Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 1 hour 56 min ago

metabolomics; +42 new citations

Tue, 26/02/2019 - 21:11
42 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 2019/02/26PubMed 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.

Global Metabolic Analyses of Acinetobacter baumannii.

Mon, 25/02/2019 - 14:56
Related Articles Global Metabolic Analyses of Acinetobacter baumannii. Methods Mol Biol. 2019;1946:321-328 Authors: Mahamad Maifiah MH, Velkov T, Creek DJ, Li J Abstract Acinetobacter baumannii is rapidly emerging as a multidrug-resistant pathogen responsible for nosocomial infections including pneumonia, bacteremia, wound infections, urinary tract infections, and meningitis. Metabolomics provides a powerful tool to gain a system-wide snapshot of cellular biochemical networks under defined conditions and has been increasingly applied to bacterial physiology and drug discovery. Here we describe an optimized sample preparation method for untargeted metabolomics studies in A. baumannii. Our method provides a significant recovery of intracellular metabolites to demonstrate substantial differences in global metabolic profiles among A. baumannii strains. PMID: 30798566 [PubMed - in process]

Dissection of the network of indolic defence compounds in Arabidopsis thaliana by multiple mutant analysis.

Mon, 25/02/2019 - 14:56
Related Articles Dissection of the network of indolic defence compounds in Arabidopsis thaliana by multiple mutant analysis. Phytochemistry. 2019 Feb 21;161:11-20 Authors: Müller TM, Böttcher C, Glawischnig E Abstract Characteristic for cruciferous plants is the synthesis of a complex array of defence-related indolic compounds. In Arabidopsis, these include indol-3-ylmethyl glucosinolates (IMGs), as well as stress-inducible indole-3-carbaldehyde (ICHO)/indole-3-carboxylic acid (ICOOH) derivatives and camalexin. Key enzymes in the biosynthesis of the inducible metabolites are the cytochrome P450 enzymes CYP71A12, CYP71A13 and CYP71B6 and Arabidopsis Aldehyde Oxidase 1 (AAO1). Multiple mutants in the corresponding genes were generated and their metabolic phenotypes were comprehensively analysed in untreated, UV exposed and silver nitrate-treated leaves. Most strikingly, ICOOH and ICHO derivatives synthesized in response to UV exposure were not metabolically related. While ICHO concentrations correlated with IMGs, ICOOH derivatives were anti-correlated with IMGs and partially dependent on CYP71B6. The AAO1 genotype was shown to not only be important for ICHO metabolism but also for the accumulation of 4-pyridoxic acid, suggesting a dual role of AAO1 in vitamin B6 metabolism and IMG degradation in Arabidopsis. PMID: 30798200 [PubMed - as supplied by publisher]

Cultivar differentiation of Citri Reticulatae Pericarpium by a combination of hierarchical three-step filtering metabolomics analysis, DNA barcoding and electronic nose.

Mon, 25/02/2019 - 14:56
Related Articles Cultivar differentiation of Citri Reticulatae Pericarpium by a combination of hierarchical three-step filtering metabolomics analysis, DNA barcoding and electronic nose. Anal Chim Acta. 2019 May 16;1056:62-69 Authors: Li SZ, Zeng SL, Wu Y, Zheng GD, Chu C, Yin Q, Chen BZ, Li P, Lu X, Liu EH Abstract The traditional Chinese medicine Citri Reticulatae Pericarpium (CRP) was mainly originated from the dried pericarp of Citrus reticulata 'Chachi' (Crc), Citrus reticulata 'Dahongpao' (Crd), Citrus reticulata 'Unshiu' (Cru) and Citrus reticulata 'Tangerina' (Crt) in China. Since these four cultivars have great similarities in morphology, reliable methods to differentiate CRP cultivars have rarely been reported. To discriminate the differences of these CRP cultivars, herein an efficient and reliable method by combining metabolomics, DNA barcoding and electronic nose was first established. The hierarchical three-step filtering metabolomics analysis based on liquid chromatography-quadrupole time-of-flight mass spectrometry (LC-QTOF-MS) indicated that 9 species-specific chemical markers including 6 flavanone glycosides and 3 polymethoxyflavones could be considered as marker metabolites for discrimination of the geoherb Crc from other cultivars. A total of 19 single nucleotide polymorphism (SNP) sites were found in nuclear internal transcribed spacer 2 (ITS2) of CRP, and three stable SNP sites (33, 128 and 174) in the ITS2 region can distinguish the four CRP cultivars. The electronic nose coupled with chemometrics could also be used to effectively distinguish Crc from other CRP cultivars. Therefore, our results indicated that the integrated method will be an effective strategy for discrimination of similar herbal medicines. PMID: 30797461 [PubMed - in process]

Endorsing and extending the repertory of nutraceutical and antioxidant sources in mangoes during postharvest shelf life.

Mon, 25/02/2019 - 14:56
Related Articles Endorsing and extending the repertory of nutraceutical and antioxidant sources in mangoes during postharvest shelf life. Food Chem. 2019 Jul 01;285:119-129 Authors: Monribot-Villanueva JL, Elizalde-Contreras JM, Aluja M, Segura-Cabrera A, Birke A, Guerrero-Analco JA, Ruiz-May E Abstract Mango byproducts, such as peels, contain high levels of antioxidants and fiber and represent important sources of nutraceuticals and pharmacological products. Fruit are collected at the mature green stage then stored and ripened, undergoing several structural and molecular changes over the course of this process. However, very little is known regarding the content and nature of antioxidant compounds in peels of elite and local cultivars during postharvest shelf life (PSL). We screened the phenolic compound content of six cultivars during PSL, including elite (Kent, Tommy, and Ataulfo) and local (Manila, Manililla, and Criollo) mangoes, using a targeted metabolomics approach. We determined that Ataulfo mangoes exhibited the highest content of phenolic compounds during PSL. Untargeted metabolomics and comparative proteomics in Ataulfo and Manililla showed these cultivars to be significant sources of phenolic and lipidic compounds, with the latter cultivar also representing an interesting candidate as a new source for nutraceutical products. PMID: 30797326 [PubMed - in process]

Plasma metabolites predict both insulin resistance and incident type 2 diabetes: a metabolomics approach within the Prevención con Dieta Mediterránea (PREDIMED) study.

Sun, 24/02/2019 - 14:35
Related Articles Plasma metabolites predict both insulin resistance and incident type 2 diabetes: a metabolomics approach within the Prevención con Dieta Mediterránea (PREDIMED) study. Am J Clin Nutr. 2019 Feb 23;: Authors: Papandreou C, Bulló M, Ruiz-Canela M, Dennis C, Deik A, Wang D, Guasch-Ferré M, Yu E, Razquin C, Corella D, Estruch R, Ros E, Fitó M, Fiol M, Liang L, Hernández-Alonso P, Clish CB, Martínez-González MA, Hu FB, Salas-Salvadó J Abstract BACKGROUND: Insulin resistance is a complex metabolic disorder and is often associated with type 2 diabetes (T2D). OBJECTIVES: The aim of this study was to test whether baseline metabolites can additionally improve the prediction of insulin resistance beyond classical risk factors. Furthermore, we examined whether a multimetabolite model predicting insulin resistance in nondiabetics can also predict incident T2D. METHODS: We used a case-cohort study nested within the Prevención con Dieta Mediterránea (PREDIMED) trial in subsets of 700, 500, and 256 participants without T2D at baseline and 1 and 3 y. Fasting plasma metabolites were semiquantitatively profiled with liquid chromatography-tandem mass spectrometry. We assessed associations between metabolite concentrations and the homeostasis model of insulin resistance (HOMA-IR) through the use of elastic net regression analysis. We subsequently examined associations between the baseline HOMA-IR-related multimetabolite model and T2D incidence through the use of weighted Cox proportional hazard models. RESULTS: We identified a set of baseline metabolites associated with HOMA-IR. One-year changes in metabolites were also significantly associated with HOMA-IR. The area under the curve was significantly greater for the model containing the classical risk factors and metabolites together compared with classical risk factors alone at baseline [0.81 (95% CI: 0.79, 0.84) compared with 0.69 (95% CI: 0.66, 0.73)] and during a 1-y period [0.69 (95% CI: 0.66, 0.72) compared with 0.57 (95% CI: 0.53, 0.62)]. The variance in HOMA-IR explained by the combination of metabolites and classical risk factors was also higher in all time periods. The estimated HRs for incident T2D in the multimetabolite score (model 3) predicting high HOMA-IR (median value or higher) or HOMA-IR (continuous) at baseline were 2.00 (95% CI: 1.58, 2.55) and 2.24 (95% CI: 1.72, 2.90), respectively, after adjustment for T2D risk factors. CONCLUSIONS: The multimetabolite model identified in our study notably improved the predictive ability for HOMA-IR beyond classical risk factors and significantly predicted the risk of T2D. PMID: 30796776 [PubMed - as supplied by publisher]

GC-QTOFMS with a low-energy electron ionization source for advancing isotopologue analysis in 13C-based metabolic flux analysis.

Sun, 24/02/2019 - 14:35
Related Articles GC-QTOFMS with a low-energy electron ionization source for advancing isotopologue analysis in 13C-based metabolic flux analysis. Anal Bioanal Chem. 2019 Feb 22;: Authors: Mairinger T, Sanderson J, Hann S Abstract For the study of different levels of (intra)cellular regulation and condition-dependent insight into metabolic activities, fluxomics experiments based on stable isotope tracer experiments using 13C have become a well-established approach. The experimentally obtained non-naturally distributed 13C labeling patterns of metabolite pools can be measured by mass spectrometric detection with front-end separation and can be consequently incorporated into biochemical network models. Here, despite a tedious derivatization step, gas chromatographic separation of polar metabolites is favorable because of the wide coverage range and high isomer separation efficiency. However, the typically employed electron ionization energy of 70 eV leads to significant fragmentation and consequently only low-abundant ions with an intact carbon backbone. Since these ions are considered a prerequisite for the analysis of the non-naturally distributed labeling patterns and further integration into modeling strategies, a softer ionization technique is needed. In the present work, a novel low energy electron ionization source is optimized for the analysis of primary metabolites and compared with a chemical ionization approach in terms of trueness, precision, and sensitivity. PMID: 30796486 [PubMed - as supplied by publisher]

Urinary metabolic variation analysis during pregnancy and application in Gestational Diabetes Mellitus and spontaneous abortion biomarker discovery.

Sun, 24/02/2019 - 14:35
Related Articles Urinary metabolic variation analysis during pregnancy and application in Gestational Diabetes Mellitus and spontaneous abortion biomarker discovery. Sci Rep. 2019 Feb 22;9(1):2605 Authors: Liu X, Wang X, Sun H, Guo Z, Liu X, Yuan T, Fu Y, Tang X, Li J, Sun W, Zhao W Abstract Pregnancy is associated with the onset of many adaptation processes that are likely to change over the course of gestation. Understanding normal metabolites' variation with pregnancy progression is crucial for gaining insights of the key nutrients for normal fetal growth, and for comparative research of pregnancy-related complications. This work presents liquid chromatography-mass spectrum-based urine metabolomics study of 50 health pregnant women at three time points during pregnancy. The influence of maternal physiological factors, including age, BMI, parity and gravity to urine metabolome was explored. Additionally, urine metabolomics was applied for early prediction of two pregnancy complications, gestational diabetes mellitus and spontaneous abortion. Our results suggested that during normal pregnancy progression, pathways of steroid hormone biosynthesis and tyrosine metabolism were significantly regulated. BMI is a factor that should be considered during cross-section analysis. Application analysis discovered potential biomarkers for GDM in the first trimester with AUC of 0.89, and potential biomarkers for SA in the first trimester with AUC of 0.90. In conclusion, our study indicated that urine metabolome could reflect variations during pregnancy progression, and has potential value for pregnancy complications early prediction. The clinical trial number for this study is NCT03246295. PMID: 30796299 [PubMed - in process]

Application of metabolomics and molecular networking in investigating the chemical profile and antitrypanosomal activity of British bluebells (Hyacinthoides non-scripta).

Sun, 24/02/2019 - 14:35
Related Articles Application of metabolomics and molecular networking in investigating the chemical profile and antitrypanosomal activity of British bluebells (Hyacinthoides non-scripta). Sci Rep. 2019 Feb 22;9(1):2547 Authors: Raheem DJ, Tawfike AF, Abdelmohsen UR, Edrada-Ebel R, Fitzsimmons-Thoss V Abstract Bulb, leaf, scape and flower samples of British bluebells (Hyacinthoides non-scripta) were collected regularly for one growth period. Methanolic extracts of freeze-dried and ground samples showed antitrypanosomal activity, giving more than 50% inhibition, for 20 out of 41 samples. High-resolution mass spectrometry was used in the dereplication of the methanolic extracts of the different plant parts. The results revealed differences in the chemical profile with bulb samples being distinctly different from all aerial parts. High molecular weight metabolites were more abundant in the flowers, shoots and leaves compared to smaller molecular weight ones in the bulbs. The anti-trypanosomal activity of the extracts was linked to the accumulation of high molecular weight compounds, which were matched with saponin glycosides, while triterpenoids and steroids occurred in the inactive extracts. Dereplication studies were employed to identify the significant metabolites via chemotaxonomic filtration and considering their previously reported bioactivities. Molecular networking was implemented to look for similarities in fragmentation patterns between the isolated saponin glycoside at m/z 1445.64 [M + formic-H]- equivalent to C64H104O33 and the putatively found active metabolite at m/z 1283.58 [M + formic-H]- corresponding to scillanoside L-1. A combination of metabolomics and bioactivity-guided approaches resulted in the isolation of a norlanostane-type saponin glycoside with antitrypanosomal activity of 98.9% inhibition at 20 µM. PMID: 30796274 [PubMed - in process]

Function, Detection and Alteration of Acylcarnitine Metabolism in Hepatocellular Carcinoma.

Sun, 24/02/2019 - 14:35
Related Articles Function, Detection and Alteration of Acylcarnitine Metabolism in Hepatocellular Carcinoma. Metabolites. 2019 Feb 21;9(2): Authors: Li S, Gao D, Jiang Y Abstract Acylcarnitines play an essential role in regulating the balance of intracellular sugar and lipid metabolism. They serve as carriers to transport activated long-chain fatty acids into mitochondria for β-oxidation as a major source of energy for cell activities. The liver is the most important organ for endogenous carnitine synthesis and metabolism. Hepatocellular carcinoma (HCC), a primary malignancy of the live with poor prognosis, may strongly influence the level of acylcarnitines. In this paper, the function, detection and alteration of acylcarnitine metabolism in HCC were briefly reviewed. An overview was provided to introduce the metabolic roles of acylcarnitines involved in fatty acid β-oxidation. Then different analytical platforms and methodologies were also briefly summarised. The relationship between HCC and acylcarnitine metabolism was described. Many of the studies reported that short, medium and long-chain acylcarnitines were altered in HCC patients. These findings presented current evidence in support of acylcarnitines as new candidate biomarkers for studies on the pathogenesis and development of HCC. Finally we discussed the challenges and perspectives of exploiting acylcarnitine metabolism and its related metabolic pathways as a target for HCC diagnosis and prognosis. PMID: 30795537 [PubMed]

metabolomics; +42 new citations

Sat, 23/02/2019 - 14:14
42 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 2019/02/23PubMed 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.

Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae.

Thu, 21/02/2019 - 13:45
Related Articles Comprehensive mass spectrometry-guided plant specialized metabolite phenotyping reveals metabolic diversity in the cosmopolitan plant family Rhamnaceae. Plant J. 2019 Feb 20;: Authors: Kang KB, Ernst M, van der Hooft JJJ, da Silva RR, Park J, Medema MH, Sung SH, Dorrestein PC Abstract Plants produce a myriad of specialized metabolites to overcome their sessile habit and combat biotic as well as abiotic stresses. Evolution has shaped specialized metabolite diversity, which drives many other aspects of plant biodiversity. However, until recently, large-scale studies investigating specialized metabolite diversity in an evolutionary context have been limited by the impossibility to identify chemical structures of hundreds to thousands of compounds in a time-feasible manner. Here, we introduce a workflow for large-scale, semi-automated annotation of specialized metabolites, and apply it for over 1000 metabolites of the cosmopolitan plant family Rhamnaceae. We enhance the putative annotation coverage dramatically, from 2.5% based on spectral library matches alone to 42.6% of total MS/MS molecular features extending annotations from well-known plant compound classes into the dark plant metabolomics matter. To gain insights in substructural diversity within the plant family, we also extract patterns of co-occurring fragments and neutral losses, so-called Mass2Motifs, from the dataset; for example, only the Ziziphoid clade developed the triterpenoid biosynthetic pathway, whereas the Rhamnoid clade predominantly developed diversity in flavonoid glycosides, including 7-O-methyltransferase activity. Our workflow provides the foundations towards the automated, high-throughput chemical identification of massive metabolite spaces, and we expect it to revolutionize our understanding of plant chemoevolutionary mechanisms. This article is protected by copyright. All rights reserved. PMID: 30786088 [PubMed - as supplied by publisher]

Metabolomic profiling reveals correlations between spermiogram parameters and the metabolites present in human spermatozoa and seminal plasma.

Thu, 21/02/2019 - 13:45
Related Articles Metabolomic profiling reveals correlations between spermiogram parameters and the metabolites present in human spermatozoa and seminal plasma. PLoS One. 2019;14(2):e0211679 Authors: Engel KM, Baumann S, Rolle-Kampczyk U, Schiller J, von Bergen M, Grunewald S Abstract In 50% of all infertility cases, the male is subfertile or infertile, however, the underlying mechanisms are often unknown. Even when assisted reproductive procedures such as in vitro fertilization and intracytoplasmic sperm injection are performed, the causes of male factor infertility frequently remain elusive. Since the overall activity of cells is closely linked to their metabolic capacity, we analyzed a panel of 180 metabolites in human sperm and seminal plasma and elucidated their associations with spermiogram parameters. Therefore, metabolites from a group of 20 healthy donors were investigated using a targeted LC-MS/MS approach. The correlation analyses of the amino acids, biogenic amines, acylcarnitines, lysophosphatidylcholines, phosphatidylcholines, sphingomyelins and sugars from sperm and seminal plasma with standard spermiogram parameters revealed that metabolites in sperm are closely related to sperm motility, whereas those in seminal plasma are closely related to sperm concentration and morphology. This study provides essential insights into the metabolome of human sperm and seminal plasma and its associations with sperm functions. This metabolomics technique could be a promising screening tool to detect the factors of male infertility in cases where the cause of infertility is unclear. PMID: 30785892 [PubMed - in process]

Pyrophosphate modulates plant stress responses via SUMOylation.

Thu, 21/02/2019 - 13:45
Related Articles Pyrophosphate modulates plant stress responses via SUMOylation. Elife. 2019 Feb 20;8: Authors: Patir-Nebioglu MG, Andrés Z, Krebs M, Fink F, Drzewicka K, Stankovic-Valentin N, Segami S, Schuck S, Büttner M, Hell R, Maeshima M, Melchior F, Schumacher K Abstract Pyrophosphate (PPi), a byproduct of macromolecule biosynthesis is maintained at low levels by soluble inorganic pyrophosphatases (sPPase) found in all eukaryotes. In plants, H+-pumping pyrophosphatases (H+-PPase) convert the substantial energy present in PPi into an electrochemical gradient. We show here, that both cold- and heat stress sensitivity of fugu5 mutants lacking the major H+-PPase isoform AVP1 is correlated with reduced SUMOylation. In addition, we show that increased PPi concentrations interfere with SUMOylation in yeast and we provide evidence that SUMO activating E1-enzymes are inhibited by micromolar concentrations of PPi in a non-competitive manner. Taken together, our results do not only provide a mechanistic explanation for the beneficial effects of AVP1 overexpression in plants but they also highlight PPi as an important integrator of metabolism and stress tolerance. PMID: 30785397 [PubMed - in process]

The effect of vegetable and spice addition on the acrylamide content and antioxidant activity of innovative cereal products.

Thu, 21/02/2019 - 13:45
Related Articles The effect of vegetable and spice addition on the acrylamide content and antioxidant activity of innovative cereal products. Food Addit Contam Part A Chem Anal Control Expo Risk Assess. 2019 Feb 20;:1-11 Authors: Jaworska D, Mojska H, Gielecińska I, Najman K, Gondek E, Przybylski W, Krzyczkowska P Abstract The aim of the work was to assess the impact of vegetable and spice addition on the acrylamide content and antioxidant activity of extruded cereal crisps. The foods were based on grain ingredients, such as brown rice, whole grain flour, wheat bran, with different vegetables. Products from one group contained green vegetables, such as broccoli and zucchini; garlic was included as a flavour additive (0.75-1.50%). The second group of crisps consisted of similar cereal ingredients with pumpkin and cinnamon; additionally ginger was included as a flavour additive (0.75-1.50%). The results indicate that the production of a new, innovative product with appropriate nutritional value and acceptable quality is a complex process. The production process significantly changed the nutritional value of the product. The content of acrylamide in zucchini and broccoli crisps was relatively low; ranging from 78 to 86 μg/kg of product. The addition of garlic did not significantly affect the acrylamide content in the final product. For cereal-pumpkin crisps, the acrylamide content was 7 times higher in comparison with zucchini and broccoli products. The acrylamide content in pumpkin and ginger crisps exceeded the benchmark level. The antioxidant activity of the pumpkin product was significantly higher (p < 0.05) than for crisps with green vegetables. PMID: 30785367 [PubMed - as supplied by publisher]

Integrated metallomic and metabolomic profiling of plasma and tissues provides deep insights into the protective effect of raw and salt-processed Achyranthes bidentata Blume extract in ovariectomia rats.

Thu, 21/02/2019 - 13:45
Related Articles Integrated metallomic and metabolomic profiling of plasma and tissues provides deep insights into the protective effect of raw and salt-processed Achyranthes bidentata Blume extract in ovariectomia rats. J Ethnopharmacol. 2019 Feb 19;234:85-95 Authors: Tao Y, Huang S, Yan J, Li W, Cai B Abstract ETHNOPHARMACOLOGICAL RELEVANCE: Achyranthes bidentata Blume (AB) is a well-known traditional Chinese medicine for treating osteoporosis and bone fracture. In the current, researches on pharmacological mechanism of AB mostly focused on molecular pathways, knowledge about its metabolic signatures is largely unclear. This study aims to develop an integrative metabolomics and metallomic approach for deciphering the biochemical basis of anti-osteoporosis effects of raw and salt-processed AB. METHOD: Gas chromatography-mass spectrometry (GC-MS) and inductively coupled plasma mass spectrometry (ICP-MS) were combined for metabolomic and metallomic profiling of rats serum, liver and kidney derived from the sham group, model group, E2, raw and salt-processed AB treated groups. Meanwhile, micro-CT and biomechanical analysis were carried out to ensure the success of the osteoporosis model and to validate the anti-osteoporosis effect of raw and salt-processed AB. Partial least squares discriminant analysis (PLS-DA) was employed to screen potential biomarkers and the MetaboAnalyst and KEGG PATHWAY Database were used to investigate the metabolic pathway. RESULTS: Raw and salt-processed AB protected the rats against osteoporosis, as evidenced by the restoration of the alkaline phosphatase activity, osteocalcin concentration, urine calcium/creatinine ratio and urine phosphorus/creatinine ratio. The combination of PCA and PLS-DA revealed deviations in ninety-four differential biomarkers between raw AB treated group and model group. The identified biomarkers were primarily engaged in the metabolic pathways including galactose metabolism, urea cycle, arginine and proline metabolism, alanine metabolism, lactose degradation, ammonia recycling and glycine and serine metabolism. The levels of these biomarkers showed significant alterations and a tendency to be restored to normal values in raw and salt-processed AB treated osteoporosis rats. Of note, the levels of trace elements, such as Zn, Se, Mn, Cu and Fe, were elevated after raw and salt-processed AB treatment. Finally, a correlation network diagram was constructed to show the biomarkers perturbed by raw and salt-processed AB. CONCLUSION: Our findings indicate that raw and salt-processed AB has positive effects on osteoporosis rats. Meanwhile, metabolomic and metallomic method coupled with metabolites enrichment analysis and pattern recognition serves as a useful tool for revealing the action mechanism of traditional Chinese medicine. PMID: 30784959 [PubMed - as supplied by publisher]

Ambient fine particulate matter exposure induces cardiac functional injury and metabolite alterations in middle-aged female mice.

Thu, 21/02/2019 - 13:45
Related Articles Ambient fine particulate matter exposure induces cardiac functional injury and metabolite alterations in middle-aged female mice. Environ Pollut. 2019 Jan 30;248:121-132 Authors: Zhang Y, Ji X, Ku T, Li B, Li G, Sang N Abstract Plenty of epidemiological studies have shown that exposure to ambient particulate matter (PM2.5) is linked to cardiovascular diseases (CVDs) in older even in middle-aged populations; however, experimental evidence through intuitive metabolic analysis to confirm the age susceptibility and explain the related molecular mechanism of PM2.5-induced cardiotoxicity is relatively rare. In the present study, C57BL/6 mice (adult (4-month) and middle-aged (10-month)) were given 3 mg/kg PM2.5 every other day by oropharyngeal aspiration for 4 weeks, and then, body and cardiac parameter, containing weight data, cardiac function, ultrastructure, metabolic analysis, and molecular detection were conducted to investigate the PM2.5-induced cardiotoxicity. The results indicated that middle-aged mice were more susceptible to PM2.5, displaying slow cardiac growth, cardiac dysfunction, abnormal mitochondrial structure and function, and cardiac metabolic disorders. The altered metabolites were enriched in carbohydrate metabolism, fatty acid metabolism, amino acid metabolism, nucleotide metabolism and nicotinate and nicotinamide metabolism. In conclusion, we speculated that the cardiac metabolic disorders may be important factors in PM2.5-induced cardiac dysfunction and mitochondrial structure destruction in middle-aged mice, providing a new direction for the study of the association between PM2.5 and CVDs. PMID: 30784831 [PubMed - as supplied by publisher]

Integrated application of transcriptomics and metabolomics provides insights into unsynchronized growth in pearl oyster Pinctada fucata martensii.

Thu, 21/02/2019 - 13:45
Related Articles Integrated application of transcriptomics and metabolomics provides insights into unsynchronized growth in pearl oyster Pinctada fucata martensii. Sci Total Environ. 2019 Feb 15;666:46-56 Authors: Hao R, Du X, Yang C, Deng Y, Zheng Z, Wang Q Abstract Similar to other marine bivalves, Pinctada fucata martensii presents unsynchronized growth, which is one of the problems farmers currently face. However, the underlying mechanisms have not been studied. In the present study, pearl oyster P. f. martensii from cultured stocks were selected to produce a progeny stock. At 180 days, the stock was sorted by size, and fast- and slow-growing individuals were separately sampled. Then, metabolomic and transcriptomic approaches were applied to assess the metabolic and transcript changes between the fast- and slow-growing P. f. martensii groups and understand the mechanism underlying their unsynchronized growth. In the metabolomics assay, 30 metabolites were considered significantly different metabolites (SDMs) between the fast- and slow-growing groups and pathway analysis indicated that these SDMs were involved in 20 pathways, including glutathione metabolism; sulfur metabolism; valine, leucine, and isoleucine biosynthesis; and tryptophan metabolism. The transcriptome analysis of different growth groups showed 168 differentially expressed genes (DEGs) and pathway enrichment analysis indicated that DEGs were involved in extracellular matrix-receptor interaction, pentose phosphate pathway, aromatic compound degradation. Integrated transcriptome and metabolome analyses showed that fast-growing individuals exhibited higher biomineralization activity than the slow-growing group, which consumed more energy than the fast-growing group in response to environmental stress. Fast-growing group also exhibited higher digestion, anabolic ability, and osmotic regulation ability than the slow-growing group. This study is the first work involving the integrated metabolomic and transcriptomic analyses to identify the key pathways to understand the molecular and metabolic mechanisms underlying unsynchronized bivalve growth. PMID: 30784822 [PubMed - as supplied by publisher]

Evaluation of the chemical consistency of Yin-Chen-Hao-Tang prepared by combined and separated decoction methods using high-performance liquid chromatography quadrupole time-of-flight mass spectrometry coupled with multivariate statistical analysis.

Thu, 21/02/2019 - 13:45
Related Articles Evaluation of the chemical consistency of Yin-Chen-Hao-Tang prepared by combined and separated decoction methods using high-performance liquid chromatography quadrupole time-of-flight mass spectrometry coupled with multivariate statistical analysis. J Sep Sci. 2019 Feb 19;: Authors: Tian Q, Liu F, Xu Z, Liu H, Yin H, Sun Z, Chen M, Li Z, Ma L, Huang C Abstract In this study, Yin-Chen-Hao-Tang prepared by two decoction methods, namely, combined decoction (modern decoction method) and separated decoction (traditional decoction method), was analyzed by high-performance liquid chromatography quadrupole time-of-flight mass spectrometry. The acquired datasets containing sample codes, tR -m/z pairs and ion intensities were processed with multivariate statistical analyses, such as principal component analysis and an orthogonal partial least squared discriminant analysis model, to globally compare the chemical differences between the different decoction samples. Then, the chemical differences between the combined and separated decoctions were screened out by S-plots generated from the orthogonal partial least squared discriminant analysis model and compared with chemical information from an established in-house library. The six components that contributed the most to the chemical differences were identified as chlorogenic acid, caffeic acid, geniposide, genipin, scopoletin, and 3,5-dicaffeoylquinic acid. The concentrations of genipin and caffeic acid from the separated decoction were higher than those from the combined decoction, indicating that the separated decoction may present a stronger hepatoprotective effect. However, the results still require further investigation through pharmacological and clinical studies. Our findings not only establish a strategy to evaluate chemical consistency of Yin-Chen-Hao-Tang but also provide the scientific basis for using traditional separated decoction method. This article is protected by copyright. All rights reserved. PMID: 30784184 [PubMed - as supplied by publisher]

A comprehensive analysis of WGCNA and serum metabolomics manifests the lung cancer-associated disordered glucose metabolism.

Thu, 21/02/2019 - 13:45
Related Articles A comprehensive analysis of WGCNA and serum metabolomics manifests the lung cancer-associated disordered glucose metabolism. J Cell Biochem. 2019 Feb 19;: Authors: Ding M, Li F, Wang B, Chi G, Liu H Abstract Lung cancer is a worldwide disease and highly heterogeneous at a molecular level. In this study, we both performed the pathway enrichment analysis and the transcriptome-based weighted gene coexpression network analysis (WGCNA) so as to find the critical pathways involved in lung cancer. Our analysis results indicated that genes in viability modules (0 < Z-summary < 2) selected by WGCNA were more reliable for identifying crucial pathways, while gene enrichment analysis provided a wide range of pathways with a little emphasis on target pathways for lung cancer. On the basis of genes, which were classified into various modules by WGCNA, we found a significant aberration of glucose metabolism in lung cancer cells, demonstrating that the glucose metabolism has been perturbed, especially the glycolysis pathway. Our study revealed that disordered glucose metabolism might be closely associated with the carcinogenesis of lung cancer based on the integrated analysis of WGCNA and metabolomics, which could be a potential therapeutic target for lung cancer. PMID: 30784104 [PubMed - as supplied by publisher]

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