Search Results (897)

The vast majority of the ocean’s microbial natural product biosynthetic potential remains undescribed. To access this chemical diversity, we employed Small Molecule In Situ Resin Capture (SMIRC) across three ecologically distinct sites in San Diego, California. Using high-resolution LC-MS/MS, we detected spatial and temporal variability in the metabolomes captured. Low annotation rates and evidence of extensive halogenation supported the chemical novelty of the compounds captured. We detected rare chlorinated polyketides in the pinnaic acid class, previously known only from filter-feeding invertebrates. We also report the first detection of chlorosulfolipids in the Pacific Ocean including one that contained 11 chlorine atoms. We linked compound abundances to weekly phytoplankton counts to identify candidate producers and found evidence that different taxa produce chlorosulfolipids of different carbon chain lengths. This study provides evidence of the chemical novelty that can be captured directly from the environment and a framework for integrating environmental metabolomics with phytoplankton counts as a method to identify candidate compound producers. Full article

Microplastics (MPs) and pesticides increasingly co-occur in agricultural ecosystems, where they may jointly affect plant physiology and plant–microorganism interactions. This study investigated the individual and combined effects of biodegradable poly(butylene adipate-co-terephthalate) (PBAT), the herbicide metolachlor (MET), and the beneficial fungus Trichoderma harzianum KKP 534 on wheat (Triticum aestivum). Plant growth, physiological responses, chlorophyll content, cell membrane damage, antioxidant enzyme activities and selected metabolomic and lipidomic biomarkers were evaluated. High PBAT concentrations negatively affected wheat growth by reducing root and shoot length and increasing oxidative stress, as evidenced by elevated TBARS levels, increased antioxidant enzyme activities (POD, GST, CAT, and SOD), and enhanced membrane damage. Metabolomic and lipidomic analyses further revealed stress-associated changes in amino acid metabolism and membrane lipid remodelling. PBAT also adsorbed MET and 2,4-di-tert-butylphenol (DTBP), potentially altering their bioavailability and environmental behaviour. Although T. harzianum KKP 534 promoted plant growth and enhanced antioxidant responses under control conditions, these beneficial effects were attenuated in the presence of PBAT MP. The results suggest that biodegradable microplastics may influence plant–microbe interactions and modify pesticide dynamics under controlled conditions, highlighting the need for further studies in soil-based systems. Full article

Moringa, a versatile tree species, has seen an increasing diversification of breeding objectives due to its rich nutritional value and potential applications in ecological restoration. The emergence and integration of multi-omics technologies have provided a revolutionary systems-level research framework for elucidating the fundamental biological mechanisms underlying Moringa’s agronomic traits and nutritional characteristics. This review systematically analyzes the application prospects and omics significance of Moringa based on research trends, and explores in depth the progress made in various omics studies of Moringa: the fourth iteration of the genome has identified specific genes encoding heat shock proteins (HSPs) in Moringa; phenomics reveals differential expression of Moringa under different environmental conditions; and the transcriptomics and metabolomics elucidate differential regulatory networks across different tissues and environments. In the future, multi-omics technologies can be integrated: genomics can further identify rare alleles and localize genetic loci for key agronomic traits; transcriptomics combined with epigenomics can elucidate the spatial regulation of gene expression and epigenetic mechanisms; and proteomics and metabolomics can be integrated to validate pathways and provide targets for improvement. Throughout the process, a high-throughput phenotyping platform utilizing drones will be introduced to dynamically monitor agronomic traits, enabling efficient breeding and accelerating genetic improvement. Full article

Anti-nutritional factors (ANFs) in terrestrial plant feeds constrain efficient herbivore production, an issue intensified by rising feed costs and growing demand for animal products. Unlike previous reviews that focus on single ANFs or feed types, this review provides an integrated, cross-species framework linking ANF chemistry, rumen microbial interactions, and mitigation strategies. It examines major ANF classes—tannins, phytates, saponins, oxalates, protease inhibitors, lectins, glucosinolates, and gossypol—and their distribution and biochemical modes of action. Mechanistic pathways are grouped into digestive effects (reduced palatability and enzyme inhibition), microbial effects (altered rumen microbiota and fermentation), metabolic effects (impaired absorption), and mineral interactions (nutrient complexation and chelation). Species-specific responses are evaluated, emphasizing the partial detoxification capacity of the rumen microbiome and the dose-dependent nature of ANF effects. Mitigation strategies—physical, chemical, microbial, enzymatic, probiotic, and genetic—are critically assessed for efficacy, scalability, and sustainability. Emerging metabolomic and metagenomic evidence shows that certain ANFs confer functional benefits at controlled doses; for example, tannins improve nitrogen retention, saponins reduce methane, and phytic acid scavenges free radicals. This synthesis supports strategic management rather than complete elimination, informing safe and sustainable use of terrestrial feeds under evolving food-security and environmental challenges. Full article

The red imported fire ant (Solenopsis invicta Buren) is a destructive invasive pest, and conventional chemical control faces challenges related to environmental contamination and resistance development, highlighting the need for novel control agents and greener management strategies. In this study, pyrethrins-mediated silver nanoparticles (Pyr-AgNPs) were synthesized via a green route, characterized, and evaluated for their insecticidal activity, environmental stability, and metabolic effects on S. invicta workers. Bait bioassays showed that Pyr-AgNPs exhibited high toxicity to S. invicta, causing 100% cumulative corrected mortality at 500 mg·kg⁻¹ after 9 days of feeding, with a 5-d LC₅₀ of 116.83 mg·kg⁻¹. Exposure assays further demonstrated that Pyr-AgNPs had good environmental stability and residual efficacy, as bait containing 1000 mg·kg⁻¹ Pyr-AgNPs still caused 100% cumulative corrected mortality after 9 days following 96 h of outdoor exposure, significantly outperforming the pyrethrins treatment. LC-MS-based untargeted metabolomic analysis revealed that treatment with Pyr-AgNPs markedly altered the metabolic profile of S. invicta workers, with 607 differential metabolites identified, mainly belonging to organic acids and derivatives, lipid and lipid-like molecules, amino acids and peptides, cofactors, and redox-related metabolites. Pathway enrichment analysis indicated that these metabolic disturbances were primarily associated with energy metabolism, redox homeostasis, and membrane lipid metabolism. Overall, these findings provide preliminary mechanistic clues into the toxicity of Pyr-AgNPs and support their potential application in the sustainable management of S. invicta. Full article

Climate change is increasing the exposure of crops to drought stress, highlighting the need for integrative approaches to assess plant responses under field conditions. In this study, telomere length (TL) was evaluated in field-grown grapevine (Vitis vinifera L., cv. Aglianico) subjected to rainfed (RF) and controlled deficit irrigation (CDI) regimes. A qPCR-based protocol was applied together with physiological measurements, UAV-derived vegetation indices, and berry metabolomic profiling to investigate plant responses to different water regimes. Physiological and metabolomic analyses confirmed distinct responses between treatments, with rainfed vines showing more negative leaf water potential, lower stomatal conductance, and increased accumulation of stress-associated metabolites, including anthocyanins and abscisic acid. Linear mixed-effects modeling showed no significant difference in TL between treatments at the beginning of the experimental period (p = 0.198), whereas rainfed vines displayed significantly lower TL values than irrigated vines at the end of the growing season (p = 0.0009). TL decreased significantly over time in both treatments. The treatment × time interaction suggested a greater TL reduction in rainfed vines in the primary model (p = 0.064), and this effect was significant in a complete-pair sensitivity analysis (p = 0.036). These findings indicate an association between irrigation regime and telomere length variation under field conditions. The study provides preliminary evidence supporting the potential application of TL measurements for investigating plant responses to environmental stress in grapevine. Full article

Yaks have long inhabited the Qinghai-Tibetan Plateau. This region features low-oxygen, frigid temperatures and pronounced seasonal variation in nutrient availability. They have evolved adaptive phenotypes centered on energy metabolism reprogramming, tissue structure remodeling, and stress homeostasis maintenance. In recent years, non-coding RNAs (ncRNAs) have been confirmed as an important component of the yak’s post-transcriptional regulatory network. They play a key bridging role between environmental stress perception and phenotypic output through mechanisms such as influencing RNA splicing, stability, translation activity, and constructing competitive endogenous RNA (ceRNA) networks. This article systematically reviews the biogenesis pathways and core regulatory patterns of circular RNAs (circRNAs), microRNAs (miRNAs), and long non-coding RNAs (lncRNAs). It focuses on summarizing the expression profile characteristics and dynamic spatiotemporal changes of these three types of ncRNAs in physiological contexts such as muscle and fat deposition, mammary gland lactation, testicular development, and hypoxia response in the heart, lungs, and vascular system of yaks. Current research evidence indicates that the regulatory network of yaks ncRNAs shows significant convergence on multiple key signaling pathways, mainly concentrating on lipid metabolism (PPAR/AMPK), nutrition and growth signals (PI3K-Akt/MAPK/mTOR), extracellular matrix remodeling (ECM-receptor interaction, Wnt/TGF-β), and cell stress fate determination (apoptosis, oxidative stress/ferroptosis) modules. Among them, some core circRNA and lncRNA-miRNA-mRNA regulatory axes have been functionally validated in vitro. Despite the phased progress, current research on ncRNA in yaks still faces bottlenecks: the multi-omics molecular atlases (encompassing genomics, transcriptomics, proteomics, and metabolomics) of key high-altitude adaptive organs remain incomplete, analysis processes lack sufficient standardization, and most studies stay at the association network level with limited causal mechanism validation. To address these limitations, future research should focus on building a standardized evidence chain, integrating multi-omics and single-cell/spatial transcriptome technologies, and conducting mechanism verification for traits in independent populations, thereby providing a solid theoretical basis for understanding the extreme environmental adaptation mechanisms of yaks and molecular breeding improvement. Full article

Due to large-scale macroalgal blooms, nutrient enrichment, and changes in ocean circulation brought on by climate change, beach-accumulated seaweed (BAS) has quickly become a global environmental and waste-governance concern. Despite degradation and contamination during beach stranding, BAS retains valuable bioactive compounds, including sulfated polysaccharides, phlorotannins, pigments, proteins, peptides, and lipids, which exhibit anti-inflammatory, antioxidant, antimicrobial, antiviral, immunomodulatory, anticancer, and metabolic regulatory activities. This review critically evaluates BAS as a sustainable bioresource by integrating current knowledge on biomass composition, degradation-associated challenges, bioactive properties, valorization pathways, advanced extraction technologies, safety validation, regulatory considerations, and emerging commercialization opportunities. Attention is given to sustainable valorization pathways, ranging from composting and bioenergy production to the recovery of high-value bioactives through enzyme-assisted, green, and advanced extraction technologies. The review further discusses policy and regulatory gaps, contamination challenges, safety validation requirements, and life-cycle sustainability considerations that currently limit industrial adoption. Finally, emerging opportunities involving metabolomics, microbial bioprocessing, artificial intelligence, automation, and nanotechnology are explored as future directions for transforming BAS into a standardized and economically viable feedstock within the circular blue bioeconomy. Establishing harmonized regulatory frameworks and integrating BAS management with Sustainable Development Goals (SDGs) 12 and 14 will be critical for enabling sustainable resource recovery and long-term coastal resilience. Full article

Cadmium (Cd) is an environmental nephrotoxicant that preferentially accumulates in the kidney and disrupts redox and energy metabolism. However, the protective effect of berberine (Ber) against Cd-induced nephrotoxicity remains insufficiently characterized. In the present study, male C57BL/6 mice were orally exposed to CdSO₄ (30 mg/kg body weight/day) for 30 days in the absence or presence of berberine (25 or 100 mg/kg/day). Renal function, histopathology, oxidative stress parameters, LC–MS/MS-based metabolomic profiling, gene and protein expression, and in silico ligand–target interactions were evaluated. Cd exposure markedly increased serum CREA, renal index, renal LDH activity, and MDA content, decreased SOD and CAT activities, and induced pronounced renal histopathological lesions. Ber significantly attenuated these abnormalities in a dose-dependent manner. Metabolomic analysis revealed that Cd broadly suppressed pyruvate metabolism, tricarboxylic acid cycle intermediates, and NAD+/NADH homeostasis, whereas berberine restored the levels of pyruvate, acetyl-CoA, oxaloacetate, citrate, isocitrate, succinate, fumarate, malate, NAD+, and NADH. In parallel, berberine normalized the expression of metabolism-related genes including the downregulation of Ldha and the upregulation of Cs, Sucnr1, G6pc, and Pfkm, with the high-dose regimen showing the most evident recovery. Western blotting further verified the lower LDHA protein expression after berberine treatment. Molecular docking demonstrated favorable potential berberine–LDHA binding, and molecular dynamics simulation supported the stability of the ligand–protein complex. Collectively, these findings indicate that berberine ameliorates Cd-induced renal injury, an effect that correlates with attenuated oxidative stress, modulation of LDHA-associated glycolytic pathways, and restoration of mitochondrial TCA-cycle activity and redox balance, highlighting berberine as a promising candidate for the prevention of heavy metal-associated nephrotoxicity. Full article

Chronic Kidney Disease of Unknown Etiology (CKDu) is an ongoing global health concern, particularly affecting agricultural communities in equatorial regions. Unlike traditional chronic kidney disease (CKD), CKDu occurs without common risk factors such as diabetes, hypertension, or kidney stones. Its etiology remains poorly understood, with environmental exposures, occupational hazards, and genetic susceptibility proposed as contributing factors. Omic technologies including genomics, transcriptomics, proteomics, metabolomics, and exposomics offer promising avenues to elucidate CKDu pathogenesis by enabling comprehensive molecular profiling and identification of biomarkers. Recent genomic studies have explored single nucleotide polymorphisms (SNPs) linked to kidney injury susceptibility, while transcriptomic analyses have identified differential expression of genes involved in oxidative stress and tubular injury pathways. Proteomic investigations have revealed candidate urinary biomarkers such as heat shock proteins and inflammatory mediators, and metabolomic profiling has highlighted alterations in amino acid and energy metabolism in affected individuals. Exposomic approaches are beginning to characterize cumulative chemical exposures, including pesticides and heavy metals, in endemic regions. This narrative review synthesizes current evidence on the application of omics approaches in CKDu research, highlights knowledge gaps, and proposes future directions for integrating multi-omics studies with machine learning and artificial intelligence approaches. Advancing omics-based investigations may provide critical insights into disease mechanisms, improve diagnostic precision, and inform targeted interventions for vulnerable populations. Full article

Cold stress is a key environmental constraint in aquaculture, but integrated host responses linking oxidative status, intestinal microbiota, and hepatic metabolism remain insufficiently characterized in Luciobarbus capito. This study aimed to evaluate the biochemical, microbial, and metabolic responses of L. capito to acute low-temperature exposure. Fish were exposed to 12 °C for 96 h, with fish maintained at 22 °C as controls; hepatic antioxidant indices, serum biochemical parameters, intestinal microbiota based on 16S rRNA gene sequencing, and liver metabolomic profiles were analyzed. Cold exposure reduced hepatic total superoxide dismutase (T-SOD) and catalase (CAT) activities and increased malondialdehyde (MDA) content, while serum alanine aminotransferase (ALT) and aspartate aminotransferase (AST) activities increased and acid phosphatase (ACP) activity decreased. The intestinal microbiota showed reduced richness and compositional shifts, including decreased Cetobacterium and increased Pseudomonas. Liver metabolomics identified 172 differential metabolites, with enriched pathways related to glycerophospholipid metabolism, α-linolenic acid metabolism, pantothenate and CoA biosynthesis, and ascorbate and aldarate metabolism. Correlation analysis indicated significant associations between altered bacterial genera and hepatic metabolites. These results suggest that acute cold stress disrupts oxidative balance, intestinal microbial composition, and hepatic metabolism in L. capito, providing an integrated view of associated physiological and metabolic responses to low-temperature stress. Full article

Lead exposure remains a pervasive environmental and public health threat, imposing a substantial burden of neurodevelopmental and cognitive dysfunction, yet safe mechanism-oriented interventions remain limited. Genistein, a soybean-derived isoflavone with antioxidant and neuroprotective potential, may counter heavy metal-induced neural injury; however, whether its efficacy is associated with redox–metabolic remodeling is unclear. Here, we evaluated genistein in lead-exposed C57BL/6J mice and lead-challenged HT22 hippocampal neurons. Genistein improved novel-arm exploration and spatial memory without altering locomotor or swimming performance, and attenuated neuronal disorganization and apoptosis in hippocampal CA1, CA3 and dentate gyrus regions. These protective effects were accompanied by reduced blood and hippocampal lead accumulation, restored glutathione redox balance, enhanced antioxidant capacity, preserved mitochondrial integrity, and suppressed Bax/Caspase-3-associated apoptotic signaling. Importantly, because genistein also reduced hippocampal lead accumulation, the in vivo neuroprotection may reflect both reduced target-tissue lead burden and improved glutathione-related redox homeostasis. Untargeted metabolomics identified 59 genistein-responsive metabolites enriched mainly in glutathione metabolism, oxidative phosphorylation, and ascorbate/aldarate metabolism, linking metabolic remodeling to behavioral recovery and reduced oxidative-apoptotic injury. In HT22 cells, blockade of glutathione synthesis by buthionine sulfoximine markedly weakened genistein-mediated cytoprotection, mitochondrial membrane potential recovery, and apoptosis inhibition. Collectively, genistein mitigates lead-induced hippocampal neurotoxicity and cognitive impairment by restoring glutathione-centered redox–mitochondrial homeostasis, supporting its further development as a mechanistically defined dietary candidate for environmental pollutant-associated neural injury. Full article

Background/Objectives: This study aims to establish a systematic phytochemical characterization and quality evaluation method to systematically evaluate the influence of multiple factors on the chemical composition of Taxillus chinensis, thereby providing a scientific basis for its development, utilization, and quality control standards. Methods: To ensure a targeted and representative metabolic screening, six representative batches covering the major geographical origins and host plants were selected for initial metabolomic profiling. An integrated analytical approach combining UPLC-MS/MS-based widely targeted metabolomics, HPLC fingerprinting, and multi-component quantitative analysis with multivariate statistical analysis was employed. Results: Significant quality variations were identified across the samples. Metabolomics results indicated that while chemical component types were qualitatively consistent across growth conditions, their contents varied significantly. Unique differential metabolites clustered according to specific geographical origins or host plants. KEGG pathway analysis revealed that geographical origin primarily regulated phenylpropanoid biosynthesis, whereas host differences mainly influenced flavonoid and monoterpenoid biosynthesis. Furthermore, HPLC fingerprinting of 20 batches demonstrated similarities greater than 0.9, with 15 common peaks determined. Based on their high relative abundance, differential significance across samples, and documented pharmacological relevance to the herb’s traditional efficacy, six bioactive components—gallic acid, catechin, epicatechin, hyperoside, isoquercitrin, and quercitrin—were identified and quantified. Notably, samples originating from Wuzhou exhibited the highest total content of these components. Consistent with PCA and HCA results, gallic acid, hyperoside, isoquercitrin, and quercitrin were identified as potential markers driving quality differences. Conclusions: This integrated approach allows for a systematic analytical screening of Taxillus chinensis, clarifying chemical variations caused by environmental and biological factors, and supporting the standardization and comprehensive utilization of this medicinal plant. Full article

Background/Objective: Bisphenol AF (BPAF), a fluorinated analogue of bisphenol A, is an environmental contaminant associated with hepatotoxicity and metabolic disruption. However, the systematic molecular mechanisms linking early transcriptional events to metabolic dysfunction in the liver remain poorly defined. The aim of this study is to elucidate the association between BPAF exposure and hepatic lipid accumulation by integrating transcriptomics, cellular metabolomics, and targeted phenotypic assays. Methods: We performed RNA-sequencing on livers from mice exposed to BPAF (0.1–10 mg/kg/day, 28 days), and performed non-targeted metabolomics on AML12 murine hepatocytes co-cultured with RAW264.7 macrophages in a Transwell system (0–2500 nM BPAF, 48 h). Key metabolic pathways were identified through integrated bioinformatics and validated using enzymatic assays, qRT-PCR, Western blotting, and phenotypic staining (lipid droplets, ROS). Results: Multi-omics integration revealed significant disruption of PPAR signaling and the tricarboxylic acid (TCA) cycle. A striking dose-dependent accumulation of succinate was observed in exposed cells, concomitant with a significant inhibition of succinate dehydrogenase (SDH) activity (52% reduction at 2500 nM, p < 0.001). Transcriptomic data confirmed the downregulation of mitochondrial fatty acid β-oxidation genes. Phenotypic validation indicated that BPAF exposure is associated with oxidative stress, pro-inflammatory cytokine release (TNF-α, IL-6), and pronounced intracellular lipid droplet accumulation in hepatocytes. Conclusions: This study suggests that BPAF exposure is associated with SDH dysfunction, TCA cycle arrest, and lipid dysregulation. Whether BPAF directly inhibits SDH or acts through upstream mitochondrial targets warrants further structural and kinetic investigation. Full article

Background: Confident chemical annotation in nontarget small-molecule mass spectrometry critically depends on the availability of high-quality tandem mass spectral (MS²) reference libraries. While community efforts have driven significant expansion of open-access repositories, technical challenges in assembling standardized, metadata-rich records continue to limit broader participation, underscoring the need for improved computational tools to assist contributors. Methods: To promote the creation and sharing of standardized reference MS² spectral records, we have developed Librarian, a free, open-access web application designed for rapid and scalable assembly of high-resolution MS² libraries. Librarian integrates automated retrieval and harmonization of chemical identifiers and metadata from PubChem, compound mixture design for high-resolution mass spectrometry (HRMS) acquisition, and assembly of curated MS² spectra into repository-ready records compatible with public spectral databases. Results: Through a simple in-browser interface, Librarian offers a flexible end-to-end workflow compatible with popular open-source pre-processing tools to lower technical barriers and facilitate broader community participation in library development. As a demonstration, we used Librarian to create and deposit a spectral library comprising over 1500 new MS² records into MassBank, which was further applied in retrospective analysis of environmental datasets. Conclusions: Librarian streamlines the creation of standardized, metadata-rich and repository-ready MS² reference records. Addressing a key bottleneck in community spectral library development and sharing, Librarian supports the continued growth of open-access resources for metabolomics, exposomics, and environmental mass spectrometry. The Librarian web application is publicly accessible via the SciLifeLab Serve platform. Full article