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 31 min ago

Aberrant Sialylation in Cancer Pathology and Metastasis, a Putative Drug Target Candidate.

Thu, 13/09/2018 - 13:04
Related Articles Aberrant Sialylation in Cancer Pathology and Metastasis, a Putative Drug Target Candidate. Anticancer Agents Med Chem. 2018 Sep 10;: Authors: Lu DY, Lu TR, Xu B, Varki A, Huang M, Zhu H, Shen Y, Yarla NS Abstract BACKGROUNDS: Neoplasm metastasis is a multi-step and multi-level pathological feature causing 90% of cancer mortality due to a shortage of effective drugs and clinical therapeutics. To change this scenario, new drug targets and developments are required. METHOD: Aberrant tumor sialylation as a putative drug target candidate has been evolving over the past half century. Some specific agents and clinical events suggested some promising therapeutic potentiality and benefits against neoplasm metastasis in a number of cellular and animal tumor models. RESULTS: Since neoplasm tissues often contain higher levels and diverse sialic acids (sia) analogues and antigens, sia-related tumor biology/pathology are emerging as cancer diagnostic categories and a series of useful agents until now. Previously some compounds enabling to inhibit sia-related pathologic pathways were reported to exhibit therapeutic activity in cellular or animal tumor models. These types of cancer treatment agents can provide excellent therapeutic outcomes by glycome/metabolomics diagnostics first. CONCLUSION: Taking together of these experimental/clinical discoveries, the "central dogma" of glycobiology might be found out via all these principle discoveries. In addition, mathematic- or physics-majored talents might render new therapeutic discoveries by computational analysis of experimental and clinical data. Overall, therapeutic targets/benefits in the clinic should be pursuit with earnest attitude. PMID: 30205804 [PubMed - as supplied by publisher]

Comprehensive Metabolomics Analysis of Mandarins (Citrus reticulata) as A Tool for Variety, Rootstock and Grove Discrimination.

Thu, 13/09/2018 - 13:04
Related Articles Comprehensive Metabolomics Analysis of Mandarins (Citrus reticulata) as A Tool for Variety, Rootstock and Grove Discrimination. J Agric Food Chem. 2018 Sep 12;: Authors: Feng S, Niu L, Suh JH, Hung WL, Wang Y Abstract The metabolite profile responsible for the quality of mandarin fruit is influenced by pre-harvest factors including genotype, rootstock, grove location, etc. In this paper, mandarin varieties were discriminated using metabolomics. Additionally, effects on metabolic profiles due to grove location and rootstock differences were also investigated. Results revealed that mandarin varieties could be differentiated using the metabolite profile, while the compositions of flavonoids have the potential for variety differentiation. With regard to fruits of the same variety, grove location might determine the overall profile of metabolites, whereas rootstock possibly affected composition of secondary metabolites. Pathway enrichment analysis demonstrated biosynthesis pathways of terpenoids and steroids involving limonene and linalool, were highly influenced by variety diversity. Moreover, the flavonoid biosynthesis pathway, involving hesperetin, naringenin, eriodictyol and taxifolin, was indicated to have a close relationship with rootstock differentiation. This study provides useful and important information with depth for breeding and optimizing pre-harvest practices. PMID: 30205680 [PubMed - as supplied by publisher]

A variable selection approach in the multivariate linear model: an application to LC-MS metabolomics data.

Thu, 13/09/2018 - 13:04
Related Articles A variable selection approach in the multivariate linear model: an application to LC-MS metabolomics data. Stat Appl Genet Mol Biol. 2018 Sep 08;: Authors: Perrot-Dockès M, Lévy-Leduc C, Chiquet J, Sansonnet L, Brégère M, Étienne MP, Robin S, Genta-Jouve G PMID: 30205662 [PubMed - as supplied by publisher]

Response of Cisplatin Resistant Skov-3 Cells to [Pt(O,O'-Acac)(γ-Acac)(DMS)] Treatment Revealed by a Metabolomic ¹H-NMR Study.

Thu, 13/09/2018 - 13:04
Related Articles Response of Cisplatin Resistant Skov-3 Cells to [Pt(O,O'-Acac)(γ-Acac)(DMS)] Treatment Revealed by a Metabolomic ¹H-NMR Study. Molecules. 2018 Sep 09;23(9): Authors: De Castro F, Benedetti M, Antonaci G, Del Coco L, De Pascali SA, Muscella A, Marsigliante S, Fanizzi FP Abstract The novel [Pt(O,O'-acac)(γ-acac)(DMS)], Ptac2S, Pt(II) complex has recently gained increasing attention as a potential anticancer agent for its pharmacological activity shown in different tumor cell lines, studied both in vitro and in vivo. The mechanism of action of Ptac2S, operating on non-genomic targets, is known to be very different from that of cis-[PtCl₂(NH₃)₂], cisplatin, targeting nucleic acids. In this work, we evaluated the cytotoxicity of Ptac2S on the cisplatin resistant Epithelial Ovarian Carcinoma (EOC), SKOV-3 cells, by the MTT assay. A ¹H-NMR metabolomic approach coupled with multivariate statistical analysis was used for the first time for Ptac2S to figure out the biological mechanisms of action of the complex. The metabolic variations of intracellular metabolites and the composition of the corresponding extracellular culture media were compared to those of cisplatin (cells were treated at the IC50 doses of both drugs). The reported comparative metabolomic analysis revealed a very different metabolic profile between Ptac2S and cisplatin treated samples, thus confirming the different mechanism of action of Ptac2S also in the Epithelial Ovarian Carcinoma (EOC), SKOV-3 cells line. In particular, higher levels of pyruvate were observed in Ptac2S treated, with respect to cisplatin treated, cells (in both aqueous and culture media). In addition, a very different lipid expression resulted after the exposure to the two drugs (Ptac2S and cisplatin). These results suggest a possible explanation for the Ptac2S ability to circumvent cisplatin resistance in SKOV-3 cells. PMID: 30205612 [PubMed - in process]

Potential Metabolomic Linkage in Blood between Parkinson's Disease and Traumatic Brain Injury.

Thu, 13/09/2018 - 13:04
Related Articles Potential Metabolomic Linkage in Blood between Parkinson's Disease and Traumatic Brain Injury. Metabolites. 2018 Sep 07;8(3): Authors: Fiandaca MS, Gross TJ, Johnson TM, Hu MT, Evetts S, Wade-Martins R, Merchant-Borna K, Bazarian J, Cheema AK, Mapstone M, Federoff HJ Abstract The etiologic basis for sporadic forms of neurodegenerative diseases has been elusive but likely represents the product of genetic predisposition and various environmental factors. Specific gene-environment interactions have become more salient owing, in part, to the elucidation of epigenetic mechanisms and their impact on health and disease. The linkage between traumatic brain injury (TBI) and Parkinson's disease (PD) is one such association that currently lacks a mechanistic basis. Herein, we present preliminary blood-based metabolomic evidence in support of potential association between TBI and PD. Using untargeted and targeted high-performance liquid chromatography-mass spectrometry we identified metabolomic biomarker profiles in a cohort of symptomatic mild TBI (mTBI) subjects (n = 75) 3⁻12 months following injury (subacute) and TBI controls (n = 20), and a PD cohort with known PD (n = 20) or PD dementia (PDD) (n = 20) and PD controls (n = 20). Surprisingly, blood glutamic acid levels in both the subacute mTBI (increased) and PD/PDD (decreased) groups were notably altered from control levels. The observed changes in blood glutamic acid levels in mTBI and PD/PDD are discussed in relation to other metabolite profiling studies. Should our preliminary results be replicated in comparable metabolomic investigations of TBI and PD cohorts, they may contribute to an "excitotoxic" linkage between TBI and PD/PDD. PMID: 30205491 [PubMed]

Sepsis: Personalized Medicine Utilizing 'Omic' Technologies-A Paradigm Shift?

Thu, 13/09/2018 - 13:04
Related Articles Sepsis: Personalized Medicine Utilizing 'Omic' Technologies-A Paradigm Shift? Healthcare (Basel). 2018 Sep 07;6(3): Authors: Itenov TS, Murray DD, Jensen JUS Abstract Sepsis has over the years proven a considerable challenge to physicians and researchers. Numerous pharmacological and non-pharmacological interventions have been tested in trials, but have unfortunately failed to improve the general prognosis. This has led to the speculation that the sepsis population may be too heterogeneous to be targeted with the traditional one treatment suits all' approach. Recent advances in genetic and biochemical analyses now allow genotyping and biochemical characterisation of large groups of patients via the 'omics' technologies. These new opportunities could lead to a paradigm shift in the approach to sepsis towards personalised treatments with interventions targeted towards specific pathophysiological mechanisms activated in the patient. In this article, we review the potentials and pitfalls of using new advanced technologies to deepen our understanding of the clinical syndrome of sepsis. PMID: 30205441 [PubMed]

A sensitive and efficient procedure for the high-throughput determination of nine urinary metabolites of pyrethroids by GC-MS/MS and its application in a sample of Japanese children.

Thu, 13/09/2018 - 13:04
Related Articles A sensitive and efficient procedure for the high-throughput determination of nine urinary metabolites of pyrethroids by GC-MS/MS and its application in a sample of Japanese children. Anal Bioanal Chem. 2018 Sep;410(24):6207-6217 Authors: Ueda Y, Oda M, Saito I, Hamada R, Kondo T, Kamijima M, Ueyama J Abstract Four pyrethroids (PYRs), metofluthrin, profluthrin, tefluthrin, and transfluthrin, which were newly developed and have relatively high vapor activity at ambient temperature, are now playing a key role in safely controlling insects in our daily lives. We developed a sensitive and high-throughput determination method for urinary metabolites derived from the newly developed PYR, e.g., 2,3,5,6-tetrafluoro-1,4-benzenedimethanol (HOCH2-FB-Al), 2,3,5,6-tetrafluorobenzyl alcohol (FB-Al), and other PYR metabolites such as trans-chrysanthemumdicarboxylic acid (trans-CDCA) and 3-phenoxybenzoic acid (3PBA). After high temperature acid hydrolysis of 2 mL urine sample in 24-deep well plate, the PYR metabolites were extracted by semi-automated liquid-liquid extraction with tert-butyl methyl ether. N,O-Bis (trimethylsilyl) trifluoroacetamide containing 1% trimethylchlorosilane or 1,1,1,3,3,3-hexafluoroisopropanol were used for the derivatization of PYR metabolites, and the derivatized metabolites were analyzed separately by GC-MS/MS equipped with dual injector system (DB-5MS and mid- to high-polarity phase Rtx-65 columns). The derivatization and evaporation conditions were mainly optimized for improving sensitivity and reproducibility. The mean within-run day precisions were less than 18.4% (relative standard deviation, %RSD) with low detection limits ranging from 0.01 μg/L for HOCH2-FB-Al to 0.06 μg/L for trans-CDCA. This method was successfully applied to urine samples obtained from 50 3-year-old children with high detection frequencies (e.g., 82% for HOCH2-FB-Al and 84% for FB-Al). This method may be a pivotal tool for developing risk assessment from PYR exposure in the general population. PMID: 30046868 [PubMed - indexed for MEDLINE]

metabolomics; +25 new citations

Wed, 12/09/2018 - 15:20
25 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 2018/09/12PubMed 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.

metabolomics; +25 new citations

Wed, 12/09/2018 - 12:10
25 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 2018/09/12PubMed 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.

metabolomics; +22 new citations

Tue, 11/09/2018 - 14:13
22 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 2018/09/11PubMed 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.

Analytical Platforms and Techniques to Study Stem Cell Metabolism.

Mon, 10/09/2018 - 13:42
Related Articles Analytical Platforms and Techniques to Study Stem Cell Metabolism. Methods Mol Biol. 2018;1842:265-281 Authors: Tang C, Chen K, Bajic A, Choi WT, Baluya DL, Maletic-Savatic M Abstract Over the past decade, advances in systems biology or 'omics techniques have enabled unprecedented insights into the biological processes that occur in cells, tissues, and on the organism level. One of these technologies is the metabolomics, which examines the whole content of the metabolites in a given sample. In a biological system, a stem cell for instance, there are thousands of single components, such as genes, RNA, proteins, and metabolites. These multiple molecular species interact with each other and these interactions may change over the life-time of a cell or in response to specific stimuli, adding to the complexity of the system. Using metabolomics, we can obtain an instantaneous snapshot of the biological status of a cell, tissue, or organism and gain insights on the pattern(s) of numerous analytes, both known and unknown, that result because of a given biological condition. Here, we outline the main methods to study the metabolism of stem cells, including a relatively recent technology of mass spectrometry imaging. Given the abundant and increasing interest in stem cell metabolism in both physiological and pathological conditions, we hope that this chapter will provide incentives for more research in these areas to ultimately reach wide network of applications in biomedical, pharmaceutical, and nutritional research and clinical medicine. PMID: 30196417 [PubMed - in process]

Ganoderma Lucidum Polysaccharide Peptide Alleviates Hepatoteatosis via Modulating Bile Acid Metabolism Dependent on FXR-SHP/FGF.

Mon, 10/09/2018 - 13:42
Related Articles Ganoderma Lucidum Polysaccharide Peptide Alleviates Hepatoteatosis via Modulating Bile Acid Metabolism Dependent on FXR-SHP/FGF. Cell Physiol Biochem. 2018 Sep 07;49(3):1163-1179 Authors: Zhong D, Xie Z, Huang B, Zhu S, Wang G, Zhou H, Lin S, Lin Z, Yang B Abstract BACKGROUND/AIMS: Non-alcoholic fatty liver disease (NAFLD) encompasses a series of pathologic changes ranging from steatosis to steatohepatitis, which may progress to cirrhosis and hepatocellular carcinoma. The purpose of this study was to determine whether ganoderma lucidum polysaccharide peptide (GLPP) has therapeutic effect on NAFLD. METHODS: Ob/ ob mouse model and ApoC3 transgenic mouse model were used for exploring the effect of GLPP on NAFLD. Key metabolic pathways and enzymes were identified by metabolomics combining with KEGG and PIUmet analyses and key enzymes were detected by Western blot. Hepatosteatosis models of HepG2 cells and primary hepatocytes were used to further confirm the therapeutic effect of GLPP on NAFLD. RESULTS: GLPP administrated for a month alleviated hepatosteatosis, dyslipidemia, liver dysfunction and liver insulin resistance. Pathways of glycerophospholipid metabolism, fatty acid metabolism and primary bile acid biosynthesis were involved in the therapeutic effect of GLPP on NAFLD. Detection of key enzymes revealed that GLPP reversed low expression of CYP7A1, CYP8B1, FXR, SHP and high expression of FGFR4 in ob/ob mice and ApoC3 mice. Besides, GLPP inhibited fatty acid synthesis by reducing the expression of SREBP1c, FAS and ACC via a FXR-SHP dependent mechanism. Additionally, GLPP reduced the accumulation of lipid droplets and the content of TG in HepG2 cells and primary hepatocytes induced by oleic acid and palmitic acid. CONCLUSION: GLPP significantly improves NAFLD via regulating bile acid synthesis dependent on FXR-SHP/FGF pathway, which finally inhibits fatty acid synthesis, indicating that GLPP might be developed as a therapeutic drug for NAFLD. PMID: 30196282 [PubMed - as supplied by publisher]

Influence of malt source on beer chemistry, flavor, and flavor stability.

Mon, 10/09/2018 - 13:42
Related Articles Influence of malt source on beer chemistry, flavor, and flavor stability. Food Res Int. 2018 Nov;113:487-504 Authors: Bettenhausen HM, Barr L, Broeckling CD, Chaparro JM, Holbrook C, Sedin D, Heuberger AL Abstract Beverage quality in the brewing industry is heavily influenced by ingredient properties. The contribution of raw ingredients such as yeast and hops to beer flavor is well understood. However, the influence of barley genotype and/or environment on flavor (the malt 'source') is largely unexplored. Here, a study was performed to determine (i) if there are metabolite differences among six commercial malt sources, (ii) if differences in malt chemistry are reflected in the chemistry of the beer, and (iii) if the differences in the beer chemistry impact sensory attributes of beer, through flavor and flavor stability. Six distinct sources of malts (six varieties from three maltsters) were brewed into six beers using a recipe designed to evaluate differences in flavor. Metabolomics and ionomics was used to characterize chemical variation among the six malts and beers using UHPLC- and HILIC-MS (non-volatile metabolites), HS-SPME/GC-MS (beer volatiles), and ICP-MS (malt metals). These analyses detected a total of 5042 compounds in malt, of which 217 were annotated and included amines, amino acids, fatty acids/lipids/fatty acyls, saccharides/glucosides/sugar acids/sugar alcohols, carboxylic acid derivatives, organic acids, phenolics/benzenoids, purines, pyrimidines/pyridines, terpenes, and organosulfurs. A total of 4568 compounds were detected in beer, of which 246 were annotated and included esters, aldehydes, and alcohols. Statistical analysis revealed chemical variation among the six malts (50/217 malt metabolites varied) and beers (150/246). The six beers were evaluated for flavor using a modified descriptive analysis for 45 sensory traits at 0, 4, and 8 weeks of storage at 4 °C. Principal component analysis of the sensory data revealed flavor differences among the six beers at 8 weeks, and the malt-type Full Pint was described as fruity and Meredith as corn chip. The metabolite and sensory data were integrated and revealed associations between flavor profiles in beer and the annotated malt and beer. The fruity or corn chip flavor profiles in beer were associated beer purines/pyrimidines, volatile ketones, amines, and phenolics, and malt lipids, saccharides, phenols, amines, and alkaloids. Taken together, these data support a role of malt source in beer flavor and flavor stability. As a raw ingredient, malting barley genotypes can be evaluated for a contribution to flavor, and this may be a future target for plant breeding, agronomy, and malting efforts to selectively improve flavor, flavor stability, and quality in beer. PMID: 30195545 [PubMed - in process]

Untargeted metabolomics reveals differences in chemical fingerprints between PDO and non-PDO Grana Padano cheeses.

Mon, 10/09/2018 - 13:42
Related Articles Untargeted metabolomics reveals differences in chemical fingerprints between PDO and non-PDO Grana Padano cheeses. Food Res Int. 2018 Nov;113:407-413 Authors: Rocchetti G, Lucini L, Gallo A, Masoero F, Trevisan M, Giuberti G Abstract The purpose of this preliminary study was to discriminate the chemical fingerprints of Protected Designation of Origin (PDO) Grana Padano cheeses from non-PDO "Grana-type" cheeses by means of an untargeted metabolomic approach based on ultra-high-pressure liquid chromatography coupled to quadrupole time-of-flight mass spectrometer (UHPLC/QTOF-MS). Hierarchical cluster analysis and Orthogonal Projections to Latent Structures Discriminant Analysis (OPLS-DA) allowed discriminating PDO vs. non-PDO cheeses. Lipids (fatty acids and their derivatives, phospholipids and monoacylglycerols), amino acids and oligopeptides, together with plant-derived compounds were the markers having the highest discrimination potential. It can be postulated that Grana Padano value chain, as strictly defined in the PDO production specification rules, can drive the biochemical processes involved in cheese making and ripening in a distinct manner, thus leaving a defined chemical signature on the final product. These preliminary findings provide the basis for further authenticity studies, aiming to protect the designation of origin of PDO Grana Padano cheese by applying a comprehensive foodomics-based approach. PMID: 30195535 [PubMed - in process]

Olive oil industry by-products. Effects of a polyphenol-rich extract on the metabolome and response to inflammation in cultured intestinal cell.

Mon, 10/09/2018 - 13:42
Related Articles Olive oil industry by-products. Effects of a polyphenol-rich extract on the metabolome and response to inflammation in cultured intestinal cell. Food Res Int. 2018 Nov;113:392-400 Authors: Di Nunzio M, Picone G, Pasini F, Caboni MF, Gianotti A, Bordoni A, Capozzi F Abstract Over the past years, researchers and food manufacturers have become increasingly interested in olive polyphenols due to the recognition of their biological properties and probable role in the prevention of various diseases such as inflammatory bowel disease. Olive pomace, one of the main by-products of olive oil production, is a potential low-cost, phenol-rich ingredient for the formulation of functional food. In this study, the aqueous extract of olive pomace was characterized and used to supplement human intestinal cell in culture (Caco-2). The effect on the cell metabolome and the anti-inflammatory potential were then evaluated. Modification in the metabolome induced by supplementation clearly evidenced a metabolic shift toward a "glucose saving/accumulation" strategy that could have a role in maintaining anorexigenic hormone secretion and could explain the reported appetite-suppressing effect of the administration of polyphenol-rich food. In both basal and inflamed condition, supplementation significantly reduced the secretion of the main pro-inflammatory cytokine, IL-8. Thus, our data confirm the therapeutic potential of polyphenols, and specifically of olive pomace in intestinal bowel diseases. Although intervention studies are needed to confirm the clinical significance of our findings, the herein reported results pave the road for exploitation of olive pomace in the formulation of new, value-added foods. In addition, the application of a foodomics approach allowed observing a not hypothesized modulation of glucose metabolism. PMID: 30195533 [PubMed - in process]

1H NMR and multivariate data analysis of the differences of metabolites in five types of dry-cured hams.

Mon, 10/09/2018 - 13:42
Related Articles 1H NMR and multivariate data analysis of the differences of metabolites in five types of dry-cured hams. Food Res Int. 2018 Nov;113:140-148 Authors: Zhang J, Ye Y, Sun Y, Pan D, Ou C, Dang Y, Wang Y, Cao J, Wang D Abstract In order to distinguish the taste styles of dry-cured hams (Jinhua, Xuanwei, Country, Parma and Bama), we established a 1H nuclear magnetic resonance spectroscopy method to identify metabolites. Totally, 33 charged metabolites, including amino acids, organic acids, nucleic acids and their derivatives, sugars, alkaloids and others were identified. The abundant glutamate, lysine, alanine, leucine and lactate could be the major contributors of taste. Total variables were explained by PC1 (67.7%) and PC2 (16.0%) which showed that Parma and Xuanwei styles were close to each other (similar amino acids, peptide, organic acids and alkaloids contents). Bama style showed the highest PC1 and amino acids, organic acids and alkaloids contents. Country style was located on the left-most area of PC1 (the lowest amino acids, organic acids and peptide, but the highest sugars contents). Sensory evaluation revealed that Bama ham had the highest overall taste score, followed by Jinhua, Parma, Xuanwei and American Country ham. We concluded that the proportions and combinations of taste components explained the specific taste instead of any single component. These findings provided a better understanding of different metabolomics among hams. PMID: 30195506 [PubMed - in process]

NMR metabolomic fingerprinting distinguishes milk from different farms.

Mon, 10/09/2018 - 13:42
Related Articles NMR metabolomic fingerprinting distinguishes milk from different farms. Food Res Int. 2018 Nov;113:131-139 Authors: Tenori L, Santucci C, Meoni G, Morrocchi V, Matteucci G, Luchinat C Abstract A fast and reproducible protocol for milk Nuclear Magnetic Resonance (NMR) metabolomic fingerprinting was developed, allowing for an accurate discrimination among milk samples from large-scale distribution, as well as among milk sample from different farms located in the same restricted geographical area. Seasonal variations in milk composition and correlations with cows' nutritional patterns are also assessed, underlining relationships between feeding and metabolites. The most important difference was related to the use of silage feeding. This finding is relevant to assess the suitability of milk for different dairy products. A prominent example is parmesan cheese, the preparation protocol of which excludes milk from silage-fed cows. PMID: 30195505 [PubMed - in process]

Dysregulated serum metabolites in staging of hepatocellular carcinoma.

Mon, 10/09/2018 - 13:42
Related Articles Dysregulated serum metabolites in staging of hepatocellular carcinoma. Clin Biochem. 2018 Sep 06;: Authors: Wang W, Lv J, Chen N, Lou B, Mao W, Wang P, Chen Y Abstract BACKGROUND: Correct staging of hepatocellular carcinoma (HCC) could help physicians to precisely select treatments for patients, such as surgery, chemotherapy, or their combination. The objective of this study was to explore potential metabolic markers for staging of hepatocellular carcinoma. METHODS: By liquid chromatography with mass spectrometry (LC-MS), the serum metabolic profiles of 60 pathologically confirmed hepatocellular carcinoma (HCC) patients were analyzed using the TNM staging system and Chinese staging system. RESULTS: The serum levels of dihydrocortisol, lysophosphatidylcholine (LPC-18:0), lysophosphatidylethanolamine (LPE-16:0), taurine, uric acid, adipic acid, tetracosatetraenoic acid, and L-octanoylcarnitine differed significantly between staging I and non-stage I HCCs (p < 0.05) based on the HCC TNM staging system, and compared to stage I sera, non-stage I sera contained higher levels of dihydrocortisol, adipic acid, tetracosatetraenoic acid, and L-octanoylcarnitine. There are significant differences were observed in serum levels of LPC (22:6), alpha-linolenylcarnitine, estrone, LPE (16:0), LPE (18:2), and taurine between stage I and stage II HCCs (p < 0.05) based on the Chinese HCC staging system, and compared to stage I sera, stage II sera had a higher level of LPC (22:6). CONCLUSION: These dysregulated metabolites in sera of HCC patients potentially could be used as biomarkers for the clinical staging of HCC. PMID: 30195484 [PubMed - as supplied by publisher]

Metabolomics in chronic kidney disease: Strategies for extended metabolome coverage.

Sun, 09/09/2018 - 13:13
Metabolomics in chronic kidney disease: Strategies for extended metabolome coverage. J Pharm Biomed Anal. 2018 Aug 25;161:313-325 Authors: Yoric G, Julien B, Belén P, Serge R Abstract Chronic kidney disease (CKD) is becoming a major public health issue as prevalence is increasing worldwide. It also represents a major challenge for the identification of new early biomarkers, understanding of biochemical mechanisms, patient monitoring and prognosis. Each metabolite contained in a biofluid or tissue may play a role as a signal or as a driver in the development or progression of the pathology. Therefore, metabolomics is a highly valuable approach in this clinical context. It aims to provide a representative picture of a biological system, making exhaustive metabolite coverage crucial. Two aspects can be considered: analytical and biological coverage. From an analytical point of view, monitoring all metabolites within one run is currently impossible. Multiple analytical techniques providing orthogonal information should be carried out in parallel for coverage improvement. The biological aspect of metabolome coverage can be enhanced by using multiple biofluids or tissues for in-depth biological investigation, as the analysis of a single sample type is generally insufficient for whole organism extrapolation. Hence, recording of signals from multiple sample types and different analytical platforms generates massive and complex datasets so that chemometric tools, including data fusion approaches and multi-block analysis, are key tools for extracting biological information and for discovery of relevant biomarkers. This review presents the recent developments in the field of metabolomic analysis, from sampling and analytical strategies to chemometric tools, dedicated to the generation and handling of multiple complementary metabolomic datasets enabling extended metabolite coverage to improve our biological knowledge of CKD. PMID: 30195171 [PubMed - as supplied by publisher]

Using metabolome data for mathematical modeling of plant metabolic systems.

Sun, 09/09/2018 - 13:13
Using metabolome data for mathematical modeling of plant metabolic systems. Curr Opin Biotechnol. 2018 Sep 05;54:138-144 Authors: Hirai MY, Shiraishi F Abstract Plant metabolism is characterized by a wide diversity of metabolites, with systems far more complicated than those of microorganisms. Mathematical modeling is useful for understanding dynamic behaviors of plant metabolic systems for metabolic engineering. Time-series metabolome data has great potential for estimating kinetic model parameters to construct a genome-wide metabolic network model. However, data obtained by current metabolomics techniques does not meet the requirement for constructing accurate models. In this article, we highlight novel strategies and algorithms to handle the underlying difficulties and construct dynamic in vivo models for large-scale plant metabolic systems. The coarse but efficient modeling enables the prediction of unknown mechanisms regulating plant metabolism. PMID: 30195121 [PubMed - as supplied by publisher]

Pages