Good = 1.61 kg/mm, Poor = 1.47 kg/mm), tibia ash (Good = 45.9%, Poor = 42.2%), plasma BAP (Good = 372.3 pg/mL, Poor = 312.4 pg/mL), and lower plasma TRAP activity (Good = 18010 U, Poor = 23590 U). These data suggest that there is a strong correlation between the eggshell quality of breeders, performance and bone strength of progeny, and plasma of concentrations of BAP and TRAP in both breeder hens and progeny.

Soybean tolerance to waterlogging is achieved by detoxifying root lactate via lactate dehydrogenase in leaves and metabolizing malate and succinate

Waterlogging is a significant stressor for crops, particularly in lowland regions where soil conditions exacerbate the problem. Waterlogged roots experience hypoxia, disrupting oxidative phosphorylation and triggering metabolic reorganization to sustain energy production. Here, we investigated the metabolic aspects that differentiate two soybean sister lines contrasting for waterlogging tolerance. After 11 days of waterlogging, roots of the tolerant line (PELBR15-7015C) modulated their fermentative metabolism by exporting key metabolites (lactate, malate, and succinate) to the shoot. These metabolites were metabolized in the leaves, supporting photosynthesis and facilitating sugar export to the roots, sustaining a root-shoot-root cycling process. In contrast, the sensitive line (PELBR15-7060) entered a quiescent state, depleting its carbon stock and accumulating protective metabolites. Our study reveals that long-term waterlogging tolerance is primarily achieved through lactate detoxification in the leaves, along with malate and succinate metabolism, enabling root metabolism to withstand hypoxia. This mechanism offers new insights into crop resilience under waterlogged conditions, with implications for modern agriculture as climate change intensifies the frequency and duration of such stress events.

Metabolomic study for the identification of symptomatic carotid plaque biomarkers

Carotid artery stenosis is mainly produced due to the progressive accumulation of atherosclerotic plaque in the vascular wall. The atherosclerotic plaque is characterized by the accumulation of lipids, low density proteins, expression of chemokines and adhesion molecules, and migration of monocytes and lymphocytes into the plaque. Its rupture can produce stroke, but embolic propensity depends principally on the composition and vulnerability of plaque rather than the severity of stenosis. It is important, then, to ascertain which patients with carotid artery stenosis have a greater risk of developing neurological symptomatology. Here, we present a metabolomic study by using nuclear magnetic resonance (NMR) spectroscopy in atheroma plaque and serum samples from patients with recently symptomatic and asymptomatic carotid stenosis to search for metabolites that could be used as biomarkers associated with plaque vulnerability and subsequent risk of rupture. Thirty-eight atheromatous plaque samples (24 asymptomatic patients and 14 symptomatic) and 70 serum samples (43 asymptomatic and 27 symptomatic) were studied by NMR spectroscopy. The data were analysed using multivariate statistics (PLS-DA) to determine a model to discriminate between symptomatic and asymptomatic samples (atheroma plaques and sera). The calculated PLS-DA models showed a 100 % sensitivity and a 96.6 % specificity for the cross validation to discriminate between symptomatic and asymptomatic plaques, and 88.37 % sensitivity and 77.78 % specificity when serum samples were analysed. According to the results of our multivariate and univariate analysis, the most discriminative metabolites for plaque vulnerability were threonine in serum samples, and glutamate in plaque samples. Also, an analysis of the main metabolic pathways involved in plaque vulnerability revealed that d-glutamine and d-glutamate metabolism, and phenylalanine, tyrosine, and tryptophan biosynthesis were the most affected pathways in plaque and serum, respectively.

Parallel multiOMIC analysis reveals glutamine deprivation enhances directed differentiation of renal organoids

Metabolic pathways play a critical role in driving differentiation but remain poorly understood in the development of kidney organoids. In this study, parallel metabolite and transcriptome profiling of differentiating human pluripotent stem cells (hPSCs) to multicellular renal organoids revealed key metabolic drivers of the differentiation process. In the early stage, transitioning from hPSCs to nephron progenitor cells (NPCs), both the glutamine and the alanine-aspartate-glutamate pathways changed significantly, as detected by enrichment and pathway impact analyses. Intriguingly, hPSCs maintained their ability to generate NPCs, even when deprived of both glutamine and glutamate. Surprisingly, single cell RNA-Seq analysis detected enhanced maturation and enrichment for podocytes under glutamine-deprived conditions. Together, these findings illustrate a novel role of glutamine metabolism in regulating podocyte development.

Deep transcriptome and metabolome analysis to dissect untapped spatial dynamics of specialized metabolism in Saussurea costus (Falc.) Lipsch

Saussurea costus (Falc.) is an endangered medicinal plant possessing diverse phytochemical compounds with clinical significance and used to treat numerous human ailments. Despite the source of enriched phytochemicals, molecular insights into spatialized metabolism are poorly understood in S. costus. This study investigated the dynamics of organ-specific secondary metabolite biosynthesis using deep transcriptome sequencing and high-throughput UHPLC-QTOF based untargeted metabolomic profiling. A de novo assembly from quality reads fetched 59,725 transcripts with structural (53.02%) and functional (66.13%) annotations of non-redundant transcripts. Of the 7,683 predicted gene families, 3,211 were categorized as 'single gene families'. Interestingly, out of the 4,664 core gene families within the Asterids, 4,560 families were captured in S. costus. Organ-specific differential gene expression analysis revealed significant variations between leaves vs. stems (23,102 transcripts), leaves vs. roots (30,590 transcripts), and roots vs. stems (21,759 transcripts). Like-wise, putative metabolites (PMs) were recorded with significant differences in leaves vs. roots (250 PMs), leaves vs. stem (350 PMs), and roots vs. stem (107 PMs). The integrative transcriptomic and metabolomic analysis identified organ-specific differences in the accumulation of important metabolites, including secologanin, menthofuran, taraxerol, lupeol, acetyleugenol, scopoletin, costunolide, and dehydrocostus lactone. Furthermore, a global gene co-expression network (GCN) identified putative regulators controlling the expression of key target genes of secondary metabolite pathways including terpenoid, phenylpropanoid, and flavonoid. The comprehensive functionally relevant genomic resource created here provides beneficial insights for upscaling targeted metabolite biosynthesis through genetic engineering, and for expediting association mapping efforts to elucidate the casual genetic elements controlling specific bioactive metabolites.

Combined metabolome and transcriptome analysis provides molecular insights into reproductive process in Chuanxiang Black and Landrace pigs

Testes are crucial for male reproduction, and transcriptomic and metabolomic analyses can help identify genes and pathways linked to reproductive performance differences in pig breeds. The present study was conducted to identify the differentially expressed genes and differentially accumulated metabolites (DAMs) through transcriptomic and metabolomic analyses of testicular tissues in Chuanxiang Black and Landrace pigs. Six testis tissue samples from each pig breed were used for transcriptomic analysis. Further liquid chromatography-mass spectrometry analysis was performed for targeted metabolomic analysis to identify differential metabolites in both breeds. RNA-sequencing data identified a total of 6,233 DEGs, including 3,417 upregulated and 2,816 downregulated genes in Chuanxiang Black compared to Landrace pigs. Comparative pathway enrichment analyses revealed that many DEGs and DAMs were associated with critical reproductive pathways, especially those related to male gametogenesis, spermatogenesis, sexual reproduction, development, and reproductive processes. Three major pathways related to signal transduction (PI3K-Akt, Rap1, and MAPK signaling pathways), lipid metabolism (linoleic acid and arachidonic acid metabolism), and cytokine-cytokine receptor interaction were identified as differentially enriched pathways in Chuanxiang Black pigs. Differential circRNA target gene enrichment analysis revealed 4,179 DEGs, including 3,022 genes involved in biological processes, 477 in cellular components, and 680 in molecular functions. Differential analysis of miRNA between the two groups revealed 2,512 DEGs, including 1,628 upregulated and 884 downregulated genes. Both miRNA and circRNA were involved in enriched KEGG pathways mainly including signaling pathways (cAMP signaling pathways, calcium signaling pathways), endocrine secretion (aldosterone synthesis and secretion and GnRH secretion), and signaling molecules and interaction (ECM-receptor interaction). These findings revealed that both circRNA and miRNA play a crucial role in regulating the differential gene expression related to reproductive processes in Chuanxiang Black compared to Landrace pigs.

Toxicity of Pentachlorophenol Exposure on Male and Female Heteropneustes fossilis Investigated Using NMR-Based Metabolomics Approach

Pentachlorophenol (PCP) is one of the most common chlorophenols utilized in numerous industrial processes, including the production of dyes, pesticides, wood preservatives, disinfectants, antiseptics, and medicines because it has fungicidal and bactericidal characteristics. Previous studies on catfish (Heteropneustes fossilis) revealed that PCP acts as a potent endocrine disruptor and also causes behavioral changes in a concentration-dependent manner. However, the toxicological effects of PCP have not been compared between male and female catfish. The present study aims to investigate the toxic effects of PCP on catfish through histopathological changes, oxidative stress, and serum metabolomics after 60 days of exposure. Chronic exposure to sublethal concentrations of PCP resulted in significant histopathological alterations in the liver and gonad, including leukocyte infiltration, hepatocyte degeneration, follicular layer dissolution, and abnormal sperm distribution. Increased levels of lipid peroxidation and hydrogen peroxide, along with decreased antioxidant enzyme activity, were observed in PCP-exposed groups. A 1H NMR-based metabolomics approach was employed to investigate the toxic effects of PCP on catfish serum, revealing alterations in various metabolites, including amino acids, organic acids, glucose, cholesterol, and neurotransmitters, in a dose-dependent manner. Multivariate partial least-squares discriminant analysis (PLS-DA) identified metabolic changes associated with oxidative stress, disruption in hormone synthesis and reproduction, disturbance in osmoregulation and membrane stabilization, energy metabolism disorder, amino acid metabolism disorder, and neurotransmitter imbalance in PCP-exposed catfish. This study demonstrates the efficacy of metabolomics in elucidating the toxicity and underlying mechanisms of wood preservatives like PCP, providing valuable insights for risk assessment in toxicology research. Overall, these findings contribute to our understanding of the toxicological effects of PCP exposure on aquatic organisms and highlight the potential of histology, oxidative stress, and metabolomics in assessing environmental contaminants' risks.

Polar Metabolite Profiles Distinguish Between Early and Severe Sub-Maintenance Nutritional States of Wild Bighorn Sheep

Background: Understanding the metabolic adaptations of wild bighorn sheep (Ovis c. canadensis) to nutritional stress is crucial for their conservation. Methods: This study employed 1H nuclear magnetic resonance (NMR) metabolomics to investigate the biochemical responses of these animals to varying sub-maintenance nutritional states. Serum samples from 388 wild bighorn sheep collected between 2014 and 2017 from December (early sub-maintenance) through March (severe sub-maintenance) across Wyoming and Montana were analyzed. Multivariate statistics and machine learning analyses were employed to identify characteristic metabolic patterns and metabolic interactions between early and severe sub-maintenance nutritional states. Results: Significant differences were observed in the levels of 15 of the 49 quantified metabolites, including formate, thymine, glucose, choline, and others, pointing to disruptions in one-carbon, amino acid, and central carbon metabolic pathways. These metabolites may serve as indicators of critical physiological processes such as nutritional intake, immune function, energy metabolism, and protein catabolism, which are essential for understanding how wild bighorn sheep adapt to nutritional stress. Conclusions: This study has generated valuable insights into molecular networks underlying the metabolic resilience of wild bighorn sheep, highlighting the potential for using specific biochemical markers to evaluate nutritional and energetic states in free-ranging ungulates. These insights may help wildlife managers and ecologists compare populations across different times in seasonal cycles, providing information to assess the adequacy of seasonal ranges and support conservation efforts. This research strengthens our understanding of metabolic adaptations to environmental stressors in wild ruminants, offering a foundation for improving management practices to maintain healthy bighorn sheep populations.

Alterations in bile acid metabolites associated with pathogenicity and IVIG resistance in Kawasaki disease

Background

Kawasaki disease (KD) primarily affects children as an acute systemic vasculitis. Numerous studies indicated an elevated risk of cardiovascular disease due to metabolic disturbances. Despite this knowledge, the specific metabolic modes involved in KD remain unclear.

Methods

We examined the metabolome of individuals with 108 KD and 52 non-KD controls (KD vs. nKD) by ultraperformance liquid chromatography (UPLC) and tandem mass spectrometry (MS).

Results

Differential analysis uncovered the disturbed production of bile acids and lipids in KD. Furthermore, we investigated the impact of treatment, intravenous immunoglobulin (IVIG) resistance, and coronary artery (CA) occurrence on the metabolome. Our findings suggested that IVIG treatment alters the lipid and amino acid metabolism of KD patients. By orthogonal projections to latent structures discriminant analysis (OPLS-DA), there was no significant difference between the coronary injury groups and non-coronary injury groups, and IVIG resistance didn't appear to cause the metabolic change in KD patients.

Conclusions

Patients with KD exhibit metabolic abnormalities, particularly in bile acids and lipids. IVIG interventions may partially ameliorate these lipid abnormalities.

Starve a cold or feed a fever? Identifying cellular metabolic changes following infection and exposure to SARS-CoV-2

Viral infections induce major shifts in cellular metabolism elicited by active viral replication and antiviral responses. For the virus, harnessing cellular metabolism and evading changes that limit replication are essential for productive viral replication. In contrast, the cellular response to infection disrupts metabolic pathways to prevent viral replication and promote an antiviral state in the host cell and neighboring bystander cells. This competition between the virus and cell results in measurable shifts in cellular metabolism that differ depending on the virus, cell type, and extracellular environment. The resulting metabolic shifts can be observed and analyzed using global metabolic profiling techniques to identify pathways that are critical for either viral replication or cellular defense. SARS-CoV-2 is a respiratory virus that can exhibit broad tissue tropism and diverse, yet inconsistent, symptomatology. While the factors that determine the presentation and severity of SARS-CoV-2 infection remain unclear, metabolic syndromes are associated with more severe manifestations of SARS-CoV-2 disease. Despite these observations a critical knowledge gap remains between cellular metabolic responses and SARS-CoV-2 infection. Using a well-established untargeted metabolomics analysis workflow, we compared SARS-CoV-2 infection of human lung carcinoma cells. We identified significant changes in metabolic pathways that correlate with either productive or non-productive viral infection. This information is critical for characterizing the factors that contribute to SARS-CoV-2 replication that could be targeted for therapeutic interventions to limit viral disease.

Plant-nanoparticles enhance anti-PD-L1 efficacy by shaping human commensal microbiota metabolites

Diet has emerged as a key impact factor for gut microbiota function. However, the complexity of dietary components makes it difficult to predict specific outcomes. Here we investigate the impact of plant-derived nanoparticles (PNP) on gut microbiota and metabolites in context of cancer immunotherapy with the humanized gnotobiotic mouse model. Specifically, we show that ginger-derived exosome-like nanoparticle (GELN) preferentially taken up by Lachnospiraceae and Lactobacillaceae mediated by digalactosyldiacylglycerol (DGDG) and glycine, respectively. We further demonstrate that GELN aly-miR159a-3p enhances anti-PD-L1 therapy in melanoma by inhibiting the expression of recipient bacterial phospholipase C (PLC) and increases the accumulation of docosahexaenoic acid (DHA). An increased level of circulating DHA inhibits PD-L1 expression in tumor cells by binding the PD-L1 promoter and subsequently prevents c-myc-initiated transcription of PD-L1. Colonization of germ-free male mice with gut bacteria from anti-PD-L1 non-responding patients supplemented with DHA enhances the efficacy of anti-PD-L1 therapy compared to controls. Our findings reveal a previously unknown mechanistic impact of PNP on human tumor immunotherapy by modulating gut bacterial metabolic pathways.

Comprehensive approaches to heavy metal bioremediation: Integrating microbial insights and genetic innovations

The increasing contamination of ecosystems with heavy metals (HMs) due to industrial activities raises significant jeopardies to environmental health and human well-being. Addressing this issue, recent advances in the field of bioremediation have highlighted the potential of plant-associated microbiomes and genetically engineered organisms (GEOs) to mitigate HMs pollution. This review explores recent advancements in bioremediation strategies for HMs detoxification, with particular attention to omics technologies such as metagenomics, metabolomics, and metaproteomics in deepening the understanding of microbial interactions and their potential for neutralizing HMs. Additionally, Emerging strategies and technologies in GEOs and microorganism-aided nanotechnology have proven to be effective bioremediation tools, particularly for alleviating HM contamination. Despite the promising strategies developed in laboratory settings, several challenges impede their practical application, including ecological risks, regulatory limitations, and public concerns regarding the practice of genetically modified organisms. A comprehensive approach that involves interdisciplinary research is essential to enhance the efficacy and safety of bioremediation technologies. This approach should be coupled with robust regulatory frameworks and active public engagement to ensure environmental integrity and societal acceptance. This review underscores the importance of developing sustainable bioremediation strategies that align with ecological conservation goals and public health priorities.

Unraveling the shifts in the belowground microbiota and metabolome of Pinus pinaster trees affected by forest decline

Pinus pinaster Aiton (maritime pine) stands are suffering a generalized deterioration due to different decline episodes throughout all its distribution area. It is well known that external disturbances can alter the plant associated microbiota and metabolome, which ultimately can entail the disruption of the normal growth of the hosts. Notwithstanding, very little is known about the shifts in the microbiota and the metabolome in pine trees affected by decline. The aim of our work was to unravel whether bacterial and fungal communities inhabiting the rhizosphere and root endosphere of P. pinaster trees with symptoms of decline and affected by Matsucoccus feytaudi in the National Park of Sierra Nevada (Granada, Spain) showed alterations in the structure, taxonomical profiles and associative patterns. We also aimed at deciphering potential changes in the rhizosphere and root metabolome. Trees infected by M. feytaudi and healthy individual harbored distinct microbial communities at both compositional and associative patterns. Unhealthy trees were enriched selectively in certain plant growth promoting microorganisms such as several ectomycorrhizal fungi (Clavulina) and Streptomyces, while other beneficial microorganisms (Micromonospora) were more abundant in unaffected pines. The rhizosphere of unhealthy trees was richer in secondary metabolites involved in plant defense than healthy pines, while the opposite trend was detected in root samples. The abundance of certain microorganisms was significantly correlated with several antimicrobial metabolites, thus, being all of them worthy of further isolation and study of their role in forest decline.

Integrated physiological and transcriptomic analysis uncovers the mechanism of moderate nitrogen application on promoting the growth and (-)-borneol accumulation of Blumea balsamifera

Introduction

Blumea balsamifera, a half-woody plant belonging to the Asteraceae family, is valued as both a medicinal and industrial crop primarily for its phytochemical component, (-)-borneol. Nitrogen (N) is essential for regulating the growth of B. balsamifera and the biosynthesis of (-)-borneol; however, the molecular mechanisms by which N influences these processes remain inadequately understood. This study aimed to elucidate the effects of N on growth and (-)-borneol synthesis at the molecular level.

Methods

A field experiment was conducted in which B. balsamifera plants were fertilized with three different nitrogen regimes: 0 kg N ha-1 (control, CK), 150 kg N ha-1 (N1 treatment), and 300 kg N ha-1 (N2 treatment). Physiological and biochemical assessments were performed to evaluate the growth and metabolic responses of the plants under these varying N conditions. Additionally, transcriptome sequencing of leaves of B. balsamifera was conducted to elucidate the underlying molecular mechanisms involved.

Results and discussion

The results indicated that both the N1 and N2 treatments significantly promoted the growth of B. balsamifera, with the 150 kg N ha-1 treatment (N1) resulting in the most favorable effects. Under the N1 treatment, the leaves harvested in October, November, and December exhibited the highest accumulation of (-)-borneol, with yields of 782 mg plant-1, 1102 mg plant-1, and 1774 mg plant-1, respectively, which were significantly different from those observed in the CK and N2 treatments. Comparative transcriptome analysis revealed a total of 6,714 differentially expressed genes (DEGs). Notably, several DEGs associated with auxin signaling and N metabolism were upregulated in the N1 and N2 treatments. In contrast, many DEGs related to carbohydrate metabolism, terpenoid backbone biosynthesis, monoterpenoid biosynthesis, and flavonoid biosynthesis were significantly upregulated in the CK treatment. Moreover, potential transcription factors (TFs) that may link N nutrition with the synthesis of medicinal components were identified. Our study demonstrates that N can enhance the accumulation of (-)-borneol in B. balsamifera when applied in appropriate quantities. These findings provide a comprehensive understanding of the relationship between N nutrition and (-)-borneol yield in B. balsamifera, offering valuable insights for future cultivation practices.

Enalomics: A Mass Spectrometry-Based Approach for Profiling, Identifying, and Semiquantifying Enals in Biological Samples

Human cells generate a bulk of aldehydes during lipid peroxidation (LPO), influencing critical cellular processes, such as oxidative stress, protein modification, and DNA damage. Enals, highly reactive α,β-unsaturated aldehydic metabolites, are implicated in various human pathologies, especially neurodegenerative disorders, cancer, and cardiovascular diseases. Despite their importance, endogenous enals remain poorly characterized, primarily due to their instability and low abundance. Herein, we introduced "enalomics," a mass spectrometry (MS)-based approach for profiling, identifying, and semiquantifying enals in biological samples. Derivatization with 2,4-dinitrophenylhydrazine and treatment with ascorbic acid stabilized enals in biological matrices and provided a unique MS fragment ([M-H-47]-) for reliable enal identification. Utilizing precursor ion scanning, dynamic multiple reaction monitoring, high-resolution MS, and mathematical correlations between retention times and carbon numbers of enals, we identified 157 enals (127 newly reported) with tissue-specific profiles in rats and 29 enals (24 newly reported) in human plasma. To the best of our knowledge, this represents the comprehensive analysis of enals, i.e., "enalomics," in biological samples. Enalomics demonstrated significant alterations in enal metabolism in rats with myocardial injury, highlighting the potential of medium- and short-chain plasma enals as sensitive diagnostic biomarkers. Further application of enalomics in patients with myocardial infarction (MI) identified 14 plasma diagnostic biomarkers. Receiver operating characteristic curves showed good discrimination (area under curve ≥ 0.8603, p ≤ 0.0043). This research advances the understanding of LPO products and emphasizes the roles of enals in human diseases, offering good prospects for early screening, diagnosis, and clinical interventions targeting LPO products in MI patients.

Metabolome Alterations Associated with Three-Month Sitting-Time Reduction Among Sedentary Postmenopausal Latinas with Cardiometabolic Disease Risk

Background: Incidence of cardiometabolic disease among U.S. Hispanics/Latinos is higher than in non-Hispanic Whites. Prolonged sitting duration is prevalent in older adults, and compounded with menopause, greatly increases cardiometabolic risk in postmenopausal women. Metabolomic analyses of interventions to reduce sitting are lacking and mechanistic understanding of health-promoting behavior change in postmenopausal Latinas is needed. Methods: To address this knowledge gap, an exploratory analysis investigated the plasma metabolome impact of a 12-week increased standing intervention among sedentary postmenopausal Latinas with overweight or obesity. From a parent-randomized controlled trial, a subset of Best Responders (n = 43) was selected using parameters of highest mean change in sitting bout duration and total sitting time; baseline variable-Matched Controls (n = 43) were selected using random forest modeling. Targeted LC-MS/MS analysis of archived baseline and 12-week plasma samples was conducted. Metabolite change was determined using a covariate-controlled general linear model and multivariate testing was performed. A false discovery rate correction was applied to all analyses. Results: Best Responders significantly changed time sitting (-110.0 ± 11.0 min; -21%), standing (104.6 ± 10.1 min; 40%), and sitting in bouts >30 min (-102.3 ± 13.9 min; -35%) compared to Matched Controls (7.1 ± 9.8 min, -7.8 ± 9.0 min, and -4.6 ± 12.7 min, respectively; all p < 0.001). Twelve-week metabolite change was significantly different between the two groups for 24 metabolites (FDR < 0.05). These were primarily related to amino acid metabolism, improved blood flow, and ATP production. Enzyme enrichment analysis predicted significant changes regulating glutamate, histidine, phenylalanine, and mitochondrial short-chain fatty acid catabolism. Pathway analysis showed significant intervention effects on glutamate metabolism and phenylalanine, tyrosine, and tryptophan biosynthesis, potentially indicating reduced cardiometabolic disease risk. Conclusions: Replacing nearly two hours of daily sitting time with standing and reduced prolonged sitting bouts significantly improved metabolomic profiles associated with cardiometabolic risk among postmenopausal Latinas.

Myricetin protects mice against colitis by activating aryl hydrocarbon receptor signaling pathway

Objective

Myricetin is a bioactive compound in many edible plants. We have previously demonstrated that myricetin could significantly protect mice against colitis by regulating Treg/Th17 balance, while underlying mechanism remains unclear. The current study aimed to unravel the potential regulating mechanism of myricetin.

Methods

The concentrations of 22 amino acids in colon were determined using HPLC-MS/MS and principal component analysis (PCA) was performed on the data. MetaboAnalyst was used to detect potential biological pathway influenced by myricetin. The results were further verified using qPCR, molecular docking method, and AhR inhibitor.

Results

Studies had found that the biosynthesis of phenylalanine, tyrosine, and tryptophan; phenylalanine metabolism; and histidine metabolism were the most important pathways related to myricetin. Therefore, the aryl hydrocarbon receptor (AhR), which is closely related to the metabolism of tryptophan, phenylalanine, and tyrosine, was postulated to be the underlying signaling pathways. Furthermore, administration of myricet in significantly increased the relative expressions of CYP1A1 and CYP1B1, whereas AhR inhibitor abolished the amelioration of myricetin on DSS-induced colitis. Moreover, AhR inhibitor weakened the regulatory effect of myricetin on Treg/Th17 balance. Furthermore, the results obtained by the molecular docking method speculated that myricetin could bind to AhR as a ligand and activate AhR.

Conclusion

The results suggested that myricetin could exert its protection against dextran sulfate sodium (DSS)-induced colitis by activating AhR signaling pathway.

Effect of H2O2 induced oxidative stress on volatile organic compounds in differentiated 3T3-L1 cells

Oxidative stress (OS) refers to the disruption in the balance between free radical generation and antioxidant defenses, leading to potential tissue damage. Reactive oxygen species (ROS) can interact with biological components, triggering processes like protein oxidation, lipid peroxidation, or DNA damage, resulting in the generation of several volatile organic compounds (VOCs). Recently, VOCs provided new insight into cellular metabolism and can serve as potential biomarkers. The objective is to investigate the impact of OS on cell metabolism by analyzing the release or alterations of VOCs in the headspace of differentiated 3T3-L1 adipocytes. An OS model in differentiated 3T3-L1 cell lines was constructed using hydrogen peroxide (H2O2) treatment. The effect of OS on cell metabolism was analyzed by detecting VOCs in the headspace of the cells using solid phase micro extraction (SPME) and gas chromatography-mass spectrometry (GCMS). Our findings indicate that H2O2 concentrations exceeding 300 µM induce significant OS, leading to adipocyte apoptosis, as evidenced by various assays. Of the twenty VOCs identified, ten were upregulated in the cells. VOCs such as diphenyl ether, 1,3,5-trioxane, 5-methyl tridecane, 2-ethyl-1-hexanol, and 2,4-di-tert-butyl phenol emerged as potential biomarkers for OS. This study demonstrates that elevated OS alters VOC profiles in differentiated 3T3-L1 adipocytes, providing insights into the effects of OS on adipose tissue and identifying potential OS biomarkers.

Essential oil and furanosesquiterpenes from myrrh oleo-gum resin: a breakthrough in mosquito vector management

Mosquitoes (Diptera: Culicidae) are vectors of various pathogens of public health concern and replacing conventional insecticides remains a challenge. In this regard, natural products represent valuable sources of potential insecticidal compounds, thus increasingly attracting research interest. Commiphora myrrha (T.Nees) Engl. (Burseraceae) is a medicinal plant whose oleo-gum resin is used in food, cosmetics, fragrances, and pharmaceuticals. Herein, the larvicidal potential of its essential oil (EO) was assessed on four mosquito species (Aedes albopictus Skuse, Aedes aegypti L., Anopheles gambiae Giles and Anopheles stephensi Liston), with LC50 values ranging from 4.42 to 16.80 μg/mL. The bio-guided EO fractionation identified furanosesquiterpenes as the main larvicidal compounds. A GC-MS-driven untargeted metabolomic analysis revealed 32 affected metabolic pathways in treated larvae. The EO non-target toxicity on Daphnia magna Straus (LC50 = 4.51 μL/L) and its cytotoxicity on a human kidney cell line (HEK293) (IC50 of 14.38 μg/mL) were also assessed. This study shows the potential of plant products as innovative insecticidal agents and lays the groundwork for the possible exploitation of C. myrrha EO in sustainable approaches for mosquito management.

Untargeted metabolomics and functional analyses reveal that the secondary metabolite quinic acid associates with Angelica sinensis flowering

Flowering is a critical step in the plant life cycle. Angelica sinensis (Oliv.) Diels is a medicinal crop whose root is a well-known herbal medicine used in Asia. Early flowering causes changes in secondary metabolic flow and results in the loss of medicinal quality. Based on untargeted metabolomics studies, quinic acid was identified as a metabolite present in significantly higher concentrations during the early-flowering stage in A. sinensis leaves. This metabolite was subsequently investigated as a potential marker for early bolting in A. sinensis under field conditions. Moreover, quinic acid was found to accelerate flowering in the model plant Arabidopsis thaliana. Importantly, the flowering time was delayed in the quinate dehydrogenase At mutant, and this delay was reversed by quinic acid. Quinic acid upregulated the expression of the GA20OX and GID1 receptors and downregulated the expression of the inhibitor DELLA, thereby affecting the levels of FT and LFY and accelerating plant flowering. Quinic acid also significantly changed the expression of genes such as LOX, JAZ1, MYC2 and MYC3 in the jasmonic acid pathway. The trends of GID1, DELLA (GAI) and LOX2 protein expression were essentially consistent with those at the transcription level. These results suggest that quinic acid may promote plant flowering primarily by regulating the expression of genes and proteins in the gibberellin and jasmonic acid pathways.

Chemical interplay between gut microbiota and epigenetics: Implications in circadian biology

Circadian rhythms are intrinsic molecular mechanisms that synchronize biological functions with the day/night cycle. The mammalian gut is colonized by a myriad of microbes, collectively named the gut microbiota. The microbiota impacts host physiology via metabolites and structural components. A key mechanism is the modulation of host epigenetic pathways, especially histone modifications. An increasing number of studies indicate the role of the microbiota in regulating host circadian rhythms. However, the mechanisms remain largely unknown. Here, we summarize studies on microbial regulation of host circadian rhythms and epigenetic pathways, highlight recent findings on how the microbiota employs host epigenetic machinery to regulate circadian rhythms, and discuss its impacts on host physiology, particularly immune and metabolic functions. We further describe current challenges and resources that could facilitate research on microbiota-epigenetic-circadian rhythm interactions to advance our knowledge of circadian disorders and possible therapeutic avenues.

Exploring the causal role of plasma metabolites and metabolite ratios in prostate cancer: a two-sample Mendelian randomization study

Background

Prostate cancer (PCa), the most prevalent malignant neoplasm in males, involves complex biological mechanisms and risk factors, many of which remain unidentified. By employing a novel two-sample Mendelian randomization (MR) approach, this study aims to elucidate the causal relationships between the circulating metabolome and PCa risk, utilizing comprehensive data on genetically determined plasma metabolites and metabolite ratios.

Methods

For the MR analysis, we utilized data from the GWAS Catalog database to analyze 1,091 plasma metabolites and 309 ratios in relation to PCa outcomes within two independent GWAS datasets. The inverse variance weighted (IVW) method was the primary approach for determining the existence of the causal relationship, supplemented by additional MR methods for heterogeneity, pleiotropy, and cross-validation. The false discovery rate (FDR) and Bonferroni correction were applied to identify the most significant causative associations. Additionally, reverse MR and Steiger filtering were conducted to ascertain whether PCa influenced the observed metabolite levels. Furthermore, metabolic pathway analysis was conducted with MetaboAnalyst 6.0 software.

Results

In the MR analysis, our findings reveal three overlapped metabolite ratios (arginine to glutamate, phosphate to uridine, and glycerol to mannitol/sorbitol) inversely associated with PCa risk. Following FDR correction (FDR < 0.05), cysteinylglycine disulfide was identified as a potential reducer of PCa risk, whereas Uridine and N-acetyl-L-glutamine (NAG) were pinpointed as potential risk factors. Notably, NAG (OR 1.044; 95% CI 1.025-1.063) emerged as a metabolite with significant causal influence, as confirmed by stringent Bonferroni correction (P < 0.05/1400). Steiger's directionality test (P < 0.001) and reverse MR confirmed the proposed causal direction. Furthermore, metabolic pathway analysis revealed a significant association between the "Glutathione Metabolism" pathway and PCa development.

Conclusion

This study provides novel insights into the potential causal effects of plasma metabolites and metabolite ratios on PCa. The identified metabolites and ratios could serve as candidate biomarkers, contributing to the elucidation of PCa's biological mechanisms.

Alanine metabolism mediates energy allocation of the brown planthopper to adapt to resistant rice

INTRODUCTION

During the adaptation to host plant resistance, herbivorous insects faced the challenge of overcoming plant defenses while ensuring their own development and reproductive success. To achieve this, a strategic allocation of energy resources for detoxification and ecological fitness maintenance became essential.

OBJECTIVE

This study aimed to elucidate the intricate energy allocation mechanisms involved in herbivore adaptation that are currently poorly understood.

METHODS

The rice Oryza sativa and its monophagous pest, the brown planthopper (BPH), Nilaparvata lugens were used as a model system. An integrated analysis of metabolomes and transcriptomes from different BPH populations were conducted to identify the biomarkers. RNA interference of key genes and exogenous injection of key metabolites were performed to validate the function of biomarkers.

RESULTS

We found that alanine was one of the key biomarkers of BPH adaptation to resistant rice variety IR36. We also found that alanine flow determined the adaptation of BPH to IR36 rice. The alanine aminotransferase (ALT)-mediated alanine transfer to pyruvate was necessary and sufficient for the adaptation. This pathway may be conserved, at least to some extent, in BPH adaptation to multiple rice cultivars with different resistance genes. More importantly, ALT-mediated alanine metabolism is the foundation of downstream energy resource allocation for the adaptation. The adapted BPH population exhibited a significantly higher level of energy reserves in the fat body and ovary when fed with IR36 rice, compared to the unadapted population. This rendered the elevated detoxification in the adapted BPH and their ecological fitness recovery.

CONCLUSION

Overall, our findings demonstrated the crucial role of ALT-mediated alanine metabolism in energy allocation during the adaptation to resistant rice in BPH. This will provide novel knowledge regarding the co-evolutionary mechanisms between herbivores and their host plants.