PubMed

J Hepatol. 2023 Jan 23:S0168-8278(23)00021-1. doi: 10.1016/j.jhep.2023.01.009. Online ahead of print.ABSTRACTBACKGROUND & AIMS: Mouse models of lineage tracing have helped to describe the important subpopulations of hepatocytes responsible for liver regeneration. However, conflicting results have been obtained from different models. Here we aimed to reconcile these conflicting reports by repeating a key lineage tracing study from pericentral hepatocytes and characterised this Axin2CreERT2 model in detail.METHODS: We performed detailed characterisation of the labelled population in the Axin2CreERT2 model. We lineage traced this cell population, quantifying the labelled population over 1 year and performed in depth phenotypic comparison including transcriptomics, metabolomics and analysis of protein through immunohistochemistry of Axin2CreERT2 mice to WT counterparts.RESULTS: We find that after careful definition of a baseline population there is marked differences in labelling between male and female mice. Upon induced lineage tracing there was no expansion of the labelled hepatocyte population in Axin2CreERT2 mice. We find substantial evidence of disrupted homeostasis in Axin2CreERT2 mice. Offspring are born with sub-Mendelian ratios and adult mice have perturbations of hepatic Wnt/β-catenin signalling and related metabolomic disturbance.CONCLUSIONS: We find no evidence of predominant expansion of the pericentral hepatocyte population during liver homeostatic regeneration. Our data highlight the importance of detailed preclinical model characterisation and the pitfalls which may occur when comparing across sexes and backgrounds of mice and the effects of genetic insertion into native loci.PMID:36702176 | DOI:10.1016/j.jhep.2023.01.009

Plant Physiol Biochem. 2023 Jan 22;196:65-74. doi: 10.1016/j.plaphy.2023.01.041. Online ahead of print.ABSTRACTTrypsin has a new activity of scavenging superoxide anion and generating hydrogen peroxide. Trypsin can significantly improve the storage quality of C. sativus. To illustrate the mechanism of trypsin-induced resistance in fruits and vegetables, an integrated analysis of widely targeted metabolomics and transcriptomics was carried out. Transcriptomic results showed that 1068 genes highly related to phenylpropanoid biosynthesis gathered in the brown module were obtained by WGCNA. In KEGG analysis, differentially expressed genes (DEGs) were also highly enriched in EIP (Environmental Information Processing) pathways "Plant hormone signal transduction (map04075)" and "MAPK signaling pathway-plant (map04016)". Next, 87 genes were identified as the leading edge by GSEA analysis. So far, CsMYC2 was highlighted as a key transcription factor that regulates phenylpropanoid biosynthesis identified by GSEA and WGCNA. Furthermore, the major route of biosynthesis of phenylpropanoid compounds including coumarins, lignins, chlorogenic acid, flavonoids, and derivatives regulated by trypsin was also illustrated by both transcriptomic and metabolomic data. Results of O2PLS showed that CsMYC2 was positively correlated with Rosmarinic acid-3-O-glucoside, Epigallocatechin, Quercetin-3-O-sophoroside (Baimaside), and so on. Correlation between CsMYC2, phenylpropanoid related genes, and metabolites in C. sativus was illustrated by co-expression networks. Roles of CsMYC2 were further checked in C. sativus by VIGS. The results of this study might give new insight into the exploration of the postharvest resistance mechanism of C. sativus induced by trypsin and provide useful information for the subsequent mining of resistance genes in C. sativus.PMID:36701992 | DOI:10.1016/j.plaphy.2023.01.041

Food Chem. 2022 Dec 28;412:135343. doi: 10.1016/j.foodchem.2022.135343. Online ahead of print.ABSTRACTDouchi is a traditional famous seasoning in China. This study adopted electronic tongue and metabolomics to analyze the taste characteristics and taste active compounds of 12 samples from three most famous types of Douchi (Liuyang Douchi, Yangjiang Douchi, Yongchuan Douchi). Thirty-six differential metabolites mainly enriched from the arginine biosynthesis were identified among these Douchis. Umami and bitterness are considered as two taste that bring positive and negative perceptions for Douchi. The succinic acid was found to be responsible for the umami in LY, YJ and YC Douchi, with the TAVs of 2054, 643, 174, respectively, rather than the glutamic acid and aspartic acid. The leucine was identified as the main metabolite for bitterness, with the TAVs of 9, 9, 7 respectively. KEGG enrichment analysis found that the umami, sourness and saltiness might be related to alanine, aspartate and glutamate metabolism and the bitterness might be related to aminoacyl-tRNA biosynthesis pathway.PMID:36701969 | DOI:10.1016/j.foodchem.2022.135343

Food Chem. 2023 Jan 21;411:135535. doi: 10.1016/j.foodchem.2023.135535. Online ahead of print.ABSTRACTEndogenous aflatoxin B1 (AFB1) was quantified in five hundred and forty Hengshan goat meat samples (0.00 ± 23.09 μg kg-1). Zanthoxylum bungeanum (Z. bungeanum), as a natural pickling spice, can ameliorate the flavor of animal-derived food (goat meat). Yet, considering the direct administration of Z. bungeanum in AFB1-contaminated goat meat, the degradation mechanisms of AFB1 remain elusive. Here, UHPLC-Q-Orbitrap HRMS-based integrative metabolomics (LOQ: 1.74-59.54 μg kg-1) and proteomics analyses were executed to determine the effects of Z. bungeanum in the biotransformation of AFB1. Z. bungeanum (1.50 %, w/w) application mediated the metabolism of xenobiotics by cytochrome P450, significantly down-regulated cytochrome P450 1A and stimulated the up-regulation of glutathione S-transferase levels in AFB1-contaminated goat meat, leading to degradation of AFB1 (20.00-3.39 μg kg-1). Metabolomics assays indicated that Z. bungeanum up-regulated l-histidine (1.43-2.21 mg kg-1) and l-arginine, manifesting potential applications for the contribution of Z. bungeanum to the nutritional value of goat meat.PMID:36701916 | DOI:10.1016/j.foodchem.2023.135535

Ecotoxicol Environ Saf. 2023 Jan 24;252:114573. doi: 10.1016/j.ecoenv.2023.114573. Online ahead of print.ABSTRACTAmbient ozone (O3) pollution can induce respiratory and cardiovascular toxicity. However, its impact on the metabolome and the underlying mechanisms remain unclear. This study first investigated the serum metabolite changes in rats exposed to 0.5 ppm O3 for 3 months using untargeted metabolomic approach. Results showed chronic ozone exposure significantly altered the serum levels of 34 metabolites with potential increased risk of digestive, respiratory and cardiovascular disease. Moreover, bile acid synthesis and secretion, and arachidonic acid (AA) metabolism became the most prominent affected metabolic pathways after O3 exposure. Further studies on the mechanisms found that the elevated serum toxic bile acid was not due to the increased biosynthesis in the liver, but the reduced reuptake from the portal vein to hepatocytes owing to repressed Ntcp and Oatp1a1, and the decreased bile acid efflux in hepatocytes as a results of inhibited Bsep, Ostalpha and Ostbeta. Meanwhile, decreased expressions of detoxification enzyme of SULT2A1 and the important regulators of FXR, PXR and HNF4α also contributed to the abnormal bile acids. In addition, O3 promoted the conversion of AA into thromboxane A2 (TXA2) and 20-hydroxyarachidonic acid (20-HETE) in the liver by up-regulation of Fads2, Cyp4a and Tbxas1 which resulting in decreased AA and linoleic acid (LA), and increased thromboxane B2 (TXB2) and 20-HETE in the serum. Furthermore, apparent hepatic chronic inflammation, fibrosis and abnormal function were found in ozone-exposed rats. These results indicated chronic ozone exposure could alter serum metabolites by interfering their metabolism in the liver, and inducing liver injury to aggravate metabolic disorders.PMID:36701875 | DOI:10.1016/j.ecoenv.2023.114573

PLoS One. 2023 Jan 26;18(1):e0280399. doi: 10.1371/journal.pone.0280399. eCollection 2023.ABSTRACTBACKGROUND: The low five-year survival rate of pancreatic ductal adenocarcinoma (PDAC) and the low diagnostic rate of early-stage PDAC via imaging highlight the need to discover novel biomarkers and improve the current screening procedures for early diagnosis. Familial pancreatic cancer (FPC) describes the cases of PDAC that are present in two or more individuals within a circle of first-degree relatives. Using innovative high-throughput proteomics, we were able to quantify the protein profiles of individuals at risk from FPC families in different potential pre-cancer stages. However, the high-dimensional proteomics data structure challenges the use of traditional statistical analysis tools. Hence, we applied advanced statistical learning methods to enhance the analysis and improve the results' interpretability.METHODS: We applied model-based gradient boosting and adaptive lasso to deal with the small, unbalanced study design via simultaneous variable selection and model fitting. In addition, we used stability selection to identify a stable subset of selected biomarkers and, as a result, obtain even more interpretable results. In each step, we compared the performance of the different analytical pipelines and validated our approaches via simulation scenarios.RESULTS: In the simulation study, model-based gradient boosting showed a more accurate prediction performance in the small, unbalanced, and high-dimensional datasets than adaptive lasso and could identify more relevant variables. Furthermore, using model-based gradient boosting, we discovered a subset of promising serum biomarkers that may potentially improve the current screening procedure of FPC.CONCLUSION: Advanced statistical learning methods helped us overcome the shortcomings of an unbalanced study design in a valuable clinical dataset. The discovered serum biomarkers provide us with a clear direction for further investigations and more precise clinical hypotheses regarding the development of FPC and optimal strategies for its early detection.PMID:36701413 | DOI:10.1371/journal.pone.0280399

Cell Rep. 2023 Jan 25;42(2):112045. doi: 10.1016/j.celrep.2023.112045. Online ahead of print.ABSTRACTThe chromatin environment at origins of replication is thought to influence DNA replication initiation in eukaryotic genomes. However, it remains unclear how and which chromatin features control the firing of early-efficient (EE) or late-inefficient (LI) origins. Here, we use site-specific recombination and single-locus chromatin isolation to purify EE and LI replication origins in Saccharomyces cerevisiae. Using mass spectrometry, we define the protein composition of native chromatin regions surrounding the EE and LI replication start sites. In addition to known origin interactors, we find the microtubule-binding Ask1/DASH complex as an origin-regulating factor. Strikingly, tethering of Ask1 to individual origin sites advances replication timing (RT) of the targeted chromosomal domain. Targeted degradation of Ask1 globally changes RT of a subset of origins, which can be reproduced by inhibiting microtubule dynamics. Thus, our findings mechanistically connect RT and chromosomal organization via Ask1/DASH with the microtubule cytoskeleton.PMID:36701236 | DOI:10.1016/j.celrep.2023.112045

Kidney360. 2023 Jan 1;4(1):23-31. doi: 10.34067/KID.0004172022.ABSTRACTBACKGROUND: The proximal tubules eliminate protein-bound toxins and drugs through secretion. Measurements or estimates of GFR do not necessarily reflect the physiologically distinct process of secretion. Clinical assessment of this important intrinsic kidney function requires endogenous markers that are highly specific for secretory transport.METHODS: We used metabolomics profiling to identify candidate markers of tubular secretory clearance in 50 participants from a kidney pharmacokinetics study. We measured metabolites in three sequential plasma samples and a concurrent 10-hour timed urine sample using hydrophilic interaction liquid chromatography/high-resolution mass spectrometry. We quantified the association between estimated kidney clearance and normalized plasma peak height of each candidate solute to the clearance of administered furosemide, a protein-bound, avidly secreted medication.RESULTS: We identified 528 metabolites present in plasma and urine, excluding pharmaceuticals. We found seven highly (>50%) protein-bound and 49 poorly bound solutes with clearances significantly associated with furosemide clearance and 18 solute clearances favoring an association with furosemide clearance by the 90th percentile compared with GFR. We also found four highly bound and 42 poorly bound plasma levels that were significantly associated with furosemide clearance.CONCLUSIONS: We found several candidate metabolites whose kidney clearances or relative plasma levels are highly associated with furosemide clearance, an avidly secreted tracer medication of the organic anion transporters, highlighting their potential as endogenous markers of proximal tubular secretory clearance.PMID:36700901 | DOI:10.34067/KID.0004172022

Microbiol Spectr. 2023 Jan 26:e0295522. doi: 10.1128/spectrum.02955-22. Online ahead of print.ABSTRACTThe maternal gut microbiome affects the duration of pregnancy, delivery, and lactation. It also coordinates the stability of maternal metabolism by regulating and modulating inflammatory cytokines and reproductive hormones. This has been shown in several species; however, the situation in ruminants remains a black box. Here, we aimed to elucidate the relationship between the hindgut microbiota, metabolism, and reproductive hormones in domestic goats (Capra hircus) during nonpregnancy, pregnancy, and lactation stages. The hindgut microbiota was altered during these three stages, with a drastic decrease in the abundance of Family_XIII_AD3011_group in the second and third trimesters of pregnancy. Additionally, a decline in the abundance of Christensenellaceae_R-7_group and Turicibacter was observed from the nonpregnancy stage to late gestation. Family_XIII_AD3011_group and Paeniclostridium were strongly correlated with decreased fecal estradiol and progesterone. Furthermore, we generated a metabolome atlas of the gut and serum from nonpregnancy to lactation to reveal the specific metabolic fingerprints of each physiological stage. Several specific gut metabolites, including carnitine C8:1, γ-aminobutyric acid, and indole-3-carboxylic acid, were negatively correlated with the fecal and serum estradiol concentrations. In contrast, 2'-deoxyinosine, deoxyadenosine, and 5'-deoxyadenosine were positively correlated with the fecal and serum estradiol concentrations. The levels of 2'-deoxyinosine, deoxyadenosine, and 5'-deoxyadenosine in fecal samples were positively correlated with Family_XIII_AD3011_group. Other serum metabolites, such as (±)12-HEPE (hydroxy eicosapentaenoic acid), (±)15-HEPE, (±)18-HEPE, cytidine, uracil, and 5-hydroxyindole-3-acetic acid, were negatively correlated with the serum concentrations of estradiol and progesterone. Finally, Corynebacterium and Clostridium_sensu_stricto_1 in the fecal samples were positively correlated with the abundance of 11,12-EET (epoxy-eicosatrienoic acid), (±)18-HEPE, (±)15-HEPE, and (±)12-HEPE in the serum. IMPORTANCE Our findings revealed that the activity of Family_XIII_AD3011_group and Corynebacterium is strongly correlated with the beneficial regulation of physiological hormones and metabolic changes during pregnancy and lactation. These findings are key for guiding targeted microbial therapeutic approaches to modulate microbiomes in gestating and lactating mammals.PMID:36700635 | DOI:10.1128/spectrum.02955-22

ACS Synth Biol. 2023 Jan 26. doi: 10.1021/acssynbio.2c00339. Online ahead of print.ABSTRACTCell-free systems derived from crude cell extracts have developed into tools for gene expression, with applications in prototyping, biosensing, and protein production. Key to the development of these systems is optimization of cell extract preparation methods. However, the applied nature of these optimizations often limits investigation into the complex nature of the extracts themselves, which contain thousands of proteins and reaction networks with hundreds of metabolites. Here, we sought to uncover the black box of proteins and metabolites in Escherichia coli cell-free reactions based on different extract preparation methods. We assess changes in transcription and translation activity from σ70 promoters in extracts prepared with acetate or glutamate buffer and the common post-lysis processing steps of a runoff incubation and dialysis. We then utilize proteomic and metabolomic analyses to uncover potential mechanisms behind these changes in gene expression, highlighting the impact of cold shock-like proteins and the role of buffer composition.PMID:36700560 | DOI:10.1021/acssynbio.2c00339

Front Public Health. 2023 Jan 9;10:871218. doi: 10.3389/fpubh.2022.871218. eCollection 2022.ABSTRACTThe exposome paradigm through an integrated approach to investigating the impact of perinatal exposure to metals on child neurodevelopment in two cohorts carried out in Slovenia (PHIME cohort) and Greece (HERACLES cohort) respectively, is presented herein. Heavy metals are well-known neurotoxicants with well-established links to impaired neurodevelopment. The links between in utero and early-life exposure to metals, metabolic pathway dysregulation, and neurodevelopmental disorders were drawn through urinary and plasma untargeted metabolomics analysis, followed by the combined application of in silico and biostatistical methods. Heavy metal prenatal and postnatal exposure was evaluated, including parameters indirectly related to exposure and health adversities, such as sociodemographic and anthropometric parameters and dietary factors. The primary outcome of the study was that the identified perturbations related to the TCA cycle are mainly associated with impaired mitochondrial respiration, which is detrimental to cellular homeostasis and functionality; this is further potentiated by the capacity of heavy metals to induce oxidative stress. Insufficient production of energy from the mitochondria during the perinatal period is associated with developmental disorders in children. The HERACLES cohort included more detailed data regarding diet and sociodemographic status of the studied population, allowing the identification of a broader spectrum of effect modifiers, such as the beneficial role of a diet rich in antioxidants such as lycopene and ω-3 fatty acids, the negative effect the consumption of food items such as pork and chicken meat has or the multiple impacts of fish consumption. Beyond diet, several other factors have been proven influential for child neurodevelopment, such as the proximity to pollution sources (e.g., waste treatment site) and the broader living environment, including socioeconomic and demographic characteristics. Overall, our results demonstrate the utility of exposome-wide association studies (EWAS) toward understanding the relationships among the multiple factors that determine human exposure and the underlying biology, reflected as omics markers of effect on neurodevelopment during childhood.PMID:36699871 | PMC:PMC9869756 | DOI:10.3389/fpubh.2022.871218

Front Plant Sci. 2023 Jan 9;13:1076871. doi: 10.3389/fpls.2022.1076871. eCollection 2022.ABSTRACTINTRODUCTION: Barleria prionitis is known for its medicinal properties from ancient times. Bioactive iridoid glycosides and phenolic compounds have been isolated from leaves of this plant. However, other parts of a medicinal plants are also important, especially roots. Therefore, it is important to screen all organs for complete chemical characterization.METHOD: All parts of B. prionitis, including leaf, root, stem and inflorescence in search of bioactive compounds, with a rapid and effective metabolomic method. X500R QTOF system with information dependent acquisition (IDA) method was used to collect high resolution accurate mass data (HRMS) on both the parent (MS signal) and their fragment ions (MS/MS signal). ESI spectra was obtained in positive ion mode from all parts of the plant. A comparative analysis of antioxidant and antibacterial activity was done and their correlation study with the identified compounds was demonstrated. Principal component analysis was performed.RESULT: Iridoid glycosides and phenolic compounds were identified from all parts of the showing variability in presence and abundance. Many of the compounds are reported first time in B. prionitis. Antioxidant and antibacterial activity was revealed in all organs, root being the most effective one. Some of the iridoid glycoside and phenolic compounds found to be positively correlated with the tested biological activity. Principal component analysis of the chemical profiles showed variability in distribution of the compounds.CONCLUSION: All parts of B. prionitis are rich source of bioactive iridoid glycosides and phenolic compounds.PMID:36699860 | PMC:PMC9868927 | DOI:10.3389/fpls.2022.1076871

Front Plant Sci. 2023 Jan 9;13:1043757. doi: 10.3389/fpls.2022.1043757. eCollection 2022.ABSTRACTOryza Sativa is one of the most important food crops in China, which is easily affected by drought during its growth and development. As a member of the calcium signaling pathway, CBL-interacting protein kinase (CIPK) plays an important role in plant growth and development as well as environmental stress. However, there is no report on the function and mechanism of OsCIPK17 in rice drought resistance. We combined transcriptional and metabonomic analysis to clarify the specific mechanism of OsCIPK17 in response to rice drought tolerance. The results showed that OsCIPK17 improved drought resistance of rice by regulating deep roots under drought stress; Response to drought by regulating the energy metabolism pathway and controlling the accumulation of citric acid in the tricarboxylic acid (TCA) cycle; Our exogenous experiments also proved that OsCIPK17 responds to citric acid, and this process involves the auxin metabolism pathway; Exogenous citric acid can improve the drought resistance of overexpression plants. Our research reveals that OsCIPK17 positively regulates rice drought resistance and participates in the accumulation of citric acid in the TCA cycle, providing new insights for rice drought resistance.PMID:36699859 | PMC:PMC9868928 | DOI:10.3389/fpls.2022.1043757

Front Plant Sci. 2023 Jan 9;13:1099362. doi: 10.3389/fpls.2022.1099362. eCollection 2022.ABSTRACTViruses often establish their own infection by altering host metabolism. How viruses co-opt plant metabolism to support their successful infection remains an open question. Here, we used untargeted metabolomics to reveal that lactate accumulates immediately before and after robust sugarcane mosaic virus (SCMV) infection. Induction of lactate-involved anaerobic glycolysis is beneficial to SCMV infection. The enzyme activity and transcriptional levels of lactate dehydrogenase (LDH) were up-regulated by SCMV infection, and LDH is essential for robust SCMV infection. Moreover, LDH relocates in viral replicase complexes (VRCs) by interacting with SCMV-encoded 6K2 protein, a key protein responsible for inducing VRCs. Additionally, lactate could promote SCMV infection by suppressing plant defense responses. Taken together, we have revealed a viral strategy to manipulate host metabolism to support replication compartment but also depress the defense response during the process of infection.PMID:36699858 | PMC:PMC9868461 | DOI:10.3389/fpls.2022.1099362

Front Plant Sci. 2023 Jan 9;13:1089009. doi: 10.3389/fpls.2022.1089009. eCollection 2022.ABSTRACT'Liuyuezao' (LYZ) pummelo (Citrus maxima) originated from a spontaneous bud sport on a 'Guanxi' (GXB) pummelo tree and was released as a new very early-season cultivar. The objective of this study was to present the sensory and nutritional profiles of LYZ fruits, and compare it with other major commercialized pummelo cultivars including GXB, 'Sanhong' (SH) and 'Hongrou' (HR). LYZ had higher contents of organic acids (12.01 mg/g), phenols (669.01 mg/L), vitamin C (75.73 mg/100 mL) and stronger antioxidant capacity (77.65 mg/100 mL) but lower levels of soluble sugars (62.85 mg/g), carotenoids (0.25 mg/L) and flavonoids (46.3 mg/L) when compared to the other pummelos. Moreover, a smaller number (49) and much less content (7.63) of fruit volatiles were detected in LYZ than them in GXB, SH and HR. The relatively high levels of fructose (20.6 mg/g) and organic acids and low levels of volatile compounds in LYZ mainly contributed to its sweet and mildly sour taste and moderate aroma of pummelo note. LYZ is presented as an alternative pummelo cultivar with the potential for commercialization.PMID:36699855 | PMC:PMC9868557 | DOI:10.3389/fpls.2022.1089009

Front Plant Sci. 2023 Jan 9;13:1029907. doi: 10.3389/fpls.2022.1029907. eCollection 2022.ABSTRACTThe leaves of Eucommia ulmoides contain various active compunds and nutritional components, and have successively been included as raw materials in the Chinese Pharmacopoeia, the Health Food Raw Material Catalogue, and the Feed Raw Material Catalogue. Core collections of E. ulmoides had been constructed from the conserved germplasm resources basing on molecular markers and morphological traits, however, the metabolite diversity and variation in this core population were little understood. Metabolite profiles of E. ulmoides leaves of 193 core collections were comprehensively characterized by GC-MS and LC-MS/MS based non-targeted metabolomics in present study. Totally 1,100 metabolites were identified and that belonged to 18 categories, and contained 120 active ingredients for traditional Chinese medicine (TCM) and 85 disease-resistant metabolites. Four leaf chemotypes of the core collections were established by integrated uses of unsupervised self-organizing map (SOM), supervised orthogonal partial least squares discriminant analysis (OPLS-DA) and random forest (RF) statistical methods, 30, 23, 43, and 23 chemomarkers were screened corresponding to the four chemotypes, respectively. The morphological markers for the chemotypes were obtained by weighted gene co-expression network analysis (WGCNA) between the chenomarkers and the morphological traits, with leaf length (LL), chlorophyll reference value (CRV), leaf dentate height (LDH), and leaf thickness (LT) corresponding to chemotypes I, II, III, and IV, respectively. Contents of quercetin-3-O-pentosidine, isoquercitrin were closely correlated to LL, leaf area (LA), and leaf perimeter (LP), suggesting the quercetin derivatives might influence the growth and development of E. ulmoides leaf shape.PMID:36699853 | PMC:PMC9868706 | DOI:10.3389/fpls.2022.1029907

Front Plant Sci. 2023 Jan 9;13:1040134. doi: 10.3389/fpls.2022.1040134. eCollection 2022.ABSTRACTBACKGROUND: Arbuscular mycorrhizal fungi (AMF) are beneficial soil fungi which can effectively help plants with acquisition of mineral nutrients and water and promote their growth and development. The effects of indigenous and commercial isolates of arbuscular mycorrhizal fungi on pear (Pyrus betulaefolia) trees, however, remains unclear.METHODS: Trifolium repens was used to propagate indigenous AMF to simulate spore propagation in natural soils in three ways: 1. the collected soil was mixed with fine roots (R), 2. fine roots were removed from the collected soil (S), and 3. the collected soil was sterilized with 50 kGy 60Co γ-radiation (CK). To study the effects of indigenous AMF on root growth and metabolism of pear trees, CK (sterilized soil from CK in T. repens mixed with sterilized standard soil), indigenous AMF (R, soil from R in T. repens mixed with sterilized standard soil; S, soil from S in T. repens mixed with sterilized standard soil), and two commercial AMF isolates (Rhizophagus intraradices(Ri) and Funneliformis mosseae (Fm)) inoculated in the media with pear roots. Effects on plant growth, root morphology, mineral nutrient accumulation, metabolite composition and abundance, and gene expression were analyzed.RESULTS: AMF treatment significantly increased growth performance, and altered root morphology and mineral nutrient accumulation in this study, with the S treatment displaying overall better performance. In addition, indigenous AMF and commercial AMF isolates displayed common and divergent responses on metabolite and gene expression in pear roots. Compared with CK, most types of flavones, isoflavones, and carbohydrates decreased in the AMF treatment, whereas most types of fatty acids, amino acids, glycerolipids, and glycerophospholipids increased in response to the AMF treatments. Further, the relative abundance of amino acids, flavonoids and carbohydrates displayed different trends between indigenous and commercial AMF isolates. The Fm and S treatments altered gene expression in relation to root metabolism resulting in enriched fructose and mannose metabolism (ko00051), fatty acid biosynthesis (ko00061) and flavonoid biosynthesis (ko00941).CONCLUSIONS: This study demonstrates that indigenous AMF and commercial AMF isolates elicited different effects in pear plants through divergent responses from gene transcription to metabolite accumulation.PMID:36699828 | PMC:PMC9868765 | DOI:10.3389/fpls.2022.1040134

Neuromethods. 2022;184:87-114. doi: 10.1007/978-1-0716-2525-5_5. Epub 2022 Aug 11.ABSTRACTMolecular composition is intricately intertwined with cellular function, and elucidation of this relationship is essential for understanding life processes and developing next-generational therapeutics. Technological innovations in capillary electrophoresis (CE) and liquid chromatography (LC) mass spectrometry (MS) provide previously unavailable insights into cellular biochemistry by allowing for the unbiased detection and quantification of molecules with high specificity. This chapter presents our validated protocols integrating ultrasensitive MS with classical tools of cell, developmental, and neurobiology to assess the biological function of important biomolecules. We use CE and LC MS to measure hundreds of metabolites and thousands of proteins in single cells or limited populations of tissues in chordate embryos and mammalian neurons, revealing molecular heterogeneity between identified cells. By pairing microinjection and optical microscopy, we demonstrate cell lineage tracing and testing the roles the dysregulated molecules play in the formation and maintenance of cell heterogeneity and tissue specification in frog embryos (Xenopus laevis). Electrophysiology extends our workflows to characterizing neuronal activity in sections of mammalian brain tissues. The information obtained from these studies mutually strengthen chemistry and biology and highlight the importance of interdisciplinary research to advance basic knowledge and translational applications forward.PMID:36699808 | PMC:PMC9872963 | DOI:10.1007/978-1-0716-2525-5_5

Front Cell Infect Microbiol. 2023 Jan 9;12:1064737. doi: 10.3389/fcimb.2022.1064737. eCollection 2022.ABSTRACTBACKGROUND: Chronic atrophic gastritis (CAG), premalignant lesions of gastric cancer (GC), greatly increases the risk of GC. Gastroscopy with tissue biopsy is the most commonly used technology for CAG diagnosis. However, due to the invasive nature, both ordinary gastroscope and painless gastroscope result in a certain degree of injury to the esophagus as well as inducing psychological pressure on patients. In addition, patients need fast for at least half a day and take laxatives.METHODS: In this study, fecal metabolites and microbiota profiles were detected by metabolomics and 16S rRNA V4-V5 region sequencing.RESULTS: Alteration of fecal metabolites and microbiota profiles was found in CAG patients, compared with healthy volunteers. To identify the most relevant features, 7 fecal metabolites and 4 microbiota were selected by random forest (RF), from A and B sample sets, respectively. Furthermore, we constructed support vector machines (SVM) classifification model using 7 fecal metabolites or 4 gut microbes, or 7 fecal metabolites with 4 gut microbes, respectively, on C sample set. The accuracy of classifification model was 0.714, 0.857, 0.857, respectively, and the AUC was 0.71, 0.88, 0.9, respectively. In C sample set, Spearman's rank correlation analysis demonstrated heptadecanoic acid and pentadecanoic acid were signifificantly negatively correlated to Erysipelotrichaceae_UCG-003 and Haemophilus, respectively. We constructed SVM classifification model using 2 correlated fecal metabolites and 2 correlated gut microbes on C sample set. The accuracy of classification model was 0.857, and the AUC was 0.88.CONCLUSION: Therefore, heptadecanoic acid and pentadecanoic acid, crosstalk with fecal-derived gut microbiota namely Erysipelotrichaceae_UCG-003 and Haemophilus, are potential non-invasive biomarkers for CAG diagnosis.PMID:36699724 | PMC:PMC9868245 | DOI:10.3389/fcimb.2022.1064737

Front Physiol. 2023 Jan 9;13:1104476. doi: 10.3389/fphys.2022.1104476. eCollection 2022.ABSTRACTNanorana parkeri (Anura, Dicroglossidae) is a unique frog living at high altitude on the Tibetan plateau where they must endure a long winter dormancy at low temperatures without feeding. Here, we presented a comprehensive transcriptomic and metabolomic analysis of liver tissue from summer-active versus overwintering N. parkeri, providing the first broad analysis of altered energy metabolism and gene expression in this frog species. We discovered that significantly up-regulated genes (2,397) in overwintering frogs mainly participated in signal transduction and immune responses, phagosome, endocytosis, lysosome, and autophagy, whereas 2,169 down-regulated genes were mainly involved in metabolic processes, such as oxidation-reduction process, amino acid metabolic process, fatty acid metabolic process, and TCA cycle. Moreover, 35 metabolites were shown to be differentially expressed, including 22 down-regulated and 13 up-regulated in winter. These included particularly notable reductions in the concentrations of most amino acids. These differentially expressed metabolites were mainly involved in amino acid biosynthesis and metabolism. To sum up, these findings suggest that gene expression and metabolic processes show adaptive regulation in overwintering N. parkeri, that contributes to maintaining homeostasis and enhancing protection in the hypometabolic state. This study has greatly expanded our understanding of the winter survival mechanisms in amphibians.PMID:36699683 | PMC:PMC9868574 | DOI:10.3389/fphys.2022.1104476