PubMed

Related Articles Biochemical mechanisms of rhizospheric Bacillus subtilis-facilitated phytoextraction by alfalfa under cadmium stress - Microbial diversity and metabolomics analyses. Ecotoxicol Environ Saf. 2021 Feb 04;212:112016 Authors: Li Q, Xing Y, Fu X, Ji L, Li T, Wang J, Chen G, Qi Z, Zhang Q Abstract The effects of Bacillus subtilis inoculation on the growth and Cd uptake of alfalfa were evaluated in this research using pot experiments, and the relevant biochemical mechanisms were first investigated by combined microbial diversity and nontarget metabolomics analyses. The results indicated that inoculation with alfalfa significantly decreased the amount of plant malondialdehyde (MDA) and improved the activities of plant antioxidant enzymes and soil nutrient cycling-involved enzymes, thereby promoting biomass by 29.4%. Inoculation also increased Cd bioavailability in rhizosphere soil by 12.0% and Cd removal efficiency by 139.3%. The biochemical mechanisms included enhanced bacterial diversity, transformed microbial community composition, regulated amounts of amino acids, fatty acids, carbohydrates, flavonoids and phenols in rhizosphere soil metabolites, and modulations of the corresponding Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. These responses were beneficial to microbial activity, nutrient cycling, and Cd mobilization, detoxification, and decontamination by alfalfa in soil. This study, especially the newly identified differential metabolites and metabolic pathways, provides new insights into mechanism revelation and strategy development in microbe-assisted phytomanagement of heavy metal-contaminated soils. PMID: 33550079 [PubMed - as supplied by publisher]

Related Articles Measurement of melanin metabolism in live cells by [U-13C]-tyrosine fate tracing using LC-MS. J Invest Dermatol. 2021 Feb 04;: Authors: Chen Q, Zhou D, Abdel-Malek Z, Zhang F, Goff PS, Sviderskaya EV, Wakamatsu K, Ito S, Gross SS, Zippin JH Abstract Melanin synthesis occurs within a specialized organelle called the melanosome. Traditional methods for measuring melanin levels rely on the detection of chemical degradation products of melanin by high-performance liquid chromatography (HPLC). Although these methods are robust, they are unable to distinguish between melanin synthesis and degradation, and are best suited to measure melanin changes over long periods of time. We developed a method that actively measures both eumelanin and pheomelanin synthesis by fate tracing [U-13C] tyrosine using liquid chromatography-mass spectrometry (LC-MS). Using this method, we confirmed previous reports of melanin synthesis differences between melanocytes derived from individuals with different skin color or MC1R genotype, and uncovered new information regarding the differential de novo synthesis of eumelanin and pheomelanin, also called mixed melanogenesis. We also revealed that distinct mechanisms that alter melanosomal pH differentially induce new eumelanin and pheomelanin synthesis. Finally, we revealed that the synthesis of L-DOPA, an important metabolite of tyrosine, is differentially controlled by multiple factors. Because tyrosine fate tracing is compatible with untargeted LC-MS based metabolomics, this approach enables the broad measurement of cellular metabolism in combination with melanin metabolism, and we anticipate that this approach will shed new light on multiple mechanisms of melanogenesis. PMID: 33549605 [PubMed - as supplied by publisher]

Related Articles Investigation of the effects of actinorhodin biosynthetic gene cluster expression and a rpoB point mutation on the metabolome of Streptomyces coelicolor M1146. J Biosci Bioeng. 2021 Feb 03;: Authors: Nitta K, Breitling R, Takano E, Putri SP, Fukusaki E Abstract The previously reported Streptomyces coelicolor M1146 is commonly used as a host strain for engineering of secondary metabolite production. In this study, absolute quantification of intracellular and extracellular metabolites of M1146 was performed in mid-log phase and stationary phase to observe major metabolites and the changes that occurred during growth. Decreased levels of central carbon metabolites (glycolysis, TCA cycle, and pentose phosphate pathway) and increased levels of amino acids were observed in stationary phase compared to mid-log phase. Furthermore, comparative metabolome analyses of M1146 upon expression of the actinorhodin biosynthetic gene cluster (M1146+ACT), a point mutation on the rpoB gene encoding RNA polymerase beta-subunit (M1152), and both expression of actinorhodin biosynthetic gene cluster and a rpoB point mutation (M1152+ACT) were performed. M1146+ACT showed higher levels of important cofactors, such as ATP, NADPH, and FMN while M1152 led to higher levels of intracellular S-adenosyl-methionine, acyl-CoAs, and extracellular nucleosides compared to M1146. M1152+ACT exhibited the highest levels of actinorhodin with elevated bases, nucleosides, and nucleotides, such as intracellular PRPP (phosphoribosyl phosphate), ATP, along with extracellular inosine, uridine, and guanine compared to the other three strains, which were considered to be combined effects of actinorhodin gene cluster expression and a rpoB point mutation. Metabolites analysis by means of absolute quantification demonstrated changes in precursors of secondary metabolites before and after phosphate depletion in M1146. Comparative metabolome analysis provided further insights into the effects of actinorhodin gene cluster expression along with a rpoB point mutation on the metabolome of S. coelicolor. PMID: 33549493 [PubMed - as supplied by publisher]

Related Articles Marine Omega-3 Fatty Acids and Cardiovascular Disease Prevention: Seeking Clearer Water. Mayo Clin Proc. 2021 Feb;96(2):277-279 Authors: Farukhi ZM, Mora S, Manson JE PMID: 33549246 [PubMed - in process]

Related Articles New insights into the role of MADS-box transcription factor gene CmANR1 on root and shoot development in chrysanthemum (Chrysanthemum morifolium). BMC Plant Biol. 2021 Feb 06;21(1):79 Authors: Sun CH, Wang JH, Gu KD, Zhang P, Zhang XY, Zheng CS, Hu DG, Ma F Abstract BACKGROUND: MADS-box transcription factors (TFs) are the key regulators of multiple developmental processes in plants; among them, a chrysanthemum MADS-box TF CmANR1 has been isolated and described as functioning in root development in response to high nitrate concentration signals. However, how CmANR1 affects root and shoot development remains unclear. RESULTS: We report that CmANR1 plays a positive role in root system development in chrysanthemum throughout the developmental stages of in vitro tissue cultures. Metabolomics combined with transcriptomics assays show that CmANR1 promotes robust root system development by facilitating nitrate assimilation, and influencing the metabolic pathways of amino acid, glycolysis, and the tricarboxylic acid cycle (TCA) cycle. Also, we found that the expression levels of TFs associated with the nitrate signaling pathways, such as AGL8, AGL21, and LBD29, are significantly up-regulated in CmANR1-transgenic plants relative to the wild-type (WT) control; by contrast, the expression levels of RHD3-LIKE, LBD37, and GATA23 were significantly down-regulated. These results suggest that these nitrate signaling associated TFs are involved in CmANR1-modulated control of root development. In addition, CmANR1 also acts as a positive regulator to control shoot growth and development. CONCLUSIONS: These findings provide potential mechanisms of MADS-box TF CmANR1 modulation of root and shoot development, which occurs by regulating a series of nitrate signaling associated TFs, and influencing the metabolic pathways of amino acid and glycolysis, as well as TCA cycle and nitrate assimilation. PMID: 33549046 [PubMed - in process]

16 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2021/02/07PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

21 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2021/02/06PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

27 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2021/02/05PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

Related Articles Characteristics and Mechanisms of a Sphingolipid-associated Childhood Asthma Endotype. Am J Respir Crit Care Med. 2021 Feb 03;: Authors: Rago D, Pedersen CT, Huang M, Kelly RS, Gürdeniz G, Brustad N, Knihtil H, Lee-Sarwar KA, Morin A, Rasmussen MA, Stokholm J, Bønnelykke K, Litonjua AA, Wheelock CE, Weiss ST, Lasky-Su J, Bisgaard H, Chawes BL Abstract RATIONALE: A link between sphingolipids, 17q21 genetic variants and childhood asthma has been suggested, but the underlying mechanisms and characteristics of such asthma endotype remain to be elucidated. OBJECTIVE: To study the sphingolipid-associated childhood asthma endotype using multi-omics data. METHODS: We used untargeted LC-MS plasma metabolomics profiles at age 6 months and 6 years from >500 children in the COPSAC2010 birth cohort focusing on sphingolipids, and integrated 17q21 genotype and nasal gene expression of serine palmitoyl-CoA transferase (SPT), i.e. the rate-limiting enzyme in the de novo sphingolipid synthesis, in relation to asthma development and lung function traits from infancy till age 6 years. Replication was sought in the independent VDAART cohort. MEASUREMENTS AND MAIN RESULTS: Lower levels of ceramides and sphingomyelins at age 6 months were associated with increased risk of developing asthma before age 3, which was also observed in VDAART. At age 6 years, lower levels of key phosphosphingolipids, e.g. sphinganine-1-phosphate were associated with increased airway resistance. This relationship was dependent on 17q21 genotype and nasal SPT gene expression with significant interaction between genotype and phosphosphingolipids levels and between genotype and SPT expression, showing lower phosphosphingolipids and reduced SPT expression with increasing number of at-risk alleles. However, the findings did not pass FDR<0.05. CONCLUSIONS: This exploratory study suggests the existence of a childhood asthma endotype with early onset and increased airway resistance that is characterized by reduced sphingolipid levels that is associated with 17q21 genetic variants and expression of the SPT enzyme. PMID: 33535020 [PubMed - as supplied by publisher]

Related Articles Plasma metabolomic profile associated with fatigue in cancer patients. Cancer Med. 2021 Feb 03;: Authors: Feng LR, Barb JJ, Regan J, Saligan LN Abstract BACKGROUND: Metabolomics is the newest -omics methodology and allows for a functional snapshot of the biochemical activity and cellular state. The goal of this study is to characterize metabolomic profiles associated with cancer-related fatigue, a debilitating symptom commonly reported by oncology patients. METHODS: Untargeted ultrahigh performance liquid chromatography/mass spectrometry metabolomics approach was used to identify metabolites in plasma samples collected from a total of 197 participants with or without cancer. Partial least squares-discriminant analysis (PLS-DA) was used to identify discriminant metabolite features, and diagnostic performance of selected classifiers was quantified using area under the receiver operating characteristics (AUROC) curve analysis. Pathway enrichment analysis was performed using Fisher's exact test and the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway database. FINDINGS: The global metabolomics approach yielded a total of 1120 compounds of known identity. Significant metabolic pathways unique to fatigued cancer versus control groups included sphingolipid metabolism, histidine metabolism, and cysteine and methionine metabolism. Significant pathways unique to non-fatigued cancer versus control groups included inositol phosphate metabolism, primary bile acid biosynthesis, ascorbate and aldarate metabolism, starch and sucrose metabolism, and pentose and glucuronate interconversions. Pathways shared between the two comparisons included caffeine metabolism, tyrosine metabolism, steroid hormone biosynthesis, sulfur metabolism, and phenylalanine metabolism. CONCLUSIONS: We found significant metabolomic profile differences associated with cancer-related fatigue. By comparing metabolic signatures unique to fatigued cancer patients with metabolites associated with, but not unique to, fatigued cancer individuals (overlap pathways) and metabolites associated with cancer but not fatigue, we provided a broad view of the metabolic phenotype of cancer-related fatigue. PMID: 33534943 [PubMed - as supplied by publisher]

Related Articles Metabolic dysfunction in pregnancy: Fingerprinting the maternal metabolome using proton nuclear magnetic resonance spectroscopy. Endocrinol Diabetes Metab. 2021 Jan;4(1):e00201 Authors: Scott HD, Buchan M, Chadwick C, Field CJ, Letourneau N, Montina T, Leung BMY, Metz GAS Abstract Aims: Maternal metabolic disorders place the mother at risk for negative pregnancy outcomes with potentially long-term health impacts for the child. Metabolic syndrome, a cluster of features associated with increased risk of metabolic disorders, such as cardiovascular disease, diabetes and stroke, affects roughly one in five Canadians. Metabolomics is a relatively new technique that may be a useful tool to identify women at risk of metabolic disorders. This study set out to characterize urinary metabolic biomarkers of pregnant women with obesity and of pregnant women who later developed gestational diabetes mellitus (pre-GDM), compared to controls. Methods and Materials: Second trimester urine samples were collected through the Alberta Pregnancy Outcomes and Nutrition (APrON) cohort and examined with 1H nuclear magnetic resonance (NMR) spectroscopy. Multivariate analysis was used to examine group differences, and machine learning feature selection tools identified the metabolites contributing to separation. Results: Obesity and pre-GDM metabolomes were distinct from controls and from each other. In each comparison, the glycine, serine and threonine pathways were the most impacted. Pantothenate, formic acid and glycine were downregulated by obesity, while formic acid, dimethylamine and galactose were downregulated in pre-GDM. The three most impacted metabolites for the comparison of obesity versus pre-GDM groups were upregulated creatine/caffeine, downregulated sarcosine/dimethylamine and upregulated maltose/sucrose in individuals who later developed GDM. Conclusion: These findings suggest a role for urinary metabolomics in the prediction of GDM and metabolic marker identification for potential diagnostics and prognostics in women at risk. PMID: 33532625 [PubMed]

Related Articles Capsule endoscopy transit-related indicators in choosing the insertion route for double-balloon enteroscopy: a systematic review. Endosc Int Open. 2021 Feb;9(2):E163-E170 Authors: Cortegoso Valdivia P, Skonieczna-Żydecka K, Pennazio M, Rondonotti E, Marlicz W, Toth E, Koulaouzidis A Abstract Background and study aims  When capsule endoscopy (CE) detects a small bowel (SB) target lesion that may be manageable with enteroscopy, the selection of the insertion route is critical. Time- and progression-based CE indices have been proposed for localization of SB lesions. This systematic review analysed the role of CE transit indicators in choosing the insertion route for double-balloon enteroscopy (DBE). Methods  A comprehensive literature search identified papers assessing the role of CE on the choice of the route selection for DBE. Data on CE, criteria for route selection, and DBE success parameters were retrieved and analyzed according to the PRISMA statement. Risk of bias was assessed through the STROBE assessment. The primary outcome evaluated was DBE success rate in reaching a SB lesion, measured as the ratio of positive initial DBE to the number of total DBE. Results  Seven studies including 262 CEs requiring subsequent DBE were selected. Six studies used time-based indices and one used the PillCam Progress indicator. SB lesions were identified and insertion route was selected according to a specific cut-off, using fixed landmarks for defining SB transit except for one study in which the mouth-cecum transit was considered. DBE success rate was high in all studies, ranging from 78.3 % to 100 %. Six of seven studies were high quality. Conclusions  The precise localization of SB lesions remains an open issue, and larger studies are required to determine the most accurate index for selecting the DBE insertion route. In the future, 3 D localization technologies and tracking systems will be essential to accomplish this tricky task. PMID: 33532554 [PubMed]

Related Articles Metabolomics study reveals the potential evidence of metabolic reprogramming towards the Warburg effect in precancerous lesions. J Cancer. 2021;12(5):1563-1574 Authors: Chen X, Yi C, Yang MJ, Sun X, Liu X, Ma H, Li Y, Li H, Wang C, He Y, Chen G, Chen S, Yu L, Yu D Abstract Background: Most tumors have an enhanced glycolysis flux, even when oxygen is available, called the aerobic glycolysis or the Warburg effect. Metabolic reprogramming promotes cancer progression, and is even related to the tumorigenesis. However, it is not clear whether the observed metabolic changes act as a driver or a bystander in cancer development. Methods: In this study, the metabolic characteristics of oral precancerous cells and cervical precancerous lesions were analyzed by metabolomics, and the expression of glycolytic enzymes in cervical precancerous lesions was evaluated by RT-PCR and Western blot analysis. Results: In total, 115 and 23 metabolites with reliable signals were identified in oral cells and cervical tissues, respectively. Based on the metabolome, oral precancerous cell DOK could be clearly separated from normal human oral epithelial cells (HOEC) and oral cancer cells. Four critical differential metabolites (pyruvate, glutamine, methionine and lysine) were identified between DOK and HOEC. Metabolic profiles could clearly distinguish cervical precancerous lesions from normal cervical epithelium and cervical cancer. Compared with normal cervical epithelium, the glucose consumption and lactate production increased in cervical precancerous lesions. The expression of glycolytic enzymes LDHA, HK II and PKM2 showed an increased tendency in cervical precancerous lesions compared with normal cervical epithelium. Conclusions: Our findings suggest that cell metabolism may be reprogrammed at the early stage of tumorigenesis, implying the contribution of metabolic reprogramming to the development of tumor. PMID: 33532002 [PubMed]

Related Articles Differences in milk metabolites in Malnad Gidda (Bos indicus) cows reared under pasture-based feeding system. Sci Rep. 2021 Feb 02;11(1):2831 Authors: Ashokan M, Ramesha KP, Hallur S, Karthikkeyan G, Rana E, Azharuddin N, Raj SR, Jeyakumar S, Kumaresan A, Kataktalware MA, Das DN, Keshava Prasad TS Abstract The milk and milk products from cows reared under grazing system are believed to be healthier and hence have high demand compared to milk from cows reared in the non-grazing system. However, the effect of grazing on milk metabolites, specifically lipids has not been fully understood. In this study, we used acetonitrile precipitation and methanol:chloroform methods for extracting the milk metabolites followed by liquid chromatography-tandem mass spectrometry (LC-MS/MS) run to identify the different metabolites between the milk of grazing and non-grazing early lactating Malnad Gidda cows. Various carbohydrates, amino acids, nucleosides and vitamin derivatives were found to be differentially abundant in grazing cows. A total of 35 metabolites were differentially regulated (fold change above 1.5) between the two groups. Tyrosyl-threonine, histidinyl-cysteine, 1-methyladenine, L-cysteine and selenocysteine showed fold change above 3 in grazing cows. The lipid profile of milk showed a lesser difference between grazing and non-grazing cows as compared to polar metabolites. To the best of our knowledge, this is the largest inventory of milk metabolomics data of an Indian cattle (Bos indicus) breed. We believe that our study would help to emerge a field of Nutri-metabolomics and veterinary omics research. PMID: 33531582 [PubMed - in process]

Related Articles A metabolomic approach to target antimalarial metabolites in the Artemisia annua fungal endophytes. Sci Rep. 2021 Feb 02;11(1):2770 Authors: Alhadrami HA, Sayed AM, El-Gendy AO, Shamikh YI, Gaber Y, Bakeer W, Sheirf NH, Attia EZ, Shaban GM, Khalifa BA, Ngwa CJ, Pradel G, Rateb ME, Hassan HM, Alkhalifah DHM, Abdelmohsen UR, Hozzein WN Abstract Fungal endophytes are a major source of anti-infective agents and other medically relevant compounds. However, their classical blinded-chemical investigation is a challenging process due to their highly complex chemical makeup. Thus, utilizing cheminformatics tools such as metabolomics and computer-aided modelling is of great help deal with such complexity and select the most probable bioactive candidates. In the present study, we have explored the fungal endophytes associated with the well-known antimalarial medicinal plant Artemisia annua for their production of further antimalarial agents. Based on the preliminary antimalarial screening of these endophytes and using LC-HRMS-based metabolomics and multivariate analyses, we suggested different potentially active metabolites (compounds 1-8). Further in silico investigation using the neural-network-based prediction software PASS led to the selection of a group of quinone derivatives (compounds 1-5) as the most possible active hits. Subsequent in vitro validation revealed emodin (1) and physcion (2) to be potent antimalarial candidates with IC50 values of 0.9 and 1.9 µM, respectively. Our approach in the present investigation therefore can be applied as a preliminary evaluation step in the natural products drug discovery, which in turn can facilitate the isolation of selected metabolites notably the biologically active ones. PMID: 33531542 [PubMed - in process]

Related Articles Lower Airway Dysbiosis Exacerbates Lung Cancer. Cancer Discov. 2021 Feb;11(2):224-226 Authors: Zitvogel L, Kroemer G Abstract Accumulating evidence supports the impact of the gut microbiota on the clinical efficacy of cancer immunotherapies against extraintestinal tumors, but it has not yet been addressed whether local commensals could also dictate the prognosis of patients with cancer. In this issue of Cancer Discovery, Tsay and colleagues demonstrate that the lower airway microbiota may harbor oral commensals that turn on IL17-mediated inflammatory pathways and reprogram host transcription to exacerbate lung cancer progression.See related article by Tsay et al., p. 293. PMID: 33531424 [PubMed - in process]

Related Articles Untargeted Lipidomic Analysis of Plasma from High-fat Diet-induced Obese Rats Using UHPLC-Linear Trap Quadrupole-Orbitrap MS. Anal Sci. 2020 Jul 10;36(7):821-828 Authors: Gowda SGB, Gao ZJ, Chen Z, Abe T, Hori S, Fukiya S, Ishizuka S, Yokota A, Chiba H, Hui SP Abstract High-fat diet (HFD)-induced obesity is a primary risk factor for serious health problems. Although much research has been performed at the genomic level, lipidomic studies were limited. In this study, we aim to obtain a comprehensive profile of circulating plasma lipids, which are altered in rodent rat obesity by untargeted liquid chromatography-mass spectrometry. Rats fed with HFD for 8 weeks had increased body weight, liver and adipose tissue weight. The analysis results revealed that polyunsaturated fatty acids (PUFAs) and their corresponding phosphatidylcholine, phosphatidylinositol, and phosphatidylserine were significantly decreased in rats fed with HFD. In contrast, less unsaturated and ether type phosphatidylglycerols were increased. The triacylglycerides (TAGs) having saturated FA were increased in the HFD condition, whereas TAGs having PUFA were decreased. The levels of many plasma lipids were altered, and interestingly PUFA derived lipids were negatively associated with obesity. This signifies the importance of a PUFAs enriched diet to overwhelm obesity associated diseases. PMID: 31956159 [PubMed - indexed for MEDLINE]

Related Articles Pheophorbide a May Regulate Jasmonate Signaling during Dark-Induced Senescence. Plant Physiol. 2020 02;182(2):776-791 Authors: Aubry S, Fankhauser N, Ovinnikov S, Pružinská A, Stirnemann M, Zienkiewicz K, Herrfurth C, Feussner I, Hörtensteiner S Abstract Chlorophyll degradation is one of the most visible signs of leaf senescence. During senescence, chlorophyll is degraded in the multistep pheophorbide a oxygenase (PAO)/phyllobilin pathway. This pathway is tightly regulated at the transcriptional level, allowing coordinated and efficient remobilization of nitrogen toward sink organs. Using a combination of transcriptome and metabolite analyses during dark-induced senescence of Arabidopsis (Arabidopsis thaliana) mutants deficient in key steps of the PAO/phyllobilin pathway, we show an unanticipated role for one of the pathway intermediates, i.e. pheophorbide a Both jasmonic acid-related gene expression and jasmonic acid precursors specifically accumulated in pao1, a mutant deficient in PAO. We propose that pheophorbide a, the last intact porphyrin intermediate of chlorophyll degradation and a unique pathway "bottleneck," has been recruited as a signaling molecule of chloroplast metabolic status. Our work challenges the assumption that chlorophyll breakdown is merely a result of senescence, and proposes that the flux of pheophorbide a through the pathway acts in a feed-forward loop that remodels the nuclear transcriptome and controls the pace of chlorophyll degradation in senescing leaves. PMID: 31753845 [PubMed - indexed for MEDLINE]

26 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2021/02/03PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

45 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2021/02/02PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.