PubMed

Nat Protoc. 2024 Jul 23. doi: 10.1038/s41596-024-01009-8. Online ahead of print.ABSTRACTA biomolecular coating, or biocorona, forms on the surface of engineered nanomaterials (ENMs) immediately as they enter biological or environmental systems, defining their biological and environmental identity and influencing their fate and performance. This biomolecular layer includes proteins (the protein corona) and other biomolecules, such as nucleic acids and metabolites. To ensure a meaningful and reproducible analysis of the ENMs-associated biocorona, it is essential to streamline procedures for its preparation, separation, identification and characterization, so that studies in different labs can be easily compared, and the information collected can be used to predict the composition, dynamics and properties of biocoronas acquired by other ENMs. Most studies focus on the protein corona as proteins are easier to monitor and characterize than other biomolecules and play crucial roles in receptor engagement and signaling; however, metabolites play equally critical roles in signaling. Here we describe how to reproducibly prepare and characterize biomolecule-coated ENMs, noting especially the steps that need optimization for different types of ENMs. The structure and composition of the biocoronas are characterized using general methods (transmission electron microscopy, dynamic light scattering, capillary electrophoresis-mass spectrometry and liquid chromatography-mass spectrometry) as well as advanced techniques, such as transmission electron cryomicroscopy, synchrotron-based X-ray absorption near edge structure and circular dichroism. We also discuss how to use molecular dynamic simulation to study and predict the interaction between ENMs and biomolecules and the resulting biocorona composition. The application of this protocol can provide mechanistic insights into the formation, composition and evolution of the ENM biocorona, ultimately facilitating the biomedical and agricultural application of ENMs and a better understanding of their impact in the environment.PMID:39044000 | DOI:10.1038/s41596-024-01009-8

Sci Rep. 2024 Jul 24;14(1):17032. doi: 10.1038/s41598-024-67869-y.ABSTRACTCorn silage can usually improve the growth performance and the meat quality of ruminants, and subsequently increase the economic benefits of farming. However, little is known about the effects of corn silage on donkeys. This experiment investigated the effects of corn silage on the weight gain, gut microbiota and metabolites of Dezhou donkeys. A total of 24 Dezhou donkeys, sourced from the same farm and exhibiting similar age and average body weight, were utilized in this experiment. The donkeys were allocated into two groups: a control group receiving a basic diet and a test group receiving a basic diet supplemented with 30% corn silage. Each group comprised 12 donkeys, evenly distributed by sex (6 males and 6 females). The experiment lasted for 100 days. Results showed that dietary supplementation with corn silage significantly (P < 0.05) improved the weight gain of Dezhou donkeys at the end of the experiment. And the supplementation of corn silage in the diet significantly altered the bacterial community composition and metabolome in the feces of the donkeys. Notably, the relative abundance ratio of Bacteroidetes to Firmicutes was 0.76 in the control group compared to 0.96 in the test group. Furthermore, members of the Bacteroidetes and Firmicutes phyla were associated with differentiated metabolites enriched in the arachidonic acid metabolism and pentose and glucuronate interconversion pathways, both of which have been reported to be related to animal growth. Specifically, Bacteroidia exhibited statistically (P < 0.05) positive correlations with 15S-HpETE, while Bacilli demonstrated statistically (P < 0.05) negative correlations with D-Xylulose. The findings of this study can advance our mechanistic understanding of the remodeling of intestinal microbiota and metabolome induced by corn silage, as well as their relationships with the growth performance of Dezhou donkeys, which in turn favor the improvement in nutrition of Dezhou donkeys.PMID:39043883 | DOI:10.1038/s41598-024-67869-y

Sci Rep. 2024 Jul 23;14(1):16929. doi: 10.1038/s41598-024-67835-8.ABSTRACTNeurodevelopmental disorders are rapidly increasing in prevalence and have been linked to various environmental risk factors. Mounting evidence suggests a potential role of vitamin D in child neurodevelopment, though the causal mechanisms remain largely unknown. Here, we investigate how vitamin D deficiency affects children's communication development, particularly in relation to Autism Spectrum Disorder (ASD). We do so by developing an integrative network approach that combines metabolomic profiles, clinical traits, and neurodevelopmental data from a pediatric cohort. Our results show that low levels of vitamin D are associated with changes in the metabolic networks of tryptophan, linoleic, and fatty acid metabolism. These changes correlate with distinct ASD-related phenotypes, including delayed communication skills and respiratory dysfunctions. Additionally, our analysis suggests the kynurenine and serotonin sub-pathways may mediate the effect of vitamin D on early life communication development. Altogether, our findings provide metabolome-wide insights into the potential of vitamin D as a therapeutic option for ASD and other communication disorders.PMID:39043876 | DOI:10.1038/s41598-024-67835-8

Sci Rep. 2024 Jul 23;14(1):16980. doi: 10.1038/s41598-024-67981-z.ABSTRACTMusk is an important animal product, but the musk secretion mechanism of forest musk deer (Moschus berezovskii) is still unclear. The musk synthesis process in forest musk deer is extremely complex, and many raw materials are directly or indirectly derived from forest musk deer blood. In this study, metabolomics was used to analyze the blood of forest musk deer in secretory and non-secretory phases for the first time, aim at explaining the secretion mechanism from the perspective of blood metabolism. We found that P450-related, choline-related, axonal regeneration and other pathways and related metabolites were significantly enriched during the musk secretion of forest musk deer. These pathways and metabolites related to P450 and choline in blood may have important implications for the mechanism of musk secretion in forest musk deer, because blood components were closely related to musk components and could provide raw materials for musk synthesis in musk gland cells.PMID:39043795 | DOI:10.1038/s41598-024-67981-z

Sci Rep. 2024 Jul 23;14(1):17007. doi: 10.1038/s41598-024-66371-9.ABSTRACTPopulation aging around the world is rapidly progressing; as a result, cognitive decline developing into dementia is becoming a social problem. There is no drug that can cure dementia, and though drugs that alleviate the symptoms of dementia have been developed, they also have side effects. Therefore, we conducted a study on improving cognitive function using natural products that have secured safety. We confirmed the effect of an extract of Scrophularia buergeriana on scopolamine-induced cognitive impairment through mouse behavioral experiments, and we observed metabolic changes in the cortex and hippocampus via brain tissue dissection after the behavioral experiment. Mitigating effects of S. buergeriana on cognitive impairment caused by scopolamine were observed in passive avoidance and Morris water maze tests. A metabolic analysis revealed biomarkers related to the alleviating effect of cognitive impairment. Niacinamide, tyrosine, uridine, and valine in the cortex and GABA, choline, creatine, formate, fumarate, hypoxanthine, leucine, myo-inositol, pyroglutamate, and taurine in the hippocampus were identified as biomarker candidates for recovering cognitive impairment. In addition to behavioral experiments, this metabolomics study using specific regions of the brain may be helpful in understanding the effects of cognitive improvement.PMID:39043762 | DOI:10.1038/s41598-024-66371-9

Nat Commun. 2024 Jul 23;15(1):6216. doi: 10.1038/s41467-024-50282-4.ABSTRACTHuman cytomegalovirus (CMV) is a highly prevalent herpesvirus that is often transmitted to the neonate via breast milk. Postnatal CMV transmission can have negative health consequences for preterm and immunocompromised infants, but any effects on healthy term infants are thought to be benign. Furthermore, the impact of CMV on the composition of the hundreds of bioactive factors in human milk has not been tested. Here, we utilize a cohort of exclusively breastfeeding full-term mother-infant pairs to test for differences in the milk transcriptome and metabolome associated with CMV, and the impact of CMV in breast milk on the infant gut microbiome and infant growth. We find upregulation of the indoleamine 2,3-dioxygenase (IDO) tryptophan-to-kynurenine metabolic pathway in CMV+ milk samples, and that CMV+ milk is associated with decreased Bifidobacterium in the infant gut. Our data indicate two opposing CMV-associated effects on infant growth; with kynurenine positively correlated, and CMV viral load negatively correlated, with infant weight-for-length at 1 month of age. These results suggest CMV transmission, CMV-related changes in milk composition, or both may be modulators of full-term infant development.PMID:39043677 | DOI:10.1038/s41467-024-50282-4

Alcohol Alcohol. 2024 Jul 21;59(5):agae050. doi: 10.1093/alcalc/agae050.ABSTRACTThe human intestine is colonized by a variety of microorganisms that influence the immune system, the metabolic response, and the nervous system, with consequences for brain function and behavior. Unbalance in this microbial ecosystem has been shown to be associated with psychiatric disorders, and altered gut microbiome composition related to bacteria, viruses, and fungi has been well established in patients with alcohol use disorder. This review describes the gut microbiome-brain communication pathways, including the ones related to the vagus nerve, the inflammatory cytokines, and the gut-derived metabolites. Finally, the potential benefits of microbiota-based therapies for the management of alcohol use disorder, such as probiotics, prebiotics, and fecal microbiota transplantation, are also discussed.PMID:39042929 | DOI:10.1093/alcalc/agae050

Gut Microbes. 2024 Jan-Dec;16(1):2379624. doi: 10.1080/19490976.2024.2379624. Epub 2024 Jul 23.ABSTRACTSymbiosis between the host and intestinal microbial communities is essential for human health. Disruption in this symbiosis is linked to gastrointestinal diseases, including inflammatory bowel diseases, as well as extra-gastrointestinal diseases. Unbalanced gut microbiome or gut dysbiosis contributes in multiple ways to disease frequency, severity and progression. Microbiome taxonomic profiling and metabolomics approaches greatly improved our understanding of gut dysbiosis features; however, the precise mechanisms involved in gut dysbiosis establishment still need to be clarified. The aim of this review is to present new actors and mechanisms underlying gut dysbiosis formation following parasitic infection or in a context of altered Paneth cells, revealing the existence of a critical crosstalk between Paneth and tuft cells to control microbiome composition.PMID:39042424 | DOI:10.1080/19490976.2024.2379624

Invest Ophthalmol Vis Sci. 2024 Jul 1;65(8):37. doi: 10.1167/iovs.65.8.37.ABSTRACTPURPOSE: Cell lines are being used in preclinical uveal melanoma (UM) research. Because not all cell lines harbor typical GNAQ or GNA11 hotspot mutations, we aimed at better classifying them and determining whether we could find genetic causes to explain the protein and mRNA expression profiles of the cell lines.METHODS: We studied protein and mRNA expression of 14 UM cell lines and determined the presence of single nucleotide variants and small insertions and deletions with next-generation sequencing and copy number alterations with a single nucleotide polymorphism array. The lists of differentially expressed proteins and genes were merged, and shared lists were created, keeping only terms with concordant mRNA and protein expression. Enrichment analyses were performed on the shared lists.RESULTS: Cell lines Mel285 and Mel290 are separate from GNA-mutated cell lines and show downregulation of melanosome-related markers. Both lack typical UM mutations but each harbors four putatively deleterious variants in CTNNB1, PPP1R10, LIMCH1, and APC in Mel285 and ARID1A, PPP1R10, SPG11, and RNF43 in Mel290. The upregulated terms in Mel285 and Mel290 did not point to a convincing alternative origin. Mel285 shows loss of chromosomes 1p, 3p, partial 3q, 6, and partial 8p, whereas Mel290 shows loss of 1p and 6. Expression in the other 12 cell lines was related to BAP1 expression.CONCLUSIONS: Although Mel285 and Mel290 have copy number alterations that fit UM, multi-omics analyses show that they belong to a separate group compared to the other analyzed UM cell lines. Therefore, they may not be representative models to test potential therapeutic targets for UM.PMID:39042403 | DOI:10.1167/iovs.65.8.37

Microbiol Spectr. 2024 Jul 23:e0010824. doi: 10.1128/spectrum.00108-24. Online ahead of print.ABSTRACTAspergillus flavus conidia are widespread in air; they attach to food and feed crops and secrete aflatoxins, which results in serious contamination. Germination of A. flavus conidia is the most critical step in contamination of food by A. flavus. This study aims to gain an insight into A. flavus conidia through dormancy to germination to provide a theoretical basis for inhibition of A. flavus conidia germination. The morphological changes and regulation mechanism of A. flavus conidia germination at 0, 4, 8, and 12 hours were observed. Transcriptomic and metabolomic analyses showed that conidia became active from dormancy (0 hour) to the initial stage of germination (4 hours), cellular respiration and energy metabolism increased, and amino acids and lipids were synthesized rapidly. The number of differentially expressed genes and differential metabolites was highest at this stage. Besides, we found that conidia germination had selectivity for different carbon and nitrogen sources. Compared with monosaccharides, disaccharides, as the only carbon source, significantly promoted the germination of conidia. Moreover, MepA, one of genes in the ammonium transporter family was studied. The gene deletion mutant ΔMepA had a significant growth defect, and the expression of MeaA was significantly upregulated in ΔMepA compared with the wild-type, indicating that both MepA and MeaA played an important role in transporting ammonium ions.IMPORTANCEThis is the first study to use combined transcriptomic and metabolomics analyses to explore the biological changes during germination of Aspergillus flavus conidia. The biological process with the highest changes occurred in 0-4 hours at the initial stage of germination. Compared with polysaccharides, monosaccharides significantly increased the size of conidia, while significantly decreasing the germination rate of conidia. Both MeaA and MepA were involved in ammonia transport and metabolism during conidia germination.PMID:39041812 | DOI:10.1128/spectrum.00108-24

Zhongguo Zhong Yao Za Zhi. 2024 Jun;49(11):3031-3039. doi: 10.19540/j.cnki.cjcmm.20231204.401.ABSTRACTHaematitum is a commonly used mineral medicine. It is toxic, as recorded in the second volume of Chinese Materia Medica. Therefore, it should not be taken for a long time. In this study, the effects of Haematitum and calcined Haematitum on multiple organ injuries in mice were investigated, and the mechanism of the toxicity of the related organs was explored by metabolomics. The mice were randomly divided into the control group, Haematitum low-dose group(ZS-L group), Haematitum high-dose group(ZS-H group), and calcined Haematitum high-dose group(DZS-H group), with 12 mice in each group. Haematitum decoction was given by continuous intragastric administration for 10 days. Then the life situation was observed, and samples were taken to detect various indicators. The results showed that the ZS-H group showed obvious toxicity, with different degrees of toxicity damage in the intestinal tract,liver, spleen, and lung. ZS-L group had no toxic reaction. The toxicity of the DZS-H group was significantly reduced, and only the lung was damaged. Metabolomics technology was used to detect the lung tissue of mice in the control group and the ZS-H group, and a total of 15 kinds of significant difference metabolites were detected, mainly involved in choline metabolism in cancer, sphingolipid metabolism, and glycerophospholipid metabolism. Immunohistochemical results showed that the INSIG1 protein expression level in the lung tissue of mice in the ZS-H group was significantly higher than that in the control group. In summary, large doses and long-time use of Haematitum decoction will cause a variety of organ damage, and the same dose of calcined Haematitum is less toxic than Haematitum. In addition, a low dose of Haematitum has no obvious toxic effect. The dysfunction of lipid metabolic pathways such as sphingolipid and glycerophospholipid metabolism may be an important factor in Haematitum-induced pulmonary toxicity. This study provides a reference for further research on the mechanism of Haematitum pulmonary toxicity.PMID:39041163 | DOI:10.19540/j.cnki.cjcmm.20231204.401

Zhongguo Zhong Yao Za Zhi. 2024 Jun;49(11):3002-3011. doi: 10.19540/j.cnki.cjcmm.20240123.402.ABSTRACTThis study aims to observe the effects of the traditional Chinese medicine prescription Dahuang Zhechong Pills(DHZCP on renal aging and explore its potential multi-target effects. Rats were assigned into the normal, model, DHZCP, and vitamin E(VE)groups. Firstly, the rat model of D-galactose(D-gal)-induced renal aging was established. During the modeling period, the rats in the 4 groups were administrated with double distilled water, double distilled water, DHZCP suspension, and VE suspension, respectively,by gavage every day. On day 60 of intervention, the indicators of renal aging and injury in rats were measured, including the function,histopathological characteristics, senescence-associated β-galactosidase( SA-β-gal) staining, and expression levels of Klotho and proteins associated with cell cycle arrest and senescence-associated secretory phenotype(SASP) in the renal tissue. Moreover, nontargeted metabolomic analysis of the renal tissue was performed for the 4 groups of rats to screen out the potential biomarkers and metabolic pathways. Finally, the signaling pathways of key targets were preliminarily validated. The results showed that DHZCP and VE significantly improved the renal function, histopathological features of renal tubular/interstitial tissue, and degree of SA-β-gal staining, up-regulated the expression level of Klotho, and down-regulated the expression levels of proteins associated with cell cycle arrest and SASP in the renal tissue of the aging rats. In addition, DHZCP and VE regulated the metabolites in the renal tissue of the aging rats. There were 21 common differential metabolites. Among them, 5 differential metabolites were significantly increased in the aging rats and recovered after DHZCP or VE treatment, and they were involved in the lipid metabolism and energy metabolism pathways. The areas under the curves of the groups in comparison varied within the range of 0. 88-1. DHZCP regulated multiple signaling pathways, such as the adenosine monophosphate-activated protein kinase(AMPK), cyclic guanosine monophosphate-protein kinase G( c GMP-PKG), cyclic adenylic acid( c AMP), phosphatidylinositol-3-kinase-protein kinase B( PI3K-Akt), mammalian target of rapamycin(mTOR), and autophagy signaling pathways. In addition, it affected the multiple metabolic pathways, such as renin secretion, longevity regulation pathway, diabetic cardiomyopathy, and niacin and nicotinamide metabolism. DHZCP and VE significantly up-regulated the expression level of the key proteins in the AMPK signaling pathway in the renal tissue of the aging rats. In all, DHZCP and VE could mitigate renal aging and injury. DHZCP exerted multi-target effects via multiple signaling pathways and metabolic pathways in the kidney, in which the AMPK signaling pathway may be one of the key targets for action.PMID:39041160 | DOI:10.19540/j.cnki.cjcmm.20240123.402

Zhongguo Zhong Yao Za Zhi. 2024 Jul;49(13):3493-3504. doi: 10.19540/j.cnki.cjcmm.20240319.302.ABSTRACTBased on the processing and compatibility, this study explored the effects of components in Corni Fructus(CF) and Astragali Radix(AR) on plasma metabolomics in diabetic nephropathy rats. SD rats were randomly divided into four groups and diabetic nephropathy rat model was induced by high-fat diet combined with 30 mg·kg~(-1) streptozotocin(STZ). Histopathological observations of kidney tissue sections of rats in each group were conducted using HE, PAS, and Masson staining. Ultra-high performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry(UHPLC-Q-TOF-MS/MS) metabolomics method was employed to investigate the effects of CF before and after wine-processing combined with AR-related components on plasma metabolites in diabetic nephropathy rats. After drug treatment, kidney tissue damage and interstitial collagen fiber deposition area in diabetic nephropathy rats were improved to varying degrees(P&lt;0.001). The detection results of plasma metabolomics showed that 71 biomarkers related to the pathogenesis of diabetic nephropathy were identified in diseased rats, mainly involving linoleic acid metabolism, caffeine metabolism, glycerophospholipid metabolism, phenylalanine, tyrosine and tryptophan biosynthesis, arachidonic acid metabolism, phenylalanine metabolism, retinol metabolism, and ether lipid metabolism. After drug intervention, 26 of them were significantly downregulated, with better efficacy observed in precision processed herb-pair group(P-CG_5). This study elucidated from the perspective of plasma metabolomics that P-CG_5 could improve metabolic disorders in diabetic nephropathy through pathways such as phenylalanine, tyrosine and tryptophan biosynthesis, phenylalanine metabolism, and caffeine metabolism, providing theoretical support and experimental basis for the clinical application of CF and AR compatibility in traditional Chinese medicine.PMID:39041121 | DOI:10.19540/j.cnki.cjcmm.20240319.302

Zhongguo Zhong Yao Za Zhi. 2024 Jul;49(13):3484-3492. doi: 10.19540/j.cnki.cjcmm.20240414.101.ABSTRACTThis study aims to reveal the differences in the species and relative content of metabolites in the leaf and root tuber of Fallopia multiflora and improve the comprehensive utilization rate of F. multiflora resources. The metabolites in the root tubers and leaves of F. multiflora were detected by widely targeted metabolomics based on ultra performance liquid chromatography-tandem mass spectrometry(UPLC-MS/MS). The principal component analysis, hierarchical cluster analysis, and orthogonal partial least squares-discriminant analysis were carried out to screen the differential metabolites between the leaf and root tuber of F. multiflora. The result showed that a total of 1 942 metabolites in 15 categories were detected in the leaf and root tuber of F. multiflora, including 1 861 metabolites in the root tuber, 1 901 metabolites in the leaf, and 1 820 metabolites in both. The metabolites were mainly phenolic acids, flavonoids, amino acids and derivatives, and alkaloids. A total of 1 200 differential metabolites were screened out, accounting for 65.9% of the total metabolites. Among these differential metabolites, 813 and 387 showed higher content in the leaf and root tuber, respectively. Flavonoids were the metabolites with the largest number and the most significant differences between the leaf and root tuber, and stilbenes and anthraquinones as the main active compounds mainly existed in the root tuber. The KEGG enrichment results suggested that the differential metabolites were mainly enriched in flavonoid and flavonol biosynthesis pathways and linoleic acid metabolism pathway. This study discovered abundant metabolites in F. multiflora. The metabolites were similar but had great differences in the content between the leaf and root tuber. The research results provide theoretical guidance for the development and utilization of F. multiflora resources.PMID:39041120 | DOI:10.19540/j.cnki.cjcmm.20240414.101

Zhongguo Zhong Yao Za Zhi. 2024 Jun;49(12):3312-3319. doi: 10.19540/j.cnki.cjcmm.20231220.401.ABSTRACTUrine metabolomics based on ultra-performance liquid chromatography-quadrupole time-of-flight tandem mass spectrometry(UHPLC-Q-TOF-MS) was utilized to investigate the metabolic regulation mechanism of Tingli Dazao Xiefei Decoction(TLDZ) in rats with allergic asthma. SD male rats were divided into a normal group, a model group, a dexamethasone group, and a TLDZ group. The allergic asthma model was established by intraperitoneal injection of ovalbumin(OVA) to induce allergy, combined with atomization excitation. Urine metabolites from all rats were collected by UHPLC-Q-TOF-MS. The metabolic profiles of rats in each group were built by principal component analysis(PCA). Besides, the differential metabolites between the model group and the TLDZ group were selected by orthogonal partial least squares discriminant analysis(OPLS-DA), t-test(P&lt;0.05), and variable importance in the projection(VIP) values of more than 3. The differential metabolites were identified through HMDB, METLIN, and other online databa-ses. Heat maps and clustering analysis for relative quantitative information of biomarkers in each group were drawn by MeV 4.8.0 software. Finally, MetaboAnalyst, MBRole, and KEGG databases were used to enrich related metabolic pathways and construct metabolic networks. The result demonstrated that TLDZ could effectively regulate the disordered urine metabolic profiles of asthmatic rats. Combined with multivariate statistical analysis and online databases, a total of 45 differential metabolites with significant changes(P&lt;0.05) between the model group and the TLDZ group were screened out. Metabolic pathways including histidine metabolism, tryptophan metabolism, and arginine and proline metabolism were enriched. TLDZ could improve asthma by regulating related metabolic pathways and interfering with pathological processes such as immune homeostasis airway inflammation. The study investigates the molecular mechanism of anti-asthma of TLDZ from the perspective of urine metabolomics, and combined with previous pharmacological studies, it provides a scientific basis for the clinical development and application of TLDZ in the treatment of asthma.PMID:39041094 | DOI:10.19540/j.cnki.cjcmm.20231220.401

Zhongguo Zhong Yao Za Zhi. 2024 Jun;49(12):3263-3269. doi: 10.19540/j.cnki.cjcmm.20240314.301.ABSTRACTNumerous studies show that Lonicera macranthoides and L. japonica have significant differences in organic matter. However, there is still a lack of research on inorganic elements between them. In this study, a non-targeted elemental metabolomics method was established by inductively coupled plasma mass spectrometry(ICP-MS), so as to compare the overall differences of inorganic elements between L. macranthoides and L. japonica. In addition, the differential markers were screened, and these differential markers were quantitatively analyzed by the targeted method. The non-targeted elemental metabolomics showed that the established mathematical model could reflect the difference in element content between L. macranthoides and L. japonica. Four inorganic elements such as ~(55)Mn, ~(209)Bi, ~(111)Cd, and ~(85)Rb were confirmed as the differential markers of L. macranthoides and L. japonica based on the screening principles of variable importance in the projection(VIP) value&gt;2.0, P&lt;0.01 and fold change(FC) value&gt;1.2 or &lt;0.80. The targeted quantitative results showed that the content of ~(209)Bi in L. japonica was significantly higher than that in L. macranthoides, while ~(55)Mn, ~(111)Cd, and ~(85)Rb in L. macranthoides were significantly higher than that in L. japonica. The non-targeted and targeted elemental metabolomics methods based on ICP-MS can significantly reflect the overall differences in inorganic elements between L. macranthoides and L. japonica. Exploring the differences between them from the perspective of elements can partly reflect the differences in their drug properties and lay a foundation for further study on the quality control mode of inorganic elements in L. macranthoides and L. japonica and their pharmacological effects.PMID:39041088 | DOI:10.19540/j.cnki.cjcmm.20240314.301

Front Sleep. 2023;2:1293941. doi: 10.3389/frsle.2023.1293941. Epub 2023 Dec 4.ABSTRACTApproximately one in three adults in the United States sleeps less than the recommended 7 h per night. Decades of epidemiological data and data from experimental sleep restriction studies demonstrate short sleep duration is associated with adverse cardiometabolic risk, including risk of type 2 diabetes and cardiovascular disease. However, the precise mechanisms underlying this risk are not fully elucidated and there is a lack of sleep-based interventions designed to mitigate such risk. One strategy to overcome these limitations is to develop biomarkers that link habitual short sleep duration with adverse cardiometabolic risk. Such biomarkers could inform biochemical mechanisms, identify new targets for interventions, support precision medicine by identifying individuals most likely to benefit from sleep-based interventions, and ultimately lead to improved cardiometabolic health in people with habitual short sleep durations. Early progress demonstrates proof-of-principle that omics-based technologies are a viable approach to create biochemical signatures (biomarkers) of short sleep duration, primarily derived from acute studies of experimental sleep restriction. Yet, much work remains. Notably, studies that translate early findings from experimental sleep restriction to free-living adults with habitual short sleep duration have high potential to advance the field. Such studies also create an exciting opportunity for larger randomized controlled trials that simultaneously identify biomarkers of habitual short sleep duration and evaluate the efficacy of sleep-based interventions. Ultimately, early progress in developing molecular biomarkers of short sleep duration combined with the prior decades of progress in the sleep and metabolism fields provide the foundation for exciting progress in the biomarker development space.PMID:39041043 | PMC:PMC11262587 | DOI:10.3389/frsle.2023.1293941

Front Genet. 2024 Jul 8;15:1416283. doi: 10.3389/fgene.2024.1416283. eCollection 2024.ABSTRACTIntroduction: Laying performance is a key factor affecting production efficiency in poultry, but its molecular mechanism is still indistinct. In this study, Yaoshan chickens, a local breed in Guizhou, China, and merchant chickens (GYR) with higher egg yield after the three-line cross improvement hybridization of Yaoshan chickens were used as animal samples. Methods: To explore the regulatory mechanism of the diversities in laying performance, RNA-seq and ultra-performance liquid chromatographytandem mass spectrometry (UPLC-MS/MS) were used to describe the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens. Results: At the transcriptional level, 288 differentially expressed genes were upregulated in Yaoshan chickens and 353 differentially expressed genes were upregulated in GYR chickens. In addition, GSEA showed that ECM-receptor interactions and the TGF-β signaling pathway were restrained, resulting in increased egg production in GYR chickens. Furthermore, the upregulation of thiamine and carnitine was identified by metabolomic analysis to facilitate the laying performance of hens. Finally, comprehensive analyses of the transcriptome and metabolome found that thiamine and carnitine were negatively correlated with ECM-receptor interactions and the TGF-β signaling pathway, which jointly regulate the laying performance of Yaoshan chickens and GYR chickens. Discussion: Taken together, our research delineates differences in the transcriptional and metabolic profiles of the ovaries of Yaoshan and GYR chickens during the peak egg production period and provides new hypotheses and clues for further research on poultry egg production performance and the improvement of economic benefits.PMID:39040995 | PMC:PMC11260793 | DOI:10.3389/fgene.2024.1416283

Front Microbiol. 2024 Jul 1;15:1383526. doi: 10.3389/fmicb.2024.1383526. eCollection 2024.ABSTRACTOBJECTIVE: Rhizosphere microorganisms play crucial roles in the growth and development of plants, disease resistance, and environmental adaptability. As the only wild pepper variety resource in China, domesticated Capsicum frutescens Linn. (Xiaomila) exhibits varying beneficial traits and affects rhizosphere microbial composition compared with its wild counterparts. In this study, we aimed to identify specific rhizosphere microbiome and metabolism patterns established during the domestication process.METHODS: The rhizosphere microbial diversity and composition of domesticated and wild C. frutescens were detected and analyzed by metagenomics. Non-targeted metabolomics were used to explore the differences of metabolites in rhizosphere soil between wild and domesticated C. frutescens.RESULTS: We found that the rhizosphere microbial diversity of domesticated variety was significantly different from that of the wild variety, with Massilia being its dominant bacteria. However, the abundance of certain beneficial microbes such as Gemmatimonas, Streptomyces, Rambibacter, and Lysobacter decreased significantly. The main metabolites identified in the wild variety included serylthreonine, deoxyloganic acid, vitamin C, among others. In contrast, those identified in the domesticated group were 4-hydroxy-l-glutamic acid and benzoic acid. Furthermore, the differentially enriched pathways were concentrated in tyrosine and tryptophan biosynthesis, histidine and purine-derived alkaloids biosynthesis, benzoic acid family, two-component system, etc.CONCLUSION: This study revealed that C. frutescens established specific rhizosphere microbiota and metabolites during domestication, which has important significance for the efficient utilization of beneficial microorganisms in breeding and cultivation practices.PMID:39040904 | PMC:PMC11261347 | DOI:10.3389/fmicb.2024.1383526

Front Mol Biosci. 2024 Jul 8;11:1393240. doi: 10.3389/fmolb.2024.1393240. eCollection 2024.ABSTRACTBACKGROUND: COVID-19 disease is characterized by a spectrum of disease phases (mild, moderate, and severe). Each disease phase is marked by changes in omics profiles with corresponding changes in the expression of features (biosignatures). However, integrative analysis of multiple omics data from different experiments across studies to investigate biosignatures at various disease phases is limited. Exploring an integrative multi-omics profile analysis through a network approach could be used to determine biosignatures associated with specific disease phases and enable the examination of the relationships between the biosignatures.AIM: To identify and characterize biosignatures underlying various COVID-19 disease phases in an integrative multi-omics data analysis.METHOD: We leveraged a multi-omics network-based approach to integrate transcriptomics, metabolomics, proteomics, and lipidomics data. The World Health Organization Ordinal Scale WHO Ordinal Scale was used as a disease severity reference to harmonize COVID-19 patient metadata across two studies with independent data. A unified COVID-19 knowledge graph was constructed by assembling a disease-specific interactome from the literature and databases. Disease-state specific omics-graphs were constructed by integrating multi-omics data with the unified COVID-19 knowledge graph. We expanded on the network layers of multiXrank, a random walk with restart on multilayer network algorithm, to explore disease state omics-specific graphs and perform enrichment analysis.RESULTS: Network analysis revealed the biosignatures involved in inducing chemokines and inflammatory responses as hubs in the severe and moderate disease phases. We observed distinct biosignatures between severe and moderate disease phases as compared to mild-moderate and mild-severe disease phases. Mild COVID-19 cases were characterized by a unique biosignature comprising C-C Motif Chemokine Ligand 4 (CCL4), and Interferon Regulatory Factor 1 (IRF1). Hepatocyte Growth Factor (HGF), Matrix Metallopeptidase 12 (MMP12), Interleukin 10 (IL10), Nuclear Factor Kappa B Subunit 1 (NFKB1), and suberoylcarnitine form hubs in the omics network that characterizes the moderate disease state. The severe cases were marked by biosignatures such as Signal Transducer and Activator of Transcription 1 (STAT1), Superoxide Dismutase 2 (SOD2), HGF, taurine, lysophosphatidylcholine, diacylglycerol, triglycerides, and sphingomyelin that characterize the disease state.CONCLUSION: This study identified both biosignatures of different omics types enriched in disease-related pathways and their associated interactions (such as protein-protein, protein-transcript, protein-metabolite, transcript-metabolite, and lipid-lipid interactions) that are unique to mild, moderate, and severe COVID-19 disease states. These biosignatures include molecular features that underlie the observed clinical heterogeneity of COVID-19 and emphasize the need for disease-phase-specific treatment strategies. The approach implemented here can be used to find associations between transcripts, proteins, lipids, and metabolites in other diseases.PMID:39040605 | PMC:PMC11260748 | DOI:10.3389/fmolb.2024.1393240