Genomes and Genes
Summary: The systematic identification and quantitation of all the metabolic products of a cell, tissue, organ, or organism under varying conditions. The METABOLOME of a cell or organism is a dynamic collection of metabolites which represent its net response to current conditions.
- Li S, Sullivan N, Rouphael N, Yu T, Banton S, Maddur M, et al. Metabolic Phenotypes of Response to Vaccination in Humans. Cell. 2017;169:862-877.e17 pubmed publisher..The MMRN reveals striking associations between orthogonal datasets, such as transcriptomic and metabolomics signatures, cell populations, and cytokine levels, and identifies immune and metabolic correlates of vaccine ..
- Li S, Huang X, Wu S, Ma Y, Shi C, Xiao X, et al. [Gas chromatography-mass spectrometry based urinary metabolomics in very low birth weight premature infants]. Zhonghua Er Ke Za Zhi. 2017;55:434-438 pubmed publisher..022?0.022?0.031?0.046)???????????12???????????????????????????????????????-?????????????????????????????????????1????2?????n-?????7????????? ??? ???????????????????????????????????-????????????????????????????????????????????????. ..
- WARREN J, Oka S, Zablocki D, Sadoshima J. Metabolic reprogramming via PPAR? signaling in cardiac hypertrophy and failure: From metabolomics to epigenetics. Am J Physiol Heart Circ Physiol. 2017;313:H584-H596 pubmed publisher..In addition, we discuss how metabolomics can contribute to a better understanding of the role of PPAR? in the progression of cardiac hypertrophy and ..
- 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..Multiple targeted and untargeted metabolomics approaches (NMR, LC-MS, HPLC-DAD, HPLC-UV) as well as artificial simplified phytocomplexes representing the ..
- Feng X, Yang Z, Chu Y, Du B, Su M, Li Y, et al. 1H nuclear magnetic resonance-based metabolomic study on efficacy of Qingrehuatan decoction against abundant phlegm-heat syndrome in young adults with essential hypertension. J Tradit Chin Med. 2015;35:28-35 pubmed..1H NMR-based metabolomic technology can provide an objective basis for the treatment of YEH patients with abundant phlegm-heat syndrome using QRHT. ..
- Steele H, Horvath R, Lyon J, Chinnery P. Monitoring clinical progression with mitochondrial disease biomarkers. Brain. 2017;140:2530-2540 pubmed publisher..This update discusses current biomarkers of mitochondrial disease progression including metabolomics, circulating serum markers, exercise physiology, and both structural and functional imaging...
- Zhang Y, Cheng Y, Liu Z, Ding L, Qiu T, Chai L, et al. Systematic screening and characterization of multiple constituents in Guizhi Fuling capsule and metabolic profiling of bioactive components in rats using ultra-high-performance liquid chromatography/quadrupole-time-of-flight mass spectrometry. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1061-1062:474-486 pubmed publisher..The chemical and metabolic profiling of GFC provided an abundant substance foundation for the extensive GFC research, especially for the pharmacodynamic mechanisms research. ..
- Breier M, Wahl S, Prehn C, Ferrari U, Sacco V, Weise M, et al. Immediate reduction of serum citrulline but no change of steroid profile after initiation of metformin in individuals with type 2 diabetes. J Steroid Biochem Mol Biol. 2017;174:114-119 pubmed publisher..In this study, we used targeted metabolomics to gain new insights into the metabolic effects of metformin in humans with T2DM...
- Spinler J, Auchtung J, Brown A, Boonma P, Oezguen N, Ross C, et al. Next-Generation Probiotics Targeting Clostridium difficile through Precursor-Directed Antimicrobial Biosynthesis. Infect Immun. 2017;85: pubmed publisher..reuteri alone was ineffective. A global unbiased microbiome and metabolomics analysis independently confirmed that glycerol precursor delivery with L...
- Guo F, Zi T, Liu L, Feng R, Sun C. A 1H-NMR based metabolomics study of the intervention effect of mangiferin on hyperlipidemia hamsters induced by a high-fat diet. Food Funct. 2017;8:2455-2464 pubmed publisher..Thus, a NMR-based metabolomics approach was conducted to explore the effects of mangiferin on hyperlipidemia hamsters and to gain a better ..
- Zheng L, Zhao X, Zhu S, Tao Y, Ji W, Geng Y, et al. A new combined method of stable isotope-labeling derivatization-ultrasound-assisted dispersive liquid-liquid microextraction for the determination of neurotransmitters in rat brain microdialysates by ultra high performance liquid chromatography tande. J Chromatogr B Analyt Technol Biomed Life Sci. 2017;1054:64-72 pubmed publisher..This provided a new method for the neurotransmitters related studies in the future. ..
- Rashid R, Cazenave Gassiot A, Gao I, Nair Z, Kumar J, Gao L, et al. Comprehensive analysis of phospholipids and glycolipids in the opportunistic pathogen Enterococcus faecalis. PLoS ONE. 2017;12:e0175886 pubmed publisher..This lipidome map is the first comprehensive analysis of membrane phospholipids and glycolipids in the important human pathogen E. faecalis, for which antimicrobial resistance and altered lipid homeostasis have been intimately linked. ..
- Cui L, Hou J, Fang J, Lee Y, Costa V, Wong L, et al. Serum Metabolomics Investigation of Humanized Mouse Model of Dengue Virus Infection. J Virol. 2017;91: pubmed publisher..Most of these disturbed pathways are similar to our previous metabolomics findings in a longitudinal cohort of adult human dengue patients across different infection stages...
- Li L, Hur M, Lee J, Zhou W, Song Z, Ransom N, et al. A systems biology approach toward understanding seed composition in soybean. BMC Genomics. 2015;16 Suppl 3:S9 pubmed publisher..With the future goal of predictive biology in mind, we have combined metabolomics, transcriptomics, and metabolic flux technologies to reveal the global developmental and metabolic networks ..
- Brandl K, Schnabl B. Intestinal microbiota and nonalcoholic steatohepatitis. Curr Opin Gastroenterol. 2017;33:128-133 pubmed publisher..NASH pathogenesis is multifactorial including genetic and environmental factors. The gut microbiota is involved in disease progression and its role is complex...
- Smith R, Mathis A, Ventura D, Prince J. Proteomics, lipidomics, metabolomics: a mass spectrometry tutorial from a computer scientist's point of view. BMC Bioinformatics. 2014;15 Suppl 7:S9 pubmed publisher..This paper will facilitate contributions from mathematicians, computer scientists, and statisticians to MS-omics that will fundamentally improve results over existing approaches and inform novel algorithmic solutions to open problems. ..
- 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. ..
- Lin Z, Zhang X, Wang Z, Jiang Y, Liu Z, Alexander D, et al. Metabolomic analysis of pathways related to rice grain chalkiness by a notched-belly mutant with high occurrence of white-belly grains. BMC Plant Biol. 2017;17:39 pubmed publisher..Based on these results, metabolic mechanism of chalkiness formation is discussed, with the role of embryo highlighted. ..
- Latorre Pellicer A, Moreno Loshuertos R, Lechuga Vieco A, Sanchez Cabo F, Torroja C, Acin Perez R, et al. Mitochondrial and nuclear DNA matching shapes metabolism and healthy ageing. Nature. 2016;535:561-5 pubmed
- Shen G, Zhou L, Liu W, Cui Y, Xie W, Chen H, et al. Di(2-ethylhexyl)phthalate Alters the Synthesis and ?-Oxidation of Fatty Acids and Hinders ATP Supply in Mouse Testes via UPLC-Q-Exactive Orbitrap MS-Based Metabonomics Study. J Agric Food Chem. 2017;65:5056-5063 pubmed publisher..These findings provided new insights to better understand the mechanisms of testicular toxicity induced by DEHP exposure. ..
- Bornstein S, Moschetta M, Kawano Y, Sacco A, Huynh D, Brooks D, et al. Metformin Affects Cortical Bone Mass and Marrow Adiposity in Diet-Induced Obesity in Male Mice. Endocrinology. 2017;158:3369-3385 pubmed publisher..Obesity was not detrimental to trabecular bone in growing mice, but bone marrow medullary expansion was observed, likely resulting from inhibition of osteoblastogenesis, and this was partially reversed by metformin treatment. ..
- Mahidhara G, Ch S, Ch V. Comparative metabolomic studies of Alkanivorax xenomutans showing differential power output in a three chambered microbial fuel cell. World J Microbiol Biotechnol. 2017;33:102 pubmed publisher..Hence, the presence of anoxic conditions governed the electrogenic bacteria to produce enhanced power output by modulating differential metabolomic profiling, compared to the culture grown in oxic conditions. ..
- Law K, Han T, Mao X, Zhang H. Tryptophan and purine metabolites are consistently upregulated in the urinary metabolome of patients diagnosed with gestational diabetes mellitus throughout pregnancy: A longitudinal metabolomics study of Chinese pregnant women part 2. Clin Chim Acta. 2017;468:126-139 pubmed publisher..on ultra-performance liquid chromatography/hybrid quadrupole time-of-flight mass spectrometry, an untargeted metabolomics study was performed to explore the differences in the urinary metabolome of GDM cases and healthy controls over ..
- 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..These findings suggest the usefulness of metabolites as salivary biomarkers for Japanese patients with OSCC. Further studies using larger patient cohorts should be conducted to validate these results. ..
- 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. ..
- Pražienková V, Holubová M, Pelantová H, Bugáňová M, Pirnik Z, Mikulášková B, et al. Impact of novel palmitoylated prolactin-releasing peptide analogs on metabolic changes in mice with diet-induced obesity. PLoS ONE. 2017;12:e0183449 pubmed publisher..products N-methyl-2-pyridone-5-carboxamide and N-methyl-4-pyridone-3-carboxamide, as shown by NMR-based metabolomics. This observation confirmed the previously reported increase in nicotinamide derivatives in obesity and type 2 ..
- Cambiaghi A, Ferrario M, Masseroli M. Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration. Brief Bioinform. 2017;18:498-510 pubmed publisherb>Metabolomics is a rapidly growing field consisting of the analysis of a large number of metabolites at a system scale...
- Potter G, Cade J, Hardie L. Longer sleep is associated with lower BMI and favorable metabolic profiles in UK adults: Findings from the National Diet and Nutrition Survey. PLoS ONE. 2017;12:e0182195 pubmed publisher..10). Contrary to our hypothesis, sleep duration was not associated with any dietary measures (p ? 0.14). Together, our findings show that short-sleeping UK adults are more likely to have obesity, a disease with many comorbidities. ..
- Rosenbaum J, Weisman P. The Evolving Role of Companion Diagnostics for Breast Cancer in an Era of Next-Generation Omics. Am J Pathol. 2017;187:2185-2198 pubmed publisher..To accommodate future needs of breast cancer patients, the companion diagnostic model will continue to adapt and evolve. ..
- Qi W, Keenan H, Li Q, Ishikado A, Kannt A, Sadowski T, et al. Pyruvate kinase M2 activation may protect against the progression of diabetic glomerular pathology and mitochondrial dysfunction. Nat Med. 2017;23:753-762 pubmed publisher..Thus, PKM2 activation may protect against DN by increasing glucose metabolic flux, inhibiting the production of toxic glucose metabolites and inducing mitochondrial biogenesis to restore mitochondrial function. ..
- 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. ..
- Kumari A, Ray K, Sadhna S, Pandey A, Sreelakshmi Y, Sharma R. Metabolomic homeostasis shifts after callus formation and shoot regeneration in tomato. PLoS ONE. 2017;12:e0176978 pubmed publisher..The network analysis indicates that shift in metabolite profiles during callus formation and shoot regeneration is governed by a complex interaction between metabolites and endogenous hormones. ..
- Wang X, Wang D, Wu J, Yu X, Lv J, Kong J, et al. Metabolic Characterization of Myocardial Infarction Using GC-MS-Based Tissue Metabolomics. Int Heart J. 2017;58:441-446 pubmed publisher..Here, we aimed to characterize the metabolic features of early MI using a tissue metabolomics method based on gas chromatography-mass spectrometry (GC-MS)...
- Hu X, Thakur K, Chen G, Hu F, Zhang J, Zhang H, et al. Metabolic Effect of 1-Deoxynojirimycin from Mulberry Leaves on db/db Diabetic Mice Using Liquid Chromatography-Mass Spectrometry Based Metabolomics. J Agric Food Chem. 2017;65:4658-4667 pubmed publisherb>Metabolomics was applied to the liquid chromatography-mass spectrometry urinary metabolic profile of type 2 diabetes (T2DM) mice treated with mulberry 1-deoxynojirimycin (DNJ)...
- Matrka M, Watanabe M, Muraleedharan R, Lambert P, Lane A, Romick Rosendale L, et al. Overexpression of the human DEK oncogene reprograms cellular metabolism and promotes glycolysis. PLoS ONE. 2017;12:e0177952 pubmed publisher..glycolysis and the tricarboxylic acid cycle (TCA) that supplies substrate for OxPhos, we carried out NMR-based metabolomics studies...
- Schoeman J, Moutloatse G, Harms A, Vreeken R, Scherpbier H, van Leeuwen L, et al. Fetal Metabolic Stress Disrupts Immune Homeostasis and Induces Proinflammatory Responses in Human Immunodeficiency Virus Type 1- and Combination Antiretroviral Therapy-Exposed Infants. J Infect Dis. 2017;216:436-446 pubmed publisher..Taken together, these data demonstrate that the fetal metabolism is impacted by maternal factors (cART and HIV-1) and skews physiological immune responses toward inflammation in the newborn infant. ..
- Geng H, Liu H, Liu J, Wang C, Wen J. Insights into the metabolic mechanism of rapamycin overproduction in the shikimate-resistant Streptomyces hygroscopicus strain UV-II using comparative metabolomics. World J Microbiol Biotechnol. 2017;33:101 pubmed publisher..3 mg/L. These findings thus provide a theoretical basis for further improvements in the production of not only rapamycin, but also of other, analogous macrolide compounds. ..
- 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..These findings would be helpful in understanding the biological background of these diseases, and distinguishing between MS and NMOSD, as well as determining the disease activity. ..
- Wahl S, Vogt S, Stückler F, Krumsiek J, Bartel J, Kacprowski T, et al. Multi-omic signature of body weight change: results from a population-based cohort study. BMC Med. 2015;13:48 pubmed publisher..At follow-up (F4), two-platform serum metabolomics and whole blood gene expression measurements were obtained for 1,631 and 689 participants, respectively...
- 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 publisherThe aim was to determine if metabolomics could be used to build a predictive model for type 2 diabetes (T2D) risk that would improve prediction of T2D over current risk markers...
- 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..animals were sacrificed and the blood serum, urine and skeletal muscle tissue were collected and 1H NMR based metabolomics studies with the application of fingerprinting PLS-DA and univariate analysis were done...
- Nitzsche R, Günay Esiyok Ö, Tischer M, Zagoriy V, Gupta N. A plant/fungal-type phosphoenolpyruvate carboxykinase located in the parasite mitochondrion ensures glucose-independent survival of Toxoplasma gondii. J Biol Chem. 2017;292:15225-15239 pubmed publisher..Isotope-resolved metabolomics of the conditional mutant revealed defective flux of glutamine-derived carbon into RNA-bound ribose sugar as ..