Search

[Display omitted] • Environmental concentrations of PS-MNPs increased body weight without affecting survivorship. • Exposures induced significant alterations in host metabolome, microbiome, and transcriptome. • Gut metabolites were correlated with the microbiome. • The observed biomarkers' responses were particle size-dependent i.e., PS-S > PS-M > PS-L. • Metabolic disorder and microbiome dysbiosis are the main mechanisms of the observed phenotype. Micro- and nanoplastics (MNPs) are emerging environmental pollutants that have raised serious concerns about their potential impact on ecosystem and organism health. Despite increasing efforts to investigate the impacts of micro- and nanoplastics (MNPs) on biota little is known about their potential impacts on terrestrial organisms, especially insects, at environmental concentrations. To address this gap, we used an insect model, silkworm Bombyx mori to examine the potential long-term impacts of different sizes of polystyrene (PS) MNPs at environmentally realistic concentrations (0.25 to 1.0 μg/mL). After exposure to PS-MNPs over most of the larval lifetime (from second to last instar), the endpoints were examined by an integrated physiological (growth and survival) and multiomics approach (metabolomics, 16S rRNA, and transcriptomics). Our results indicated that dietary exposures to PS-MNPs had no lethal effect on survivorship, but interestingly, increased host body weight. Multiomics analysis revealed that PS-MNPs exposure significantly altered multiple pathways, particularly lipid metabolism, leading to enriched energy reserves. Furthermore, the exposure changed the structure and composition of the gut microbiome and increased the abundance of gut bacteria Acinetobacter and Enterococcus. Notably, the predicted functional profiles and metabolite expressions were significantly correlated with bacterial abundance. Importantly, these observed effects were particle size-dependent and were ranked as PS-S (91.92 nm) > PS-M (5.69 µm) > PS-L (9.7 µm). Overall, PS-MNPs at environmentally realistic concentrations exerted stimulatory effects on energy metabolism that subsequently enhanced body weight in silkworms, suggesting that chronic PS-MNPs exposure might trigger weight gain in animals and humans by influencing host energy and microbiota homeostasis. [ABSTRACT FROM AUTHOR]

Metabolic differences have been reported between individuals with and without major depressive disorder (MDD), but their consistency and causal relevance have been unclear. We conducted a metabolome-wide association study of MDD with 249 metabolomic measures available in the UK Biobank (n = 29,757). We then applied two-sample bidirectional Mendelian randomization and colocalization analysis to identify potentially causal relationships between each metabolite and MDD. A total of 191 metabolites tested were significantly associated with MDD (false discovery rate–corrected p <.05), which decreased to 129 after adjustment for likely confounders. Lower abundance of omega-3 fatty acid measures and a higher omega-6 to omega-3 ratio showed potentially causal effects on liability to MDD. There was no evidence of a causal effect of MDD on metabolite levels. Furthermore, genetic signals associated with docosahexaenoic acid colocalized with loci associated with MDD within the fatty acid desaturase gene cluster. Post hoc Mendelian randomization of gene-transcript abundance within the fatty acid desaturase cluster demonstrated a potentially causal association with MDD. In contrast, colocalization analysis did not suggest a single causal variant for both transcript abundance and MDD liability, but rather the likely existence of two variants in linkage disequilibrium with one another. Our findings suggest that decreased docosahexaenoic acid and increased omega-6 to omega-3 fatty acids ratio may be causally related to MDD. These findings provide further support for the causal involvement of fatty acids in MDD. [ABSTRACT FROM AUTHOR]

Psoraleae Fructus (Bu Gu Zhi) is the fruit of Psoralea corylifolia L. (PCL) and has been used for centuries in traditional Chinese medicine formulas to treat osteoporosis (OP). A new drug called "BX" has been developed from PCL, but its mechanism for treating OP is not yet fully understood. To explore the mechanism of action of BX in the treatment of ovariectomy-induced OP based function-oriented multi-omics analysis of gut microbiota (GM) and metabolites. C57BL/6 mice were bilaterally ovariectomized to replicate the OP model. The therapeutic efficacy of BX was evaluated by bone parameters (BMD, BV/TV, Tb.N, Tb.Sp), hematoxylin and eosin (H&E) staining results, and determination of bone formation markers procollagen type Ⅰ amino-terminal peptide (PⅠNP) and bone-specific alkaline phosphatase (BALP). Serum and fecal metabolomics and high-throughput 16S rDNA sequencing were performed to evaluate effects on endogenous metabolites and GM. In addition, an enzyme-based functional correlation algorithm (EBFC) algorithm was used to investigate functional correlations between GM and metabolites. BX improved OP in OVX mice by increasing BMD, BV/TV, serum PⅠNP, BALP, and improving Tb.N and Tb.Sp. A total of 59 differential metabolites were identified, and 9 metabolic pathways, including arachidonic acid metabolism, glycerophospholipid metabolism, purine metabolism, and tryptophan metabolism, were found to be involved in the progression of OP. EBFC analysis results revealed that the enzymes related to purine and tryptophan metabolism, which are from Lachnospiraceae_NK4A136_group , Blautia , Rs-E47_termite_group , UCG-009, and Clostridia_UCG-014 , were identified as the intrinsic link between GM and metabolites. The regulation of GM and restoration of metabolic disorders may be the mechanisms of action of BX in alleviating OP. This research provides insights into the function-oriented mechanism discovery of traditional Chinese medicine in the treatment of OP. [Display omitted] • BX exhibited therapeutic effects in the treatment of osteoporosis (OP). • BX modulated the gut microbiota (GM) composition and metabolism. • Functional correlations between GM and differential metabolites were discovered. • BX regulated purine and tryptophan metabolism-related GM and its metabolites. [ABSTRACT FROM AUTHOR]

High concentrations of copper can pollute coastal waters, primarily from agricultural runoff and mining activities, which can harm marine organisms, including seagrasses. The molecular mechanism of copper toxicity to seagrass currently remains unclear. To determine the response to copper, physiological and multi-omic analyses were conducted to explore the molecular mechanism by which copper affects the global threatened seagrass Halophila beccarii Asch. Excessive copper stress causes oxidative damage and stimulates the activity of the antioxidant enzyme system to remove excess reactive oxygen species (ROS), thereby reducing the damage caused by copper stress. Cu increases the activities of superoxide dismutase (EC 1.15.1.1), catalase (EC 1.11.1.6), peroxidase (EC 1.11.1.7), ascorbate peroxidase (EC 1.11.1.11), glutathione peroxidase (EC 1.11.1.9), ascorbate oxidase (EC 1.10.3.3), glutathione reductase (EC 1.6.4.2), and dehydroascorbate reductase (EC 1.8.5.1) and the content of malondialdehyde and reduces the activity of monodehydroascorbate reductase (EC 1.6.5.4). Under copper stress, H. beccarii upregulates the metabolic pathways of steroid biosynthesis and cutin, suberin, and wax biosynthesis, downregulates the metabolic pathways of arginine and proline metabolism and fructose and mannose metabolism; the levels of expression of the ribosome-related genes; upregulates the levels of expression of circadian rhythm-related proteins and downregulates the levels of glutathione metabolism and the proteins related to carbon fixation. This study provides new insights into the response of seagrass to copper stress and reports potential candidate metabolites, genes, and proteins that can be considered as biomarkers to improve the protection and management of seagrass meadows. • Copper increases antioxidant enzyme activity. • Copper affects arginine and proline metabolism. • Copper affects ribosome and flavonoid biosynthesis at the level of transcription. • Copper downregulates glutathione metabolism and carbon fixation. [ABSTRACT FROM AUTHOR]

The relationship between PM 2.5 and metabolic diseases, including type 2 diabetes (T2D), has become increasingly prominent, but the molecular mechanism needs to be further clarified. To help understand the mechanistic association between PM 2.5 exposure and human health, we investigated short-term PM 2.5 exposure trajectory-related multi-omics characteristics from stool metagenome and metabolome and serum proteome and metabolome in a cohort of 3267 participants (age: 64.4 ± 5.8 years) living in Southern China. And then integrate these features to examine their relationship with T2D. We observed significant differences in overall structure in each omics and 193 individual biomarkers between the high- and low-PM 2.5 groups. PM 2.5 -related features included the disturbance of microbes (carbohydrate metabolism-associated Bacteroides thetaiotaomicron), gut metabolites of amino acids and carbohydrates, serum biomarkers related to lipid metabolism and reducing n-3 fatty acids. The patterns of overall network relationships among the biomarkers differed between T2D and normal participants. The subnetwork membership centered on the hub nodes (fecal rhamnose and glycylproline, serum hippuric acid, and protein TB182) related to high-PM 2.5 , which well predicted higher T2D prevalence and incidence and a higher level of fasting blood glucose, HbA1C, insulin, and HOMA-IR. Our findings underline crucial PM 2.5 -related multi-omics biomarkers linking PM 2.5 exposure and T2D in humans. [Display omitted] • Trajectory grouping in short-term PM 2.5 exposures effectively capture variations in microbiota composition. • Novel PM 2.5 -related multi-omics biomarkers well predicted higher T2D prevalence and incidence. • The crucial PM 2.5 -related biomarkers include fecal rhamnose and glycylproline, serum hippuric acid, and protein TB182. • The subnetwork correlation provides critical insights into the molecular mechanisms underlying PM 2.5 -related T2D impacts. [ABSTRACT FROM AUTHOR]

Dissolved oxygen is an environmental factor that affects fish survival. Aquatic environments suffer from an increasing oxygen deficiency resulting from global warming and environmental pollution. In this study, we combined high-throughput transcriptome analysis with non-targeted liquid chromatography-mass spectrometry-based metabolome sequencing to assess the metabolic response to hypoxia in the liver of Pelteobagrus fulvidraco. Healthy fish with body weight of 12.39 ± 1.37 g were subjected to hypoxic conditions at a concentration of 1.02 ± 0.09 mg/L for durations of 6, 24 and 48 h. Hypoxia exposure increased the content of MDA, lactate, glucose and the level of T-AOC, enhanced the activity of T-SOD, CAT, GPx and LDH, and decreased SDH activity. Histological examination revealed that liver tissue was damaged after exposure, and the degree of damage increased with the prolongation of hypoxia time. In the liver transcriptome, 1527 DEGs were identified, of which 240 were co-identified in the three comparison groups. These DEGs showed significant enrichment in pathways associated with oxidation-reduction and metabolic processes. RT- qPCR confirmed transcriptional induction of metabolism-related genes in response to hypoxia. Metabolomic results showed that the SDMs were related to amino acid, carbohydrate, and lipid metabolism. Moreover, a conjoint analysis demonstrated an increase in the activity of several key enzymes, such as phosphoenolpyruvate carboxykinase, phospholipid phosphatase 1a, and betaine-homocysteine methyltransferase. An integrated regulatory network was observed to be involved in glycine, serine, and threonine metabolism; glycolysis/gluconeogenesis; tricarboxylic acid cycle; protein digestion and absorption; and lipid metabolism in response to hypoxia exposure. Overall, the findings indicated that hypoxia can cause oxidative stress in yellow catfish and that their bodies can resist stress by activating the antioxidant defense system and mobilizing multiple metabolic pathways to meet the energy demand. These results will aid in the development of strategies aimed at mitigating the adverse effects of hypoxic exposure on fish. • The metabolic response of yellow catfish to acute hypoxia was studied. • Hypoxia induces oxidative stress and activates antioxidant system in P. fulvidraco. • Glycolysis is the main source of energy under hypoxic stress. • Endogenous metabolic small molecules maintain homeostasis. • A metabolic regulatory network was constructed under hypoxia for 48 h. [ABSTRACT FROM AUTHOR]

Mangroves are of important economic and environmental value and research suggests that their carbon sequestration and climate change mitigation potential is significantly larger than other forests. However, increasing salinity and heavy metal pollution significantly affect mangrove ecosystem function and productivity. This study investigates the tolerance mechanisms of rhizobacteria in the rhizosphere of Avicennia marina under salinity and copper (Cu) stress during a 4-y stress period. The results exhibited significant differences in antioxidant levels, transcripts, and secondary metabolites. Under salt stress, the differentially expressed metabolites consisted of 30% organic acids, 26.78% nucleotides, 16.67% organic heterocyclic compounds, and 10% organic oxides as opposed to 27.27% organic acids, 24.24% nucleotides, 15.15% organic heterocyclic compounds, and 12.12% phenyl propane and polyketides under Cu stress. This resulted in differential regulation of metabolic pathways, with phenylpropanoid biosynthesis being unique to Cu stress and alanine/aspartate/glutamate metabolism and α-linolenic acid metabolism being unique to salt stress. The regulation of metabolic pathways enhanced antioxidant defenses, nutrient recycling, accumulation of osmoprotectants, stability of plasma membrane, and chelation of Cu, thereby improving the stress tolerance of rhizobacteria and A. marina. Even though the abundance and community structure of rhizobacteria were significantly changed, all the samples were dominated by Proteobacteria, Chloroflexi, Actinobacteriota, and Firmicutes. Since the response mechanisms were unbalanced between treatments, this led to differential growth trends for A. marina. Our study provides valuable inside on variations in diversity and composition of bacterial community structure from mangrove rhizosphere subjected to long-term salt and Cu stress. It also clarifies rhizobacterial adaptive mechanisms to these stresses and how they are important for mitigating abiotic stress and promoting plant growth. Therefore, this study can serve as a reference for future research aimed at developing long-term management practices for mangrove forests. [Display omitted] • Salt-copper (Cu) stress decreased bacterial abundance but increased diversity. • Low and high salt stress significantly increased bacterial abundance. • High salt stress significantly downregulated the content of free amino acids in the rhizosphere. • High Cu and salt-Cu stress promoted N reduction function but inhibited C metabolism. • Phenylpropanoid biosynthesis was unique to copper stress. [ABSTRACT FROM AUTHOR]

The hypoglycemic effects of low-molecular-weight Laminaria japonica polysaccharide (LJO) were investigated in type 2 diabetes mellitus (T2DM) mice, focusing on its effect on the microbiome, metabolome, and transcriptome. The findings demonstrated that LJO significantly reduced fasting blood glucose levels, insulin levels, and inflammatory factors. Additionally, LJO induced changes in gut microbiota composition and increased the concentrations of cecal short-chain fatty acids. Analysis of transcriptomics and metabolomics data revealed that LJO primarily altered the endocrine and digestive systems, signal transduction, and lipid metabolism. It led to a decrease in palmitic acid levels and an increase in glutathione levels. Real-time quantitative polymerase chain reaction assay suggested that LJO upregulated Irs1 expression, consequently reducing insulin resistance. These findings strongly suggest that LJO holds promise in ameliorating T2DM and may serve as a potential dietary supplement for patients with T2DM. • Polysaccharide from Laminaria japonica (LJO) has hypoglycemic effects. • LJO modulated the diabetes-associated bacterial taxa and short-chain fatty acids (SCFAs). • Using multi-omics to analyze the underlying mechanisms of LJO to ameliorate type 2 diabetes in mice. • LJO may serve as a potential prebiotic agent against metabolic disorders in diabetic patients. [ABSTRACT FROM AUTHOR]

Cadmium (Cd) is a highly toxic heavy metal that can be readily absorbed by plants and enriched in human body. Rice (Oryza sativa L.) yield and grain quality are affected by excessive Cd in the soil. Therefore, understanding the mechanisms of Cd absorption, accumulation and detoxification in the root apex is crucial for developing low-Cd rice cultivars. After Cd treatment, Cd concentration in rice root tips (RT) was 1.4 times higher than that in basal roots (BR). To uncover the distinct molecular responses to Cd toxicity, we conducted transcriptomic, proteomic, and metabolomic analyses on the two root sections. The results revealed that the RT exhibited 1.2–2.0 fold higher transcript or protein abundance of several Cd-related transporters than the BR, including Nramp1, Nramp5, IRT1, and HMA3, thereby contributing to more Cd accumulation in the RT. Furthermore, multi-omics analysis unveiled that the RT had enhanced activity in 'phenylpropanoid metabolism', 'AsA-GSH cycle' and 'tryptophan metabolism', conferring the stronger antioxidant system. While the BR showed higher activation in 'cell wall remodeling' and 'terpenoid biosynthesis'. This comprehensive study provides insights into the regulatory network of genes, proteins and metabolites involved in the differential responses to Cd toxicity between rice root tips and mature zones. [Display omitted] • Cd accumulation in root tip (RT) was higher than that in mature zone (BR) in rice. • RT exhibited higher protein abundances of Cd transporters Nramp1, Nramp 5 and IRT1. • Cd toxicity impaired cell wall remodeling in the RT but not in the BR. • Under Cd conditions, AsA-GSH cycle and tryptophan metabolism were enhanced in RT. • Terpenoid biosynthesis was induced in the BR when exposed to Cd stress. [ABSTRACT FROM AUTHOR]

Exposure to air pollutants has been associated with various adverse health outcomes, including chronic obstructive pulmonary disease (COPD). However, the precise underlying mechanism by which air pollution impacts COPD through remains insufficiently understood. To elucidated the molecular mechanism by which air pollutant exposure contributes to alterations in the gut microbiome and metabolism in AECOPD patients, we employed metagenomics and untargeted metabolomics to analyse the gut microbial, faecal, and serum metabolites. The correlations among air pollutants, gut microbes, serum metabolites, and blood biochemical markers were assessed using generalised additive mixed models and Spearman correlation analysis. The findings revealed that for every 10 μg/m3 increase in PM 2.5 concentration, the α-diversity of the gut flora decreased by 2.16% (95% CI: 1.80%−2.53%). We found seven microorganisms that were significantly associated with air pollutants, of which Enterococcus faecium , Bacteroides fragilis , Ruthenibacterium lactatiformans , and Subdoligranulum sp.4_3_54A2FAA were primarily associated with glycolysis. We identified 13 serum metabolites and 17 faecal metabolites significantly linked to air pollutants. Seven of these metabolites, which were strongly associated with air pollutants and blood biochemical indices, were found in both serum and faecal samples. Some of these metabolites, such as 2,5-furandicarboxylic acid, C-8C1P and melatonin, were closely associated with disturbances in lipid and fatty acid metabolism in AECOPD patients. These findings underscore the impact of air pollutants on overall metabolism based on influencing gut microbes and metabolites in AECOPD patients. Moreover, these altered biomarkers establish the biologic connection between air pollutant exposure and AECOPD outcomes.The identification of pertinent biomarkers provides valuable insights for the development of precision COPD prevention strategies. • Present a theoretical foundation for COPD prevention and treatment strategies. • Establish the connection between air pollutant exposure and AECOPD outcomes. • Reveal disturbances in lipid and fatty acid metabolism in AECOPD patients. [ABSTRACT FROM AUTHOR]

[Display omitted] • A multi-omics approach investigates O 3 -induced pulmonary molecular changes in mice. • Acute O 3 exposure exacerbates inflammation and oxidative stress in obese mice. • Arachidonic acid and the PPAR pathway are important in O 3 exposure response. • Obesity disrupts pulmonary lipidome, and O 3 exacerbates glycerophospholipid disruption. Certain sub-groups, including men and obese individuals, are more susceptible to ozone (O 3) exposure, but the underlying molecular mechanisms remain unclear. In this study, the male mice were divided into two dietary groups: one fed a high-fat diet (HFD), mimicking obesity conditions, and the other fed a normal diet (ND), then exposed to 0.5 ppm and 2 ppm O 3 for 4 h per day over two days. The HFD mice exhibited significantly higher body weight and serum lipid biochemical indicators compared to the ND mice. Obese mice also exhibited more severe pulmonary inflammation and oxidative stress. Using a multi-omics approach including proteomics, metabolomics, and lipidomics, we observed that O 3 exposure induced significant pulmonary molecular changes in both obese and normal mice, primarily arachidonic acid metabolism and lipid metabolism. Different molecular biomarker responses to acute O 3 exposure were also observed between two dietary groups, with immune-related proteins impacted in obese mice and PPAR pathway-related proteins affected in normal mice. Furthermore, although not statistically significant, O 3 exposure tended to aggravate HFD-induced disturbances in lung glycerophospholipid metabolism. Overall, this study provides valuable molecular insights into the responses of lung to O 3 exposure and highlights the potential impact of O 3 on obesity-induced metabolic changes. [ABSTRACT FROM AUTHOR]

[Display omitted] • A multi-omics approach was first used to explore stress resistance mechanisms. • Pseudomonas sp. LW60 removed 100 % nitrogen at C/N 10 and 4 °C. • High ammonia nitrogen removal efficiency (81.31 %) at C/N < 6 and 4 °C. • Central carbon and amino acid pathways were enhanced under low C/N ratio stress. In practical engineering, nitrogen removal at low temperatures or low C/N ratios is difficult. Although strains can remove nitrogen well at low temperatures, there is no research on the performance and deep mechanism of strains under low C/N ratio stress. In this study, Pseudomonas sp. LW60 with superior nitrogen removal efficiency under low C/N ratio stress was isolated at 4 °C. With a C/N ratio of 2–10, the NH 4 +-N removal efficiency was 40.02 %-100 % at 4 °C. Furthermore, the resistance mechanism of Pseudomonas sp. LW60 to low C/N ratio stress was deeply investigated by multi-omics. The results of transcriptome, proteome, and metabolome revealed that the resistance of strain LW60 to low C/N ratio stress was attributed to enhanced central carbon metabolism, amino acid metabolism, and ABC transporters, rather than nitrogen removal pathways. This study isolated a strain with low C/N ratio tolerance and deeply explored its tolerance mechanism by multi-omics. [ABSTRACT FROM AUTHOR]

Camellia oleifera is an important industrial crop whose leaf, flower, pericarp, and seed have multiple application values. Grafting is the main means of C. oleifera propagation, and the quality of grafted seedlings is directly related to the propagation coefficient and yield promotion. However, the research on C. oleifera grafting is lacking, and there is little comprehensive understanding of the growth characteristics, metabolic patterns, and molecular mechanisms of different grafting combinations of C. oleifera. In this study, the phenotypic, metabolomic, and transcriptomic profiles of four grafting combinations [ C. oleifera (Co), C. yuhsienensis (Cy), C. chekiangoleosa (Cc), and C. gigantocarpa (Cg) four kinds of scions grafted onto one rootstock, C. oleifera (Co)] were investigated. The phenotypic analysis showed that hetero-grafting inhibited the growth vigor of grafted unions. The abundance of shikimic acid and phenylethylamine in hetero-grafting was lower than in auto-grafting based on the differential metabolite analysis, and the exogenous addition of both metabolites promoted the growth of grafted unions. Multi-omics analysis revealed that hetero-grafting could significantly affect the differential expression of hub genes (aroD , aroE , aroK , pheA , tyrB) in the biosynthesis of shikimic acid and phenylethylamine and that AP2/ERF , MYB , and GRAS transcription factors were involved in regulating the expression of the above hub genes. These findings innovatively characterized the important role of shikimic acid and phenethylamine in the growth of C. oleifera grafted seedlings and provided new insights for promoting the propagation and industry development of C. oleifera. [Display omitted] • Hetero-grafting inhibited the growth vigor of Camellia oleifera. • Shikimic acid and phenylethylamine have positive effects on grafted C. oleifera. • The hub genes involved in shikimic acid and phenylethylamine accumulation were screened. • The transcriptional regulation model of the hub genes was established. [ABSTRACT FROM AUTHOR]

• Omics techniques provides new tools for forensic entomological research. • Genomics, transcriptomics, proteomics, metabolomics, and microbiomics are reviewed. • Omics techniques play an important role in the study of forensically related species. • Multi-omics and combination with other techniques will be applied in future research. With the advent of the post-genome era, omics technologies have developed rapidly and are widely used, including in genomics, transcriptomics, proteomics, metabolomics, and microbiome research. These omics techniques are often based on comprehensive and systematic analysis of biological samples using high-throughput analysis methods and bioinformatics, to provide new insights into biological phenomena. Currently, omics techniques are gradually being applied to forensic entomology research and are useful in species identification, phylogenetics, screening for developmentally relevant differentially expressed genes, and the interpretation of behavioral characteristics of forensic-related species at the genetic level. These all provide valuable information for estimating the postmortem interval (PMI). This review mainly discusses the available omics techniques, summarizes the application of omics techniques in forensic entomology, and their future in the field. [ABSTRACT FROM AUTHOR]

Green pepper is regarded as one of the globally essential commercial crops with bright color and rich nutrition. However, green pepper is susceptible to mechanical injuries as a result of vibration, compression and impact events during postharvest handling and transportation. These injuries can induce physiological and biochemical abnormalities in fruit, thus accelerating fruit senescence and leading to economic losses. Calcium chloride (CaCl 2) treatment is a safe, effective and economical method to maintain fruit quality during postharvest storage. Here, the impact of calcium treatment on the fruit quality of mechanically injured green pepper was investigated. The results indicated that calcium treatment maintained the sensory quality and hardness of green pepper fruit, inhibited redness development and elevation in the level of malondialdehyde (MDA). The combination of transcriptomics, metabolomics and assay for transposase accessible chromatin with high-throughput sequencing (ATAC-seq) revealed treatment effects of the expression of key genes related to fruit color change, fruit softening, active oxygen metabolism and hormone response, as well as changes of metabolites concentrations, and chromatin accessibility changes. A construction of regulatory network model of calcium treatment on post-harvest mechanical injury of green pepper fruit was developed based on these effects. Overall, the study provides valuable insights into the impact of mechanical injury on fruit after harvest and its amelioration by calcium. [Display omitted] • CaCl 2 treatment maintained sensory quality and hardness of green pepper fruit. • CaCl 2 treatment inhibited redness development and increase of MDA content. • CaCl 2 treatment improved the adverse effect of mechanical injury on fruit quality. • CaCl 2 treatment regulated color, texture, ROS and phytohormone related processes [ABSTRACT FROM AUTHOR]

Dietary intake of a large amount of soybean meal (SBM) adversely affects the physiological condition and growth of fish, while SBM is a commonly used substitute for fish meal (FM) in aquaculture feed. In the present study, we investigated the effects of feeding an SBM-based diet (SBMD) for 8 weeks on hepatopancreatic metabolic condition in red seabream Pagrus major , using comprehensive analyses of the transcriptome and metabolome. Compared with fish fed an FM-based control diet (FMD), fish fed the SBMD showed delayed growth, decreases in hepatopancreatic somatic index and serum cholesterol concentration, and hepatopancreatic tissue degeneration. Transcriptome sequencing analysis identified 454, 353, and 566 differentially expressed genes at 2, 4, and 8 weeks, respectively. Analysis of the hepatopancreas metabolome using capillary electrophoresis-time-of-flight mass spectrometry identified 301 quantifiable metabolites in the FMD and SBMD groups. Transcriptome analysis showed increases in gene expression levels in the terpenoid and steroid biosynthesis pathways, suggesting that hepatic cholesterol biosynthesis was up-regulated in the SBMD group. In addition, the results of transcriptome and metabolome analyses suggested that the SBMD affects glutathione and glycine metabolism. These findings provide valuable information that enhances our understanding of the effects of dietary SBM intake on red seabream metabolism. • Red seabream were fed a soybean meal–based diet (SBMD) for 8 weeks. • Fish fed SBMD showed delayed growth and several physiological abnormalities. • The results of omics analyses suggest SBMD affects cholesterol metabolism. • Hepatic glutathione and glycine metabolism were also affected by SBMD feeding. [ABSTRACT FROM AUTHOR]

Sulfide is a common harmful substance in sediments, with an especially high risk for deposit feeder organisms. The sea cucumber Apostichopus japonicus is a typical benthic feeder, and its intestine is the first line of defense and serves as a crucial barrier function. In this study, histological, physiological, gut microbiota, and metabolomic analyses were performed to explore the toxic response in the intestine of juvenile A. japonicus exposed to 0, 0.8, and 1.6 mg/L sulfide stress for 96 h. The results revealed sulfide-induced intestinal inflammatory symptoms and oxidative stress. Moreover, gut bacterial composition was observed after sulfide exposure, with an increase in Proteobacteria and a decrease in Cyanobacteria and Planctomycetes. Specifically, sulfide increased a set of sulfide-removing bacteria and opportunistic pathogens while decreasing several putative beneficial substance-producing bacteria. The metabolomic analysis indicated that sulfide also disturbed metabolic homeostasis, especially lipid and energy metabolism, in intestine. Interestingly, several intestinal bacteria were further identified to be significantly correlated with metabolic changes; for example, the decreased abundance levels of Bacillus, Corynebacterium , and Psychromonas were positively correlated with important energy metabolites, including maleic acid, farnesyl pyrophosphate, thiamine, butynoic acid, and deoxycholic acid. Thus, our research provides new insights into the mechanisms associated with the intestinal metabolic and microbiota response involved in sulfide stress adaptation strategies of juvenile A. japonicus. [ABSTRACT FROM AUTHOR]

[Display omitted] • Key volatile organic compounds associated with watermelon aroma were identified. • Key aroma compounds are closely related to the sugar content and flesh color. • Linkage markers and candidate genes of key aroma compounds were obtained. A range of volatile organic compounds played an important role in the formation of watermelon fruit aroma, while due to the low content and difficulty in detection, it is often neglected in watermelon breeding programs, resulting in a decline in fruit flavor. VOCs in the flesh of 194 watermelon accessions and seven cultivars at four developmental stages were determined by SPME-GC–MS. Ten metabolites with significant differences in the natural population and positive accumulation during fruit development are considered to be the key metabolite related to watermelon fruit aroma. And the link between metabolite and, flesh color and sugar content by correlation analysis was established. The results of the genome-wide association study showed that (5E)-6,10-dimethylundeca-5,9-dien-2-one, and 1-(4-methylphenyl) ethanone were colocalized with watermelon flesh color on chromosome 4, which may be regulated by LCYB and CCD. (E)-4-(2,6,6-trimethylcyclohexen-1-yl)but-3-en-2-one is the VOC produced by the cleavage of carotenoids, which has a positive correlation with the sugar content of the fruit, and the candidate gene Cla97C05G092490 on chromosome 5 may interact with PSY to influence the accumulation of this metabolite. In addition, Cla97C02G049790 (enol reductase), Cla97C03G051490 (omega-3 fatty acid desaturase gene), LOX , and ADH may play important roles in the synthesis of fatty acids and their derived VOCs. Taken together, our findings provide molecular insights into the accumulation and natural variation of VOCs in watermelon, and give data support for breeding watermelon cultivars with better flavor. [ABSTRACT FROM AUTHOR]

[Display omitted] Emerging epidemiological evidence has linked per- and polyfluoroalkyl substances (PFAS) exposure could be linked to the disturbance of gestational glucolipid metabolism, but the toxicological mechanism is unclear, especially when the exposure is at a low level. This study examined the glucolipid metabolic changes in pregnant rats treated with relatively low dose perfluorooctanesulfonic acid (PFOS) through oral gavage during pregnancy [gestational day (GD): 1–18]. We explored the molecular mechanisms underlying the metabolic perturbation. Oral glucose tolerance test (OGTT) and biochemical tests were performed to assess the glucose homeostasis and serum lipid profiles in pregnant Sprague-Dawley (SD) rats randomly assigned to starch, 0.03 and 0.3 mg/kg·bw·d groups. Transcriptome sequencing combined with non-targeted metabolomic assays were further performed to identify differentially altered genes and metabolites in the liver of maternal rats, and to determine their correlation with the maternal metabolic phenotypes. Results of transcriptome showed that differentially expressed genes at 0.03 and 0.3 mg/kg·bw·d PFOS exposure were related to several metabolic pathways, such as peroxisome proliferator-activated receptors (PPARs) signaling, ovarian steroid synthesis, arachidonic acid metabolism, insulin resistance, cholesterol metabolism, unsaturated fatty acid synthesis, bile acid secretion. The untargeted metabolomics identified 164 and 158 differential metabolites in 0.03 and 0.3 mg/kg·bw·d exposure groups, respectively under negative ion mode of Electrospray Ionization (ESI-), which could be enriched in metabolic pathways such as α-linolenic acid metabolism, glycolysis/gluconeogenesis, glycerolipid metabolism, glucagon signaling pathway, glycine, serine and threonine metabolism. Co-enrichment analysis indicated that PFOS exposure may disturb the metabolism pathways of glycerolipid, glycolysis/gluconeogenesis, linoleic acid, steroid biosynthesis, glycine, serine and threonine. The key involved genes included down-regulated Ppp1r3c and Abcd2, and up-regulated Ogdhl and Ppp1r3g , and the key metabolites such as increased glycerol 3-phosphate and lactosylceramide were further identified. Both of them were significantly associated with maternal fasting blood glucose (FBG) level. Our findings may provide mechanistic clues for clarifying metabolic toxicity of PFOS in human, especially for susceptible population such as pregnant women. [ABSTRACT FROM AUTHOR]

Since dementia is preventable with early interventions, biomarkers that assist in diagnosing early stages of dementia, such as mild cognitive impairment (MCI), are urgently needed. Multiomics analysis of amnestic MCI (aMCI) peripheral blood (n = 25) was performed covering the transcriptome, microRNA, proteome, and metabolome. Validation analysis for microRNAs was conducted in an independent cohort (n = 12). Artificial intelligence was used to identify the most important features for predicting aMCI. We found that hsa-miR-4455 is the best biomarker in all omics analyses. The diagnostic index taking a ratio of hsa-miR-4455 to hsa-let-7b-3p predicted aMCI patients against healthy subjects with 97% overall accuracy. An integrated review of multiomics data suggested that a subset of T cells and the GCN (general control nonderepressible) pathway are associated with aMCI. The multiomics approach has enabled aMCI biomarkers with high specificity and illuminated the accompanying changes in peripheral blood. Future large-scale studies are necessary to validate candidate biomarkers for clinical use. [ABSTRACT FROM AUTHOR]