Genomes and Genes
Summary: The dynamic collection of metabolites which represent a cell's or organism's net metabolic response to current conditions.
- Figueiredo A, Kouril T, Esser D, Haferkamp P, Wieloch P, Schomburg D, et al. Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus. PLoS ONE. 2017;12:e0180331 pubmed publisher..These new results reveal how enzyme kinetics and metabolomics synergizes with mathematical modelling to unveil new systemic properties of the ED pathway in S.solfataricus in terms of its adaptation and robustness. ..
- Ji J, Zhu P, Cui F, Pi F, Zhang Y, Sun X. The disorder metabolic profiling in kidney and spleen of mice induced by mycotoxins deoxynivalenol through gas chromatography mass spectrometry. Chemosphere. 2017;180:267-274 pubmed publisher..Furthermore, DON could lead to the disorder in immunity function and nucleotide metabolism in spleen, with decreasing trend of cytidine and alanine. ..
- Kostidis S, Kokova D, Dementeva N, Saltykova I, Kim H, Choi Y, et al. 1H-NMR analysis of feces: new possibilities in the helminthes infections research. BMC Infect Dis. 2017;17:275 pubmed publisher..The compounds cover a wide range of the metabolome including amino acids and their derivatives, short chain fatty acids (SCFAs), carboxylic acids and their ..
- Amiri M, Ramezani Tehrani F, Nahidi F, Kabir A, Azizi F, Carmina E. Effects of oral contraceptives on metabolic profile in women with polycystic ovary syndrome: A meta-analysis comparing products containing cyproterone acetate with third generation progestins. Metabolism. 2017;73:22-35 pubmed publisher..Instead, OC use does not affect body weight, BP or glucose levels, with only some minor increase of fasting insulin levels. ..
- Hurst C, Alder O, Platt F, Droop A, Stead L, Burns J, et al. Genomic Subtypes of Non-invasive Bladder Cancer with Distinct Metabolic Profile and Female Gender Bias in KDM6A Mutation Frequency. Cancer Cell. 2017;32:701-715.e7 pubmed publisher..More mutations in the histone lysine demethylase KDM6A were present in non-invasive tumors from females than males. ..
- Price N, Magis A, Earls J, Glusman G, Levy R, Lausted C, et al. A wellness study of 108 individuals using personal, dense, dynamic data clouds. Nat Biotechnol. 2017;35:747-756 pubmed publisher..Our results show that measurement of personal data clouds over time can improve our understanding of health and disease, including early transitions to disease states. ..
- Toprak O, Kurt H, Sari Y, Sarkis C, Us H, Kırık A. Magnesium Replacement Improves the Metabolic Profile in Obese and Pre-Diabetic Patients with Mild-to-Moderate Chronic Kidney Disease: A 3-Month, Randomised, Double-Blind, Placebo-Controlled Study. Kidney Blood Press Res. 2017;42:33-42 pubmed publisher..071) blood pressure did not achieve to a significant level after study. Our data support the argument that magnesium supplementation improves the metabolic status in hypomagnesemic CKD patients with pre-diabetes and obesity. ..
- Gao B, Chi L, Mahbub R, Bian X, Tu P, Ru H, et al. Multi-Omics Reveals that Lead Exposure Disturbs Gut Microbiome Development, Key Metabolites, and Metabolic Pathways. Chem Res Toxicol. 2017;30:996-1005 pubmed publisher..Taken together, these results demonstrated that lead exposure not only altered the gut microbiome community structures/diversity but also greatly affected metabolic functions, leading to gut microbiome toxicity. ..
- Pedersen H, Gudmundsdottir V, Nielsen H, Hyötyläinen T, Nielsen T, Jensen B, et al. Human gut microbes impact host serum metabolome and insulin sensitivity. Nature. 2016;535:376-81 pubmed..Here we show how the human gut microbiome impacts the serum metabolome and associates with insulin resistance in 277 non-diabetic Danish individuals...
- Habu J, Ibeh B. In vitro antioxidant capacity and free radical scavenging evaluation of active metabolite constituents of Newbouldia laevis ethanolic leaf extract. Biol Res. 2015;48:16 pubmed publisher..The extract is a potential source of antioxidants/free radical scavengers having important metabolites which maybe linked to its ethno-medicinal use. ..
- Chen J, Li C, Kuo C, Tsai K, Hou M, Hung W. Cancer/stroma interplay via cyclooxygenase-2 and indoleamine 2,3-dioxygenase promotes breast cancer progression. Breast Cancer Res. 2014;16:410 pubmed publisher..Integration of metabolomics and molecular and pathological approaches reveals the interplay between cancer and stroma via COX-2, and IDO promotes tumor progression and predicts poor patient survival. ..
- Liu H, Lin J, Zhu X, Li Y, Fan M, Zhang R, et al. Effects of R219K polymorphism of ATP-binding cassette transporter 1 gene on serum lipids ratios induced by a high-carbohydrate and low-fat diet in healthy youth. Biol Res. 2014;47:4 pubmed publisher..Body mass index (BMI), waist-to-hip ratios (WHR), log(TG/HDL-C), TC/HDL-C, LDL-C/HDL-C and apoA-1/apoB-100 were calculated. ABCA1 R219K was analyzed by a PCR-RFLP method...
- Si Hung L, Causon T, Hann S. Comparison of fully wettable RPLC stationary phases for LC-MS-based cellular metabolomics. Electrophoresis. 2017;38:2287-2295 pubmed publisher..Due to the difficulties in analyzing a wide range of polarities encountered in the metabolome, 100%-wettable reversed-phase materials are frequently used to maximize metabolome coverage within a single ..
- Stark H, Wolf J, Albersmeier A, Pham T, Hofmann J, Siebers B, et al. Oxidative Stickland reactions in an obligate aerobic organism - amino acid catabolism in the Crenarchaeon Sulfolobus solfataricus. FEBS J. 2017;284:2078-2095 pubmed publisher..In this work, we performed metabolic modelling as well as metabolome, transcriptome and proteome analysis on cells grown on caseinhydrolysate as carbon source in order to draw a ..
- Mathews J, Kasahara D, Cho Y, Bell L, Gunst P, Karoly E, et al. Effect of acute ozone exposure on the lung metabolomes of obese and lean mice. PLoS ONE. 2017;12:e0181017 pubmed publisher..Both obesity and ozone caused changes in the lung metabolome. Of 321 compounds identified, 101 were significantly impacted by obesity in air-exposed mice...
- Pecaut M, Mao X, Bellinger D, Jonscher K, Stodieck L, Ferguson V, et al. Is spaceflight-induced immune dysfunction linked to systemic changes in metabolism?. PLoS ONE. 2017;12:e0174174 pubmed publisher..Given the clear link between immune function and metabolism in many ground-based diseases, we propose a similar link may be involved in spaceflight-induced decrements in immune and metabolic function. ..
- Commisso M, Bianconi M, Di Carlo F, Poletti S, Bulgarini A, Munari F, et al. Multi-approach metabolomics analysis and artificial simplified phytocomplexes reveal cultivar-dependent synergy between polyphenols and ascorbic acid in fruits of the sweet cherry (Prunus avium L.). PLoS ONE. 2017;12:e0180889 pubmed publisher..Our data therefore indicate that the total antioxidant activity of sweet cherry fruits may originate from cultivar-dependent interactions among different classes of metabolite. ..
- Qiao S, Wu W, Chen M, Tang Q, Xia Y, Jia W, et al. Seminal plasma metabolomics approach for the diagnosis of unexplained male infertility. PLoS ONE. 2017;12:e0181115 pubmed publisher..By pathway enrichment analysis, we identified several major changed metabolic pathways related to UMI. Our findings provide new perspective for the diagnosis of UMI. ..
- ..Using conventional drug discovery and novel synthetic biology approaches, some investigators and companies are mining our resident microbes and their metabolites for targets in small-molecule drug programs. Ken Garber reports. ..
- Durani L, Hamezah H, Ibrahim N, Yanagisawa D, Makpol S, Damanhuri H, et al. Age-related changes in the metabolic profiles of rat hippocampus, medial prefrontal cortex and striatum. Biochem Biophys Res Commun. 2017;493:1356-1363 pubmed publisher..Thus, our findings might be useful for understanding the complexity of metabolic mechanisms in aging and provide insight for aging and health span...
- Silva V, Pereira L, Murata R. Oral microbe-host interactions: influence of ?-glucans on gene expression of inflammatory cytokines and metabolome profile. BMC Microbiol. 2017;17:53 pubmed publisher..Acetophenone, benzoic acid, and pinitol presented reduced concentrations only when treated with 10 ?g/mL of ?-glucan. Treatment with ?-glucans positively modulated the immune response and production of metabolites. ..
- Kadi A, Al Shakliah N, Yin W, Rahman A. In vitro investigation of metabolic profiling of newly developed topoisomerase inhibitors (ethyl fluorescein hydrazones, EtFLHs) in RLMs by LC-MS/MS. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1054:93-104 pubmed publisher..No metabolites were observed in the absence of either NADPH or microsomes for the compounds (1-5), indicating a likely involvement of CYP450 enzymes and cofactor NADPH in the metabolisms. ..
- Lee Y, Ku K, Becker T, Juvik J. Chemopreventive glucosinolate accumulation in various broccoli and collard tissues: Microfluidic-based targeted transcriptomics for by-product valorization. PLoS ONE. 2017;12:e0185112 pubmed publisher..This study provides basic information of the glucosinolate metabolome and transcriptome for various tissues of Brassica oleracea that maybe utilized as potential byproducts for the ..
- Xiao X, Hu M, Zhang X, Hu J. NMR-based Metabolomics Analysis of Liver from C57BL/6 Mouse Exposed to Ionizing Radiation. Radiat Res. 2017;188:44-55 pubmed publisher..In particular, metabolites such as 4-hydroxyphenylacetate, betaine, glutamine, choline and trimethylamine N-oxide may be prediagnostic biomarkers candidates for ionizing exposure of the liver. ..
- Arias Mutis O, Marrachelli V, Ruiz Sauri A, Alberola A, Morales J, Such Miquel L, et al. Development and characterization of an experimental model of diet-induced metabolic syndrome in rabbit. PLoS ONE. 2017;12:e0178315 pubmed publisher..This experimental model should provide a valuable tool for studies into the mechanisms of cardiovascular problems related to MetS, with special relevance in the study of cardiovascular remodeling, arrhythmias and SCD. ..
- Warner D, Liu H, Miller M, Ramsden C, Gao B, Feldstein A, et al. Dietary Linoleic Acid and Its Oxidized Metabolites Exacerbate Liver Injury Caused by Ethanol via Induction of Hepatic Proinflammatory Response in Mice. Am J Pathol. 2017;187:2232-2245 pubmed publisher..This study demonstrates that OXLAM-mediated induction of a proinflammatory response in macrophages is one of the potential mechanisms underlying the progression from alcohol-induced steatosis to alcoholic steatohepatitis. ..
- Schneider R, Bellenberg B, Hoepner R, Kolb E, Ellrichmann G, Haghikia A, et al. Metabolic profiles by 1H-magnetic resonance spectroscopy in natalizumab-associated post-PML lesions of multiple sclerosis patients who survived progressive multifocal leukoencephalopathy (PML). PLoS ONE. 2017;12:e0176415 pubmed publisher..In particular, Choline/Creatine levels, Lipid levels, and N-Acetyl- Aspartate/Choline are relevant markers in the post-PML setting, taking also the JCV status into account. ..
- Sriyudthsak K, Sawada Y, Chiba Y, Yamashita Y, Kanaya S, Onouchi H, et al. A U-system approach for predicting metabolic behaviors and responses based on an alleged metabolic reaction network. BMC Syst Biol. 2014;8 Suppl 5:S4 pubmed publisher..Thus, it can be a useful first-line tool of data analysis, model diagnostics and aid the design of next-step experiments. ..
- Lilja E, Johnson D. Metabolite toxicity determines the pace of molecular evolution within microbial populations. BMC Evol Biol. 2017;17:52 pubmed publisher..Given the ubiquity of toxic metabolites, they could also have implications for understanding the evolutionary histories of biological organisms. ..
- Gapper N, Hertog M, Lee J, Buchanan D, Leisso R, Fei Z, et al. Delayed response to cold stress is characterized by successive metabolic shifts culminating in apple fruit peel necrosis. BMC Plant Biol. 2017;17:77 pubmed publisher..The metabolome and transcriptome of peel destined to develop scald began to diverge from peel where scald was controlled using ..
- Ohshima M, Sugahara K, Kasahara K, Katakura A. Metabolomic analysis of the saliva of Japanese patients with oral squamous cell carcinoma. Oncol Rep. 2017;37:2727-2734 pubmed publisher..patients with oral squamous cell carcinoma (OSCC) using capillary electrophoresis-mass spectrometry (CE-MS) metabolome analysis of saliva samples...
- Walker H, Burrell M, Flatley J, Powers H. A metabolite profiling method for diagnosis of precancerous cervical lesions and HPV persistence. Bioanalysis. 2017;9:601-608 pubmed publisher..Data were interpreted using principal component analysis. The results indicate strongly that a simple metabolite profiling method could be used to rapidly identify women at increased risk of cervical cancer. ..
- Gao W, Wu Z, Sun J, Ni X, Xia H. Modulation of kanamycin B and kanamycin A biosynthesis in Streptomyces kanamyceticus via metabolic engineering. PLoS ONE. 2017;12:e0181971 pubmed publisher..kanamyceticus. Moreover, based on the clarified biosynthetic pathway, we obtained a kanamycin B-high-yield strain and an optimized kanamycin A-producing strain with minimal byproduct. ..
- Kovarik J, Kernbauer E, Hölzl M, Hofer J, Gualdoni G, Schmetterer K, et al. Fasting metabolism modulates the interleukin-12/interleukin-10 cytokine axis. PLoS ONE. 2017;12:e0180900 pubmed publisher..In conclusion, we showed that fasting metabolism modulates the IL-12/IL-10 cytokine balance, establishing novel targets for metabolism-based immune-modulation. ..
- Wagner G, Bhatt D, O Connell T, Thompson J, DuBois L, Backos D, et al. A Class of Reactive Acyl-CoA Species Reveals the Non-enzymatic Origins of Protein Acylation. Cell Metab. 2017;25:823-837.e8 pubmed publisher..These data uncover a fundamental relationship between reactive acyl-CoA species and proteins and define a new regulatory paradigm in metabolism. ..
- Mercurio L, Cecchetti S, Ricci A, Pacella A, Cigliana G, Bozzuto G, et al. Phosphatidylcholine-specific phospholipase C inhibition down- regulates CXCR4 expression and interferes with proliferation, invasion and glycolysis in glioma cells. PLoS ONE. 2017;12:e0176108 pubmed publisher..The intracellular metabolome was investigated by magnetic resonance spectroscopy; lactate levels and lactate dehydrogenase (LDH) activity ..
- Clendenen N, Nunns G, Moore E, Reisz J, Gonzalez E, Peltz E, et al. Hemorrhagic shock and tissue injury drive distinct plasma metabolome derangements in swine. J Trauma Acute Care Surg. 2017;83:635-642 pubmed publisher..These findings indicate that optimized resuscitative interventions in critically ill patients are possible based on identifying the severity of tissue injury and hemorrhage. ..
- de Candia P, De Rosa V, Gigantino V, Botti G, Ceriello A, Matarese G. Immunometabolism of human autoimmune diseases: from metabolites to extracellular vesicles. FEBS Lett. 2017;591:3119-3134 pubmed publisher..It will then discuss the new discoveries concerning how EVs may act as nanometric vehicles integrating immune/metabolic responses at the level of the extracellular environment and affecting pathological processes. ..
- Lim S, Lee J, Lee E. Comparison of fruit quality and GC-MS-based metabolite profiling of kiwifruit 'Jecy green': Natural and exogenous ethylene-induced ripening. Food Chem. 2017;234:81-92 pubmed publisher..The application of ethylene to 'Jecy green' kiwifruit to regulate ripening for commercial purposes can result in good quality fruit without side effects. ..
- Patel D, Krausz K, Xie C, Beyoglu D, Gonzalez F, Idle J. Metabolic profiling by gas chromatography-mass spectrometry of energy metabolism in high-fat diet-fed obese mice. PLoS ONE. 2017;12:e0177953 pubmed publisher..The novel SIM GCMS assay provided new insights into metabolic effects of HFD in mice. ..
- Krishnaiah S, Wu G, Altman B, Growe J, Rhoades S, Coldren F, et al. Clock Regulation of Metabolites Reveals Coupling between Transcription and Metabolism. Cell Metab. 2017;25:961-974.e4 pubmed publisher..These results provide the first comprehensive views of circadian liver and cell-autonomous metabolism. ..
- Savolainen O, Fagerberg B, Vendelbo Lind M, Sandberg A, Ross A, Bergstrom G. Biomarkers for predicting type 2 diabetes development-Can metabolomics improve on existing biomarkers?. PLoS ONE. 2017;12:e0177738 pubmed publisher..Additional markers detected using metabolomics are likely related to these measures as they did not enhance the overall prediction in a combined model. ..
- VanderSluis B, Hess D, Pesyna C, Krumholz E, Syed T, Szappanos B, et al. Broad metabolic sensitivity profiling of a prototrophic yeast deletion collection. Genome Biol. 2014;15:R64 pubmed publisher..We demonstrate utility in characterizing genes of unknown function and illustrate how these data can be integrated with other whole-genome screens to interpret similarities between seemingly diverse perturbation types. ..
- Lee D, Lee S, Singh D, Jang E, Shin H, Moon B, et al. Time-resolved comparative metabolomes for Koji fermentation with brown-, white-, and giant embryo-rice. Food Chem. 2017;231:258-266 pubmed publisher..The present study holistically underpins the dynamic metabolomes and enzymatic states during rice Koji fermentation with varying substrate types. The present study finds applications in optimization of commercial Koji production. ..
- Kim H, Jeong I, Hyun J, Kong B, Kim H, Park S. Metabolomic profiling of CSF in multiple sclerosis and neuromyelitis optica spectrum disorder by nuclear magnetic resonance. PLoS ONE. 2017;12:e0181758 pubmed publisher..Although several studies have characterized the metabolome in the cerebrospinal fluid (CSF) from MS and NMOSD patients, comparative analyses between them and between the ..
- Ząbek A, Paslawski R, Paslawska U, Wojtowicz W, Drozdz K, Polakof S, et al. The influence of different diets on metabolism and atherosclerosis processes-A porcine model: Blood serum, urine and tissues 1H NMR metabolomics targeted analysis. PLoS ONE. 2017;12:e0184798 pubmed publisher..Moreover, we revealed that once initiated, molecular changes did not return to homeostatic equilibrium, at least for the duration of this experiment...