PubMed

Combining DI-ESI-MS and NMR datasets for metabolic profiling. Metabolomics. 2015 Apr;11(2):391-402 Authors: Marshall DD, Lei S, Worley B, Huang Y, Garcia-Garcia A, Franco R, Dodds ED, Powers R Abstract Metabolomics datasets are commonly acquired by either mass spectrometry (MS) or nuclear magnetic resonance spectroscopy (NMR), despite their fundamental complementarity. In fact, combining MS and NMR datasets greatly improves the coverage of the metabolome and enhances the accuracy of metabolite identification, providing a detailed and high-throughput analysis of metabolic changes due to disease, drug treatment, or a variety of other environmental stimuli. Ideally, a single metabolomics sample would be simultaneously used for both MS and NMR analyses, minimizing the potential for variability between the two datasets. This necessitates the optimization of sample preparation, data collection and data handling protocols to effectively integrate direct-infusion MS data with one-dimensional (1D) (1)H NMR spectra. To achieve this goal, we report for the first time the optimization of (i) metabolomics sample preparation for dual analysis by NMR and MS, (ii) high throughput, positive-ion direct infusion electrospray ionization mass spectrometry (DI-ESI-MS) for the analysis of complex metabolite mixtures, and (iii) data handling protocols to simultaneously analyze DI-ESI-MS and 1D (1)H NMR spectral data using multiblock bilinear factorizations, namely multiblock principal component analysis (MB-PCA) and multiblock partial least squares (MB-PLS). Finally, we demonstrate the combined use of backscaled loadings, accurate mass measurements and tandem MS experiments to identify metabolites significantly contributing to class separation in MB-PLS-DA scores. We show that integration of NMR and DI-ESI-MS datasets yields a substantial improvement in the analysis of neurotoxin involvement in dopaminergic cell death. PMID: 25774104 [PubMed - as supplied by publisher]

Metabolomic composition of normal aged and cataractous human lenses. Exp Eye Res. 2015 Mar 12; Authors: Tsentalovich YP, Verkhovod TD, Yanshole VV, Kiryutin AS, Yanshole LV, Fursova AZ, Stepakov DA, Novoselov VP, Sagdeev RZ Abstract Quantitative metabolomic profiles of normal and cataractous human lenses were obtained with the combined use of high-frequency nuclear magnetic resonance (NMR) and high-performance liquid chromatography with high-resolution mass-spectrometric detection (LC-MS) methods. The concentration of more than fifty metabolites in the lens cortex and nucleus has been determined. For the majority of metabolites, their concentrations in the lens cortex and nucleus are similar, which confirms low metabolic activity in the lens core. The difference between the metabolite levels in the cortex and nucleus of the normal lens is observed for antioxidants and UV filters, which demonstrates the activity of redox processes in the lens. A huge difference is found between the metabolomic compositions of normal and age-matched cataractous lenses: the concentrations of almost all metabolites in the normal lens are higher than in the cataractous one. The most pronounced difference is observed for compounds playing a key role in the lens cell protection and metabolic activity, including antioxidants, UV filters, and osmolytes. The results obtained imply that the development of the age-related cataracts might originate from the metabolic dysfunction of the lens epithelial cells. PMID: 25773987 [PubMed - as supplied by publisher]

Parallelized small-scale production of uniformly (13)C-labeled cell-extract for quantitative metabolome analysis. Anal Biochem. 2015 Mar 12; Authors: Weiner M, Tröndle J, Schmideder A, Albermann C, Binder K, Sprenger GA, Weuster-Botz D Abstract The need of quantitative intracellular metabolome information is a central requirement in modern applied biotechnology and systems biology. In most cases, sample preparation and metabolite analysis result in degradation of metabolites and signal suppression due to metabolite instability and matrix effects during LC-MS analysis. Therefore application of uniformly (U) labeled (13)C-cell-extract as internal standard has gained raising interest in recent years. In this study a multiple step protocol has been developed for efficient preparation of U-(13)C-labeled E. coli cell-extracts in stirred-tank bioreactors on a milliliter-scale with minimized supply of costly (13)C-labeled substrate. Significant reduction of fermentation media-salt concentration in the U-(13)C-labeled cell-extract was achieved to reduce ion-suppression effects during mass-spectrometric analysis. Additionally, variation of reaction conditions in parallel operated stirred-tank bioreactors on a milliliter-scale enables the simultaneous preparation of U-(13)C-labeled cell extracts with varying metabolite concentrations which was shown by the example of the labeled phosphoenolpyruvate level in E. coli. PMID: 25772305 [PubMed - as supplied by publisher]

Warming differentially influences the effects of drought on stoichiometry and metabolomics in shoots and roots. New Phytol. 2015 Mar 13; Authors: Gargallo-Garriga A, Sardans J, Pérez-Trujillo M, Oravec M, Urban O, Jentsch A, Kreyling J, Beierkuhnlein C, Parella T, Peñuelas J Abstract Plants in natural environments are increasingly being subjected to a combination of abiotic stresses, such as drought and warming, in many regions. The effects of each stress and the combination of stresses on the functioning of shoots and roots have been studied extensively, but little is known about the simultaneous metabolome responses of the different organs of the plant to different stresses acting at once. We studied the shift in metabolism and elemental composition of shoots and roots of two perennial grasses, Holcus lanatus and Alopecurus pratensis, in response to simultaneous drought and warming. These species responded differently to individual and simultaneous stresses. These responses were even opposite in roots and shoots. In plants exposed to simultaneous drought and warming, terpenes, catechin and indole acetic acid accumulated in shoots, whereas amino acids, quinic acid, nitrogenous bases, the osmoprotectants choline and glycine betaine, and elements involved in growth (nitrogen, phosphorus and potassium) accumulated in roots. Under drought, warming further increased the allocation of primary metabolic activity to roots and changed the composition of secondary metabolites in shoots. These results highlight the plasticity of plant metabolomes and stoichiometry, and the different complementary responses of shoots and roots to complex environmental conditions. PMID: 25772030 [PubMed - as supplied by publisher]

Tetranychus urticae-triggered responses promote genotype-dependent conspecific repellence or attractiveness in citrus. New Phytol. 2015 Mar 13; Authors: Agut B, Gamir J, Jaques JA, Flors V Abstract The citrus rootstocks sour orange and Cleopatra mandarin display differential resistance against Tetranychus urticae. Sour orange plants support reduced oviposition, growth rates and damage compared with Cleopatra mandarin plants. Jasmonic acid signalling and flavonoid accumulation have been revealed as key mechanisms for the enhanced resistance of sour orange plants. In this study, we observed that the release of T. urticae herbivore-induced plant volatiles (HIPVs) from sour orange plants has a marked repellent effect on conspecific mites associated with the production of the terpenes α-ocimene, α-farnesene, pinene and d-limonene, and the green leaf volatile 4-hydroxy-4-methyl-2-pentanone. By contrast, T. urticae HIPVs from Cleopatra mandarin plants promote conspecific mite attraction associated with an increase in (2-butoxyethoxy) ethanol, benzaldehyde and methyl salicylate levels. HIPVs released from sour orange plants following T. urticae infestation induce resistance in Cleopatra mandarin plants, thereby reducing oviposition rates and stimulating the oxylipin biosynthetic gene lipoxygenase2 (LOX2). Cleopatra HIPVs do not affect the response to T. urticae of these rootstocks. We conclude that sour orange plants promote herbivore-induced resistance in Cleopatra mandarin plants and, despite the weak basal resistance of these rootstocks, herbivore resistance can be induced through the combination of HIPVs, such as α-ocimene and d-limonene. PMID: 25771705 [PubMed - as supplied by publisher]

A metabolomic assessment of NAC154 transcription factor overexpression in field grown poplar stem wood. Phytochemistry. 2015 Mar 11; Authors: Jervis J, Hildreth SB, Sheng X, Beers EP, Brunner AM, Helm RF Abstract Several xylem-associated regulatory genes have been identified that control processes associated with wood formation in poplar. Prominent among these are the NAC domain transcription factors (NACs). Here, the putative involvement of PopulusNAC154, a co-ortholog of the Arabidopsis gene SND2, was evaluated as a regulator of "secondary" biosynthetic processes in stem internode tissues by interrogating aqueous methanolic extracts from control and transgenic trees. Comprehensive untargeted metabolite profiling was accomplished with a liquid chromatography-mass spectrometry platform that utilized two different chromatographic supports (HILIC and reversed phase) and both positive and negative ionization modes. Evaluation of current and previous year tissues provided datasets for assessing the effects of NAC154 overexpression in wood maturation processes. Phenolic glycoside levels as well as those of oligolignols, sucrose and arginine were modulated with phenotypic and chemotypic traits exhibiting similar trends. Specifically, increased levels of arginine in the NAC154 overexpressing tissues supports a role for the transcription factor in senescence/dormancy-associated processes. PMID: 25771508 [PubMed - as supplied by publisher]

Effect of the DGAT1 K232A genotype of dairy cows on the milk metabolome and proteome. J Dairy Sci. 2015 Mar 11; Authors: Lu J, Boeren S, van Hooijdonk T, Vervoort J, Hettinga K Abstract Diglyceride O-acyltransferase 1 (DGAT1) is the enzyme that catalyzes the synthesis of triglycerides from diglycerides and acyl-coenzyme A. The DGAT1 K232A polymorphism was previously shown to have a significant influence on bovine milk production characteristics (milk yield, protein content, fat content, and fatty acid composition). The mechanism of this influence has, however, not been elucidated. In this study, metabolomics ((1)H-nuclear magnetic resonance) and proteomics (laser chromatography-tandem mass spectrometry) were applied to determine the serum and lipid metabolite composition and milk fat globule membrane proteome of milk samples from cows with the DGAT1 KK and AA genotypes. The milk samples from cows with the DGAT1 KK genotype contained more stomatin, sphingomyelin, choline, and carnitine, and less citrate, creatine or phosphocreatine, glycerol-phosphocholine, mannose-like sugar, acetyl sugar phosphate, uridine diphosphate (UDP)-related sugar, and orotic acid compared with milk samples from cows with the DGAT1 AA genotype. Based on these results, we propose that the differences between the DGAT1 genotypes may be related to stomatin-sphingomyelin lipid rafts as well as structural (cell membrane) differences in epithelial cells of the mammary gland. In conclusion, our study shows that, in addition to previously described changes in triglyceride composition, cows differing in DGAT1 polymorphism differ in their milk proteome and metabolome, which may help in further understanding the effect of the DGAT1 K232A polymorphism on milk production characteristics. PMID: 25771043 [PubMed - as supplied by publisher]

Liquid-liquid extraction and liquid chromatography-mass spectrometry detection of curcuminoids from bacterial culture medium. J Chromatogr B Analyt Technol Biomed Life Sci. 2015 Feb 24;988:116-120 Authors: Tan S, Rupasinghe TW, Tull DL, Augustin MA, Gras SL Abstract Liquid chromatography-mass spectrometry (LC-MS) has been used to detect polyphenolic curcuminoids found in turmeric but studies of metabolism by bacterial and mammalian cells in vitro are compromised by poor recovery from the culture medium. We report a liquid-liquid extraction procedure with ethyl acetate and use LC-MS to quantify extracted curcuminoids. Ethyl acetate allows recoveries of ∼80-86% of curcuminoids from the bacterial growth medium, bacterial cell lysate and combined bacterial cell and growth medium matrices; a clear improvement over acetonitrile where recoveries were ∼25-66%. This optimised method will enable studies of curcuminoid metabolism and may be applicable to other hydrophobic polyphenolic compounds. PMID: 25770788 [PubMed - as supplied by publisher]

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Related Articles Metabolic analysis reveals changes in the mevalonate and juvenile hormone synthesis pathways linked to the mosquito reproductive physiology. Insect Biochem Mol Biol. 2014 Aug;51:1-9 Authors: Rivera-Perez C, Nouzova M, Lamboglia I, Noriega FG Abstract Juvenile hormone (JH) regulates reproductive maturation in insects; therefore interruption of JH biosynthesis has been considered as a strategy for the development of target-specific insecticides. The corpora allata (CA) from mosquitoes is highly specialized to supply variable levels of JH, which are linked to ovarian developmental stages and influenced by nutritional signals. However, very little is known about how changes in JH synthesis relate to reproductive physiology and how JH synthesis regulation is translated into changes in the CA machinery. With the advent of new methods that facilitate the analysis of transcripts, enzymes and metabolites in the minuscule CA, we were able to provide comprehensive descriptions of the mevalonic (MVA) and JH synthesis pathways by integrating information on changes in the basic components of those pathways. Our results revealed remarkable dynamic changes in JH synthesis and exposed part of a complex mechanism that regulates CA activity. Principal component (PC) analyses validated that both pathways (MVAP and JH-branch) are transcriptionally co-regulated as a single unit, and catalytic activities for the enzymes of the MVAP and JH-branch also changed in a coordinate fashion. Metabolite studies showed that global fluctuations in the intermediate pool sizes in the MVAP and JH-branch were often inversely related. PC analyses suggest that in female mosquitoes, there are at least 4 developmental switches that alter JH synthesis by modulating the flux at distinctive points in both pathways. PMID: 24833260 [PubMed - indexed for MEDLINE]

NMR ((1)H and (13)C) based Signatures of Abnormal Choline Metabolism in Oral Squamous Cell Carcinoma with no Prominent Warburg Effect. Biochem Biophys Res Commun. 2015 Mar 10; Authors: Bag S, Banerjee DR, Basak A, Das AK, Pal M, Banerjee R, Paul RR, Chatterjee J Abstract At functional levels, besides genes and proteins, changes in metabolome profiles are instructive for a biological system in health and disease including malignancy. It is understood that metabolomic alterations in association with proteomic and transcriptomic aberrations are very fundamental to unravel malignant micro-ambient criticality and oral cancer is no exception. Hence deciphering intricate dimensions of oral cancer metabolism may be contributory both for integrated appreciation of its pathogenesis and to identify any critical but yet unexplored dimension of this malignancy with high mortality rate. Although several methods do exist, NMR provides higher analytical precision in identification of cancer metabolomic signature. Present study explored abnormal signatures in choline metabolism in oral squamous cell carcinoma (OSCC) using (1)H and (13)C NMR analysis of serum. It has demonstrated down-regulation of choline with concomitant up-regulation of its break-down product in the form of trimethylamine N-oxide in OSCC compared to normal counterpart. Further, no significant change in lactate profile in OSCC possibly indicated that well-known Warburg effect was not a prominent phenomenon in such malignancy. Amongst other important metabolites, malonate has shown up-regulation but D-glucose, saturated fatty acids, acetate and threonine did not show any significant change. Analyzing these metabolomic findings present study proposed trimethyl amine N-oxide and malonate as important metabolic signature for oral cancer with no prominent Warburg effect. PMID: 25769954 [PubMed - as supplied by publisher]

New developments in Cryptosporidium research. Int J Parasitol. 2015 Mar 10; Authors: Ryan U, Hijjawi N Abstract Cryptosporidium is an enteric parasite that is considered the second greatest cause of diarrhoea and death in children after rotavirus. Currently, 27 species are recognized as valid and of these, Cryptosporidium hominis and Cryptosporidium parvum are responsible for the majority of infections in humans. Molecular and biological studies indicate that Cryptosporidium is more closely related to gregarine parasites rather than to coccidians. The identification of gregarine-like gamont stages and the ability of Cryptosporidium to complete its life cycle in the absence of host cells further confirm its relationship with gregarines. This opens new avenues into the investigation of pathogenesis, epidemiology, treatment and control of Cryptosporidium. Effective drug treatments and vaccines are not yet available due, in part, to the technical challenges of working on Cryptosporidium in the laboratory. Whole genome sequencing and metabolomics have expanded our understanding of the biochemical requirements of this organism and have identified new drug targets. To effectively combat this important pathogen, increased funding is essential. PMID: 25769247 [PubMed - as supplied by publisher]

Modulation of Cell Metabolic Pathways and Oxidative Stress Signaling Contribute to Acquired Melphalan Resistance in Multiple Myeloma Cells. PLoS One. 2015;10(3):e0119857 Authors: Zub KA, Sousa MM, Sarno A, Sharma A, Demirovic A, Rao S, Young C, Aas PA, Ericsson I, Sundan A, Jensen ON, Slupphaug G Abstract Alkylating agents are widely used chemotherapeutics in the treatment of many cancers, including leukemia, lymphoma, multiple myeloma, sarcoma, lung, breast and ovarian cancer. Melphalan is the most commonly used chemotherapeutic agent against multiple myeloma. However, despite a 70-80% initial response rate, virtually all patients eventually relapse due to the emergence of drug-resistant tumour cells. By using global proteomic and transcriptomic profiling on melphalan sensitive and resistant RPMI8226 cell lines followed by functional assays, we discovered changes in cellular processes and pathways not previously associated with melphalan resistance in multiple myeloma cells, including a metabolic switch conforming to the Warburg effect (aerobic glycolysis), and an elevated oxidative stress response mediated by VEGF/IL8-signaling. In addition, up-regulated aldo-keto reductase levels of the AKR1C family involved in prostaglandin synthesis contribute to the resistant phenotype. Finally, selected metabolic and oxidative stress response enzymes were targeted by inhibitors, several of which displayed a selective cytotoxicity against the melphalan-resistant cells and should be further explored to elucidate their potential to overcome melphalan resistance. PMID: 25769101 [PubMed - as supplied by publisher]

Metabolomic Profiling of Urine Samples from Mice Exposed to Protons Reveals Radiation Quality and Dose Specific Differences. Radiat Res. 2015 Mar 13; Authors: Laiakis EC, Trani D, Moon BH, Strawn SJ, Fornace AJ Abstract As space travel is expanding to include private tourism and travel beyond low-Earth orbit, so is the risk of exposure to space radiation. Galactic cosmic rays and solar particle events have the potential to expose space travelers to significant doses of radiation that can lead to increased cancer risk and other adverse health consequences. Metabolomics has the potential to assess an individual's risk by exploring the metabolic perturbations in a biofluid or tissue. In this study, C57BL/6 mice were exposed to 0.5 and 2 Gy of 1 GeV/nucleon of protons and the levels of metabolites were evaluated in urine at 4 h after radiation exposure through liquid chromatography coupled to time-of-flight mass spectrometry. Significant differences were identified in metabolites that map to the tricarboxylic acid (TCA) cycle and fatty acid metabolism, suggesting that energy metabolism is severely impacted after exposure to protons. Additionally, various pathways of amino acid metabolism (tryptophan, tyrosine, arginine and proline and phenylalanine) were affected with potential implications for DNA damage repair and cognitive impairment. Finally, presence of products of purine and pyrimidine metabolism points to direct DNA damage or increased apoptosis. Comparison of these metabolomic data to previously published data from our laboratory with gamma radiation strongly suggests a more pronounced effect on metabolism with protons. This is the first metabolomics study with space radiation in an easily accessible biofluid such as urine that further investigates and exemplifies the biological differences at early time points after exposure to different radiation qualities. PMID: 25768838 [PubMed - as supplied by publisher]

Persistent Organic Pollutants Modify Gut Microbiota-Host Metabolic Homeostasis in Mice Through Aryl Hydrocarbon Receptor Activation. Environ Health Perspect. 2015 Mar 13; Authors: Zhang L, Nichols RG, Correll J, Murray IA, Tanaka N, Smith P, Hubbard TD, Sebastian A, Albert I, Hatzakis E, Gonzalez FJ, Perdew GH, Patterson AD Abstract BACKGROUND: Alteration of the gut microbiota through diet and environmental contaminants may disturb physiological homeostasis, leading to various diseases including obesity and type 2 diabetes. Since most exposure to environmentally-persistent organic pollutants (POPs) occurs through the diet, the host gastrointestinal tract and commensal gut microbiota are likely to be exposed to POPs. OBJECTIVES: We report that 2,3,7,8-tetrachlorodibenzofuran (TCDF), a persistent environmental contaminant, profoundly impacts the gut microbiota and host metabolism in an aryl hydrocarbon receptor (AHR)-dependent manner. METHODS: Six-week-old male wild-type and Ahr(-/-) mice on the C57BL/6J background were treated with 24 µg/kg TCDF in the diet for five days. 16S rRNA gene sequencing, (1)H nuclear magnetic resonance (NMR) metabolomics, targeted ultra-performance liquid chromatography coupled with triplequadrupole mass spectrometry (UPLC-TQMS) and biochemical assays were used to determine the microbiota compositions and the physiological and metabolic effects of TCDF. RESULTS: Dietary TCDF altered the gut microbiota by shifting the ratio of Firmicutes to Bacteroidetes. TCDF-treated mouse cecal contents were enriched with Butyrivibrio spp., but depleted in Oscillobacter spp. in comparison with vehicle-treated mice. These changes in the gut microbiota were associated with altered bile acid metabolism. Further, dietary TCDF inhibited the farnesoid X receptor (FXR) signaling pathway, and triggered significant inflammation and host metabolic disorders as a result of activation of bacterial fermentation, and altering hepatic lipogenesis, gluconeogenesis and glycogenolysis, in an AHR-dependent manner. CONCLUSION: These findings provide new insights into the biochemical consequences of TCDF exposure involving the alteration of the gut microbiota, modulation of nuclear receptor signaling, and disruption of host metabolism. PMID: 25768209 [PubMed - as supplied by publisher]

Risk factors and effective management of preeclampsia. Integr Blood Press Control. 2015;8:7-12 Authors: English FA, Kenny LC, McCarthy FP Abstract Preeclampsia, a hypertensive disorder of pregnancy is estimated to complicate 2%-8% of pregnancies and remains a principal cause of maternal and fetal morbidity and mortality. Preeclampsia may present at any gestation but is more commonly encountered in the third trimester. Multiple risk factors have been documented, including: family history, nulliparity, egg donation, diabetes, and obesity. Significant progress has been made in developing tests to predict risk of preeclampsia in pregnancy, but these remain confined to clinical trial settings and center around measuring angiogenic profiles, including placental growth factor or newer tests involving metabolomics. Less progress has been made in developing new treatments and therapeutic targets, and aspirin remains one of the few agents shown to consistently reduce the risk of developing preeclampsia. This review serves to discuss recent advances in risk factor identification, prediction techniques, and management of preeclampsia in antenatal, intrapartum, and postnatal patients. PMID: 25767405 [PubMed - as supplied by publisher]

Quantification of serum apolipoproteins A-I and B-100 in clinical samples using an automated SISCAPA-MALDI-TOF-MS workflow. Methods. 2015 Mar 9; Authors: van den Broek I, Nouta J, Razavi M, Yip R, Bladergroen MR, Romijn FP, Smit NP, Drews O, Paape R, Suckau D, Deelder AM, van der Burgt YE, Pearson TW, Leigh Anderson N, Cobbaert CM Abstract A fully automated workflow was developed and validated for simultaneous quantification of the cardiovascular disease risk markers apolipoproteins A-I (apoA-I) and B-100 (apoB-100) in clinical sera. By coupling of stable-isotope standards and capture by anti-peptide antibodies (SISCAPA) for enrichment of proteotypic peptides from serum digests to matrix-assisted laser desorption/ionisation time-of-flight (MALDI-TOF) MS detection, the standardized platform enabled rapid, liquid chromatography-free quantification at a relatively high throughput of 96 samples in 12 hours. The average imprecision in normo- and triglyceridemic serum pools was 3.8% for apoA-I and 4.2% for apoB-100 (4 replicates over 5 days). If stored properly, the MALDI target containing enriched apoA-1 and apoB-100 peptides could be re-analysed without any effect on bias or imprecision for at least 7 days after initial analysis. Validation of the workflow revealed excellent linearity for daily calibration with external, serum-based calibrators (R(2) of 0.984 for apoA-I and 0.976 for apoB-100 as average over five days), and absence of matrix effects or interference from triglycerides, protein content, hemolysates, or bilirubins. Quantification of apoA-I in 93 normo- and hypertriglyceridemic clinical sera showed good agreement with immunoturbidimetric analysis (slope = 1.01, R(2)=0.95, mean bias = 4.0%). Measurement of apoB-100 in the same clinical sera using both methods, however, revealed several outliers in SISCAPA-MALDI-TOF-MS measurements, possibly as a result of the lower MALDI-TOF-MS signal intensity (slope = 1.09, R(2)=0.91, mean bias = 2.0%). The combination of analytical performance, rapid cycle time and automation potential validate the SISCAPA-MALDI-TOF-MS platform as a valuable approach for standardized and high-throughput quantification of apoA-I and apoB-100 in large sample cohorts. PMID: 25766926 [PubMed - as supplied by publisher]

Molecular mechanisms of ethanol-associated oro-esophageal squamous cell carcinoma. Cancer Lett. 2015 Mar 9; Authors: Liu Y, Chen H, Sun Z, Chen X Abstract Alcohol drinking is a major etiological factor of oro-esophageal squamous cell carcinoma (OESCC). Both local and systemic effects of ethanol may promote carcinogenesis, especially among chronic alcoholics. However, molecular mechanisms of ethanol-associated OESCC are still not well understood. In this review, we summarize current understandings and propose three mechanisms of ethanol-associated OESCC: (1) Disturbance of systemic metabolism of nutrients: during ethanol metabolism in the liver, systemic metabolism of retinoids, zinc, iron and methyl groups is altered. These nutrients are known to be associated with the development of OESCC. (2) Disturbance of redox metabolism in squamous epithelial cells: when ethanol is metabolized in oro-esophageal squamous epithelial cells, reactive oxygen species are generated and produce oxidative damage. Meanwhile, ethanol may also disturb fatty-acid metabolism in these cells. (3) Disturbance of signaling pathways in squamous epithelial cells: due to its physico-chemical properties, ethanol changes cell membrane fluidity and shape, and may thus impact multiple signaling pathways. Advanced molecular techniques in genomics, epigenomics, metabolomics and microbiomics will help us elucidate how ethanol promotes OESCC. PMID: 25766659 [PubMed - as supplied by publisher]

A Targeted Metabolomics Approach toward Understanding Metabolic Variations in Rice under Pesticide Stress. Anal Biochem. 2015 Mar 9; Authors: Mahdavi V, Farimani MM, Fathi F, Ghassempour A Abstract Diazinon insecticide is widely applied throughout rice (Oryza sativa L.) fields in Iran. However, concerns are now being raised about its potential adverse impacts on rice fields. In this study, a time-course metabolic change in rice plants was investigated after diazinon treatment using gas chromatography-mass spectrometry (GC-MS) and subsequently, statistical strategy of Random Forest (RF) was performed in order to find the stress-associated effects. According to the results, a wide range of metabolites were dynamically varied as a result of the plant response to diazinon such as biosynthesis and metabolism of sugars, amino acids, organic acids and Phenylpropanoids, all correlating with the exposure time. Plant response was involved in multiple metabolic pathways, most of which were correlated with the exposure time. In this study, RF was explored as a potential multivariate method for GC/MS analysis of metabolomics data of rice (Oryza sativa L.) plants under diazinon stress; more than 31 metabolites were quantitatively determined and time-course metabolic response of the plant during different days after treatment was measured. Results demonstrated RF as a potential multivariate method for gas chromatography-mass spectrometry analysis of changes in plant metabolome under insecticide stress. PMID: 25766578 [PubMed - as supplied by publisher]

A genome-wide scan for signatures of directional selection in domesticated pigs. BMC Genomics. 2015 Feb 25;16(1):130 Authors: Moon S, Kim TH, Lee KT, Kwak W, Lee T, Lee SW, Kim MJ, Cho K, Kim N, Chung WH, Sung S, Park T, Cho S, Groenen M, Nielsen R, Kim Y, Kim H Abstract BACKGROUND: Animal domestication involved drastic phenotypic changes driven by strong artificial selection and also resulted in new populations of breeds, established by humans. This study aims to identify genes that show evidence of recent artificial selection during pig domestication. RESULTS: Whole-genome resequencing of 30 individual pigs from domesticated breeds, Landrace and Yorkshire, and 10 Asian wild boars at ~16-fold coverage was performed resulting in over 4.3 million SNPs for 19,990 genes. We constructed a comprehensive genome map of directional selection by detecting selective sweeps using an FST-based approach that detects directional selection in lineages leading to the domesticated breeds and using a haplotype-based test that detects ongoing selective sweeps within the breeds. We show that candidate genes under selection are significantly enriched for loci implicated in quantitative traits important to pig reproduction and production. The candidate gene with the strongest signals of directional selection belongs to group III of the metabolomics glutamate receptors, known to affect brain functions associated with eating behavior, suggesting that loci under strong selection include loci involved in behaviorial traits in domesticated pigs including tameness. CONCLUSIONS: We show that a significant proportion of selection signatures coincide with loci that were previously inferred to affect phenotypic variation in pigs. We further identify functional enrichment related to behavior, such as signal transduction and neuronal activities, for those targets of selection during domestication in pigs. PMID: 25765548 [PubMed - as supplied by publisher]