PubMed

Related Articles An integrative omics perspective for the analysis of chemical signals in ecological interactions. Chem Soc Rev. 2017 Nov 08;: Authors: Brunetti AE, Carnevale Neto F, Vera MC, Taboada C, Pavarini DP, Bauermeister A, Lopes NP Abstract All living organisms emit, detect, and respond to chemical stimuli, thus creating an almost limitless number of interactions by means of chemical signals. Technological and intellectual advances in the last two decades have enabled chemical signals analyses at several molecular levels, including gene expression, molecular diversity, and receptor affinity. These advances have also deepened our understanding of nature to encompass interactions at multiple organism levels across different taxa. This tutorial review describes the most recent analytical developments in 'omics' technologies (i.e., genomics, transcriptomics, proteomics, and metabolomics) and provide recent examples of its application in studies of chemical signals. We highlight how studies have integrated an enormous amount of information generated from different omics disciplines into one publicly available platform. In addition, we stress the importance of considering different signal modalities and an evolutionary perspective to establish a comprehensive understanding of chemical communication. PMID: 29114668 [PubMed - as supplied by publisher]

Related Articles Cancer Metabolism and Tumor Heterogeneity: Imaging Perspectives Using MR Imaging and Spectroscopy. Contrast Media Mol Imaging. 2017;2017:6053879 Authors: Lin G, Keshari KR, Park JM Abstract Cancer cells reprogram their metabolism to maintain viability via genetic mutations and epigenetic alterations, expressing overall dynamic heterogeneity. The complex relaxation mechanisms of nuclear spins provide unique and convertible tissue contrasts, making magnetic resonance imaging (MRI) and magnetic resonance spectroscopy (MRS) pertinent imaging tools in both clinics and research. In this review, we summarized MR methods that visualize tumor characteristics and its metabolic phenotypes on an anatomical, microvascular, microstructural, microenvironmental, and metabolomics scale. The review will progress from the utilities of basic spin-relaxation contrasts in cancer imaging to more advanced imaging methods that measure tumor-distinctive parameters such as perfusion, water diffusion, magnetic susceptibility, oxygenation, acidosis, redox state, and cell death. Analytical methods to assess tumor heterogeneity are also reviewed in brief. Although the clinical utility of tumor heterogeneity from imaging is debatable, the quantification of tumor heterogeneity using functional and metabolic MR images with development of robust analytical methods and improved MR methods may offer more critical roles of tumor heterogeneity data in clinics. MRI/MRS can also provide insightful information on pharmacometabolomics, biomarker discovery, disease diagnosis and prognosis, and treatment response. With these future directions in mind, we anticipate the widespread utilization of these MR-based techniques in studying in vivo cancer biology to better address significant clinical needs. PMID: 29114178 [PubMed - in process]

Related Articles Glucose Metabolic Alterations in Hippocampus of Diabetes Mellitus Rats and the Regulation of Aerobic Exercise. Behav Brain Res. 2017 Nov 04;: Authors: Li J, Liu B, Cai M, Lin X, Lou S Abstract Diabetes could negatively affect the structures and functions of the brain, especially could cause the hippocampal dysfunction, however, the potential metabolic mechanism is unclear. The aim of this study was to investigate the changes of glucose metabolism in hippocampus of diabetes mellitus rats and the regulation of aerobic exercise, and to analyze the possible mechanisms. A rat model of type 2 diabetes mellitus was established by high-fat diet feeding in combination with STZ intraperitoneal injection, then 4 weeks of aerobic exercise was conducted. The glucose metabolites and key enzymes involved in glucose metabolism in hippocampus were respectively detected by GC/MS based metabolomics and western blot. Metabolomics results showed that compared with control rats, the level of citric acid was significantly decreased, while the levels of lactic acid, ribose 5-phosphate, xylulose 5-phosphate and glucitol were significantly increased in the diabetic rat. Compared with diabetic rats, the level of citric acid was significantly increased, while the lactic acid, ribose 5-phosphate and xylulose 5-phosphate were significantly decreased in the diabetic exercise rats. Western blot results showed that lower level of citrate synthase and oxoglutarate dehydrogenase, higher level of aldose reductase and glucose 6-phosphatedehydrogenase were found in the diabetic rats when compared to control rats. After 4 weeks of aerobic exercise, citrate synthase was upregulated and glucose 6-phosphatedehydrogenase was downregulated in the diabetic rats. These results suggest that diabetes could cause abnormal glucose metabolism, and aerobic exercise plays an important role in regulating diabetes-induced disorder of glucose metabolism in the hippocampus. PMID: 29113873 [PubMed - as supplied by publisher]

Related Articles Follicular metabolic changes and effects on oocyte quality in polycystic ovary syndrome patients. Oncotarget. 2017 Oct 06;8(46):80472-80480 Authors: Zhang Y, Liu L, Yin TL, Yang J, Xiong CL Abstract Polycystic ovary syndrome (PCOS) is a common complex and heterogeneous disorder, affecting up to 10% women at reproductive age. It causes three fourth of the ovulatory infertility and PCOS patients often give poor IVF quality. Although some metabolic profiles have been investigated in PCOS patient sera and urine, the follicular fluid, providing fruitful biochemical information about oocyte environment during development has been ignored. In this work, based on NMR metabolomics approach, metabolic profile of follicular fluid of PCOS patients has been explored and compared with healthy controls. Significant increases of glycoprotein, acetate, cholesterol, significant decreases of lactic acid, glutamine, pyruvate, and alanine, have been discovered in PCOS follicular fluids. Furthermore, the Pearson correlations analysis indicated significant relationship existed between ART results and NMR detected follicular metabolites. All these results indicated that PCOS may induce dyslipidemia, low-grade inflammation, and disorder of glycolysis, pyruvate and amino acid metabolism in follicular fluids. PMID: 29113318 [PubMed]

Related Articles Metabolic and proteomic analyses of product selectivity and redox regulation in Clostridium pasteurianum grown on glycerol under varied iron availability. Microb Cell Fact. 2017 Apr 19;16(1):64 Authors: Groeger C, Wang W, Sabra W, Utesch T, Zeng AP Abstract BACKGROUND: Clostridium pasteurianum as an emerging new microbial cell factory can produce both n-butanol (BuOH) and 1,3-propanediol (1,3-PDO), and the pattern of product formation changes significantly with the composition of the culture medium. Among others iron content in the medium was shown to strongly affect the products selectivity. However, the mechanism behind this metabolic regulation is still unclear. For a better understanding of such metabolic regulation and for process optimization, we carried out fermentation experiments under either iron excess or iron limitation conditions, and performed metabolic, stoichiometric and proteomic analyses. RESULTS: 1,3-PDO is most effectively produced under iron limited condition (Fe-), whereas 1,3-PDO and BuOH were both produced under iron rich condition (Fe+). With increased iron availability the BuOH/1,3-PDO ratio increased significantly from 0.27 mol/mol (at Fe-) to 1.4 mol/mol (at Fe+). Additionally, hydrogen production was enhanced significantly under Fe+ condition. Proteomic analysis revealed differentiated expression of many proteins including several ones of the central carbon metabolic pathway. Among others, pyruvate: ferredoxin oxidoreductase, hydrogenases, and several electron transfer flavoproteins was found to be strongly up-regulated under Fe+ condition, pointing to their strong involvement in the regeneration of the oxidized form of ferredoxin, and consequently their influences on the product selectivity in C. pasteurianum. Of particular significance is the finding that H2 formation in C. pasteurianum is coupled to the ferredoxin-dependent butyryl-CoA dehydrogenase catalyzed reaction, which significantly affects the redox balance and thus the product selectivity. CONCLUSIONS: The metabolic, stoichiometric and proteomic results clearly show the key roles of hydrogenases and ferredoxins dependent reactions in determining the internal redox balance and hence product selectivity. Not only the NADH pool but also the regulation of the ferredoxin pool could explain such product variation under different iron conditions. PMID: 28424096 [PubMed - indexed for MEDLINE]

Related Articles Metabolic profile provides prognostic value better than galectin-3 in patients with heart failure. J Cardiol. 2017 Jul;70(1):92-98 Authors: Wang CH, Cheng ML, Liu MH, Kuo LT, Shiao MS Abstract BACKGROUND: Metabolic profiles have been shown to provide prognostic information in patients with heart failure (HF). Galectin-3 (Gal-3), indicating cardiac fibrosis, is a documented biomarker of prognosis in HF. It is unknown whether metabolic profiles provide prognostic value better than Gal-3. METHODS AND RESULTS: This study analyzed 212 hospitalized HF patients, measuring metabolic score (composed by butyrylcarnitine, dimethylarginine/arginine ratio, spermidine, and total essential amino acids) and Gal-3. Endpoints were composite events (death/HF-related re-hospitalization). The median of metabolic scores and Gal-3 levels were 3.1 (1.3-5.2) and 17.8ng/mL (4.7-100ng/mL), respectively. Patients with higher metabolic scores had worse functional classes, higher atrial fibrillation incidences, levels of Gal-3 and B-type natriuretic peptide (BNP), but lower albumin levels and glomerular filtration rate. Correlations of metabolic score to Gal-3 and BNP were significant, but weak (r=0.34 and 0.41, respectively, both p<0.001). During a follow-up period of 4.2±1.4 years, there were 91 (42.9%) composite events. In univariate analysis, significant predictors of composite events were age, functional class, atrial fibrillation, levels of hemoglobin, log (Gal-3), log (BNP) and metabolic score. In multivariable analysis, adjusted for above variables, metabolic score remained a strong predictor of combined endpoints (hazard ratio=2.596, 95% confidence interval=1.649-4.087, p<0.001). C-statistics for the prediction of composite events significantly increased when metabolic score was incorporated into the model with established risk factors, BNP and Gal-3 [0.76 (0.70-0.83) vs. 0.66 (0.58-0.74), p=0.032]. CONCLUSIONS: Metabolic profile provides prognostic value for HF patients better than Gal-3. PMID: 28318874 [PubMed - indexed for MEDLINE]

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 2017/11/08PubMed 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.

20 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 2017/11/07PubMed 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.

20 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 2017/11/07PubMed 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.

A Decade of Genetic and Metabolomic Contributions to Type 2 Diabetes Risk Prediction. Curr Diab Rep. 2017 Nov 04;17(12):135 Authors: Merino J, Udler MS, Leong A, Meigs JB Abstract PURPOSE OF REVIEW: The purpose of this review was to summarize and reflect on advances over the past decade in human genetic and metabolomic discovery with particular focus on their contributions to type 2 diabetes (T2D) risk prediction. RECENT FINDINGS: In the past 10 years, a combination of advances in genotyping efficiency, metabolomic profiling, bioinformatics approaches, and international collaboration have moved T2D genetics and metabolomics from a state of frustration to an abundance of new knowledge. Efforts to control and prevent T2D have failed to stop this global epidemic. New approaches are needed, and although neither genetic nor metabolomic profiling yet have a clear clinical role, the rapid pace of accumulating knowledge offers the possibility for "multi-omic" prediction to improve health. PMID: 29103096 [PubMed - in process]

Corrigendum to "Non-invasive metabolomics for improved determination of embryonic sex markers in chemically defined culture medium" [J. Chromatogr. A 1474 (2016) 138-144]. J Chromatogr A. 2017 Oct 25;: Authors: Gómez E, Muñoz M, Simó C, Ibáñez C, Carrocera S, Martín-González D, Cifuentes A PMID: 29102058 [PubMed - as supplied by publisher]

Lipidomics reveals accumulation of the oxidized cholesterol in erythrocytes of heart failure patients. Redox Biol. 2017 Oct 26;14:499-508 Authors: Tang HY, Wang CH, Ho HY, Wu PT, Hung CL, Huang CY, Wu PR, Yeh YH, Cheng ML Abstract Lipids play an important role in the pathogenesis of cardiovascular disease. Changes in lipids of erythrocytes are indicative of the outcome of pathophysiological processes. In the present study, we assessed whether the lipid profiles of erythrocytes from heart failure (HF) patients are informative of their disease risk. The lipidomes of erythrocytes from 10 control subjects and 29 patients at different HF stages were analyzed using liquid chromatography time-of-flight mass spectrometry. The lipid composition of erythrocytes obtained from HF patients was significantly different from that of normal controls. The levels of phosphatidylcholines (PCs), phosphatidylethanolamines (PEs), and sphingomyelins decreased in HF erythrocytes as compared with those of control subjects; however, the levels of lysoPCs, lysoPEs, and ceramides increased in HF erythrocytes. Notably, the oxidized cholesterol 7-ketocholesterol (7KCh) accumulated to higher level in HF erythrocytes than in plasma from the same patients. We further validated our findings with a cohort of 115 subjects of control subjects (n=28) and patients (n=87). Mechanistically, 7KCh promoted reactive oxygen species (ROS) formation in cardiomyocytes; and induced their death, probably through an ATF4-dependent pathway. Our findings suggest that erythrocytic 7KCh can be a risk factor for HF, and is probably implicated in its pathophysiology. PMID: 29101899 [PubMed - as supplied by publisher]

Related Articles Tracking maize pollen development by the Leaf Collar Method. Plant Reprod. 2017 Nov 04;: Authors: Begcy K, Dresselhaus T Abstract KEY MESSAGE: An easy and highly reproducible nondestructive method named the Leaf Collar Method is described to identify and characterize the different stages of pollen development in maize. In plants, many cellular events such as meiosis, asymmetric cell division, cell cycle regulation, cell fate determination, nucleus movement, vacuole formation, chromatin condensation and epigenetic modifications take place during pollen development. In maize, pollen development occurs in tassels that are confined within the internal stalk of the plant. Hence, identification of the different pollen developmental stages as a tool to investigate above biological processes is impossible without dissecting the entire plant. Therefore, an efficient and reproducible method is necessary to isolate homogeneous cell populations at individual stages throughout pollen development without destroying the plant. Here, we describe a method to identify the various stages of pollen development in maize. Using the Leaf Collar Method in the maize inbreed line B73, we have determined the duration of each stage from pollen mother cells before meiosis to mature tricellular pollen. Anther and tassel size as well as percentage of pollen stages were correlated with vegetative stages, which are easily recognized. The identification of stage-specific genes indicates the reproducibility of the method. In summary, we present an easy and highly reproducible nondestructive method to identify and characterize the different stages of pollen development in maize. This method now opens the way for many subsequent physiological, morphological and molecular analyses to study, for instance, transcriptomics, metabolomics, DNA methylation and chromatin patterns during normal and stressful conditions throughout pollen development in one of the economically most important grass species. PMID: 29101473 [PubMed - as supplied by publisher]

Related Articles Shifts in microbial communities in soil, rhizosphere and roots of two major crop systems under elevated CO2 and O3. Sci Rep. 2017 Nov 03;7(1):15019 Authors: Wang P, Marsh EL, Ainsworth EA, Leakey ADB, Sheflin AM, Schachtman DP Abstract Rising atmospheric concentrations of CO2 and O3 are key features of global environmental change. To investigate changes in the belowground bacterial community composition in response to elevated CO2 and O3 (eCO2 and eO3) the endosphere, rhizosphere and soil were sampled from soybeans under eCO2 and maize under eO3. The maize rhizosphere and endosphere α-diversity was higher than soybean, which may be due to a high relative abundance of Rhizobiales. Only the rhizosphere microbiome composition of the soybeans changed in response to eCO2, associated with an increased abundance of nitrogen fixing microbes. In maize, the microbiome composition was altered by the genotype and linked to differences in root exudate profiles. The eO3 treatment did not change the microbial communities in the rhizosphere, but altered the soil communities where hybrid maize was grown. In contrast to previous studies that focused exclusively on the soil, this study provides new insights into the effects of plant root exudates on the composition of the belowground microbiome in response to changing atmospheric conditions. Our results demonstrate that plant species and plant genotype were key factors driving the changes in the belowground bacterial community composition in agroecosystems that experience rising levels of atmospheric CO2 and O3. PMID: 29101364 [PubMed - in process]

Related Articles Butyrate reduces appetite and activates brown adipose tissue via the gut-brain neural circuit. Gut. 2017 Nov 03;: Authors: Li Z, Yi CX, Katiraei S, Kooijman S, Zhou E, Chung CK, Gao Y, van den Heuvel JK, Meijer OC, Berbée JFP, Heijink M, Giera M, Willems van Dijk K, Groen AK, Rensen PCN, Wang Y Abstract OBJECTIVE: Butyrate exerts metabolic benefits in mice and humans, the underlying mechanisms being still unclear. We aimed to investigate the effect of butyrate on appetite and energy expenditure, and to what extent these two components contribute to the beneficial metabolic effects of butyrate. DESIGN: Acute effects of butyrate on appetite and its method of action were investigated in mice following an intragastric gavage or intravenous injection of butyrate. To study the contribution of satiety to the metabolic benefits of butyrate, mice were fed a high-fat diet with butyrate, and an additional pair-fed group was included. Mechanistic involvement of the gut-brain neural circuit was investigated in vagotomised mice. RESULTS: Acute oral, but not intravenous, butyrate administration decreased food intake, suppressed the activity of orexigenic neurons that express neuropeptide Y in the hypothalamus, and decreased neuronal activity within the nucleus tractus solitarius and dorsal vagal complex in the brainstem. Chronic butyrate supplementation prevented diet-induced obesity, hyperinsulinaemia, hypertriglyceridaemia and hepatic steatosis, largely attributed to a reduction in food intake. Butyrate also modestly promoted fat oxidation and activated brown adipose tissue (BAT), evident from increased utilisation of plasma triglyceride-derived fatty acids. This effect was not due to the reduced food intake, but explained by an increased sympathetic outflow to BAT. Subdiaphragmatic vagotomy abolished the effects of butyrate on food intake as well as the stimulation of metabolic activity in BAT. CONCLUSION: Butyrate acts on the gut-brain neural circuit to improve energy metabolism via reducing energy intake and enhancing fat oxidation by activating BAT. PMID: 29101261 [PubMed - as supplied by publisher]

Related Articles Protein-bound uremic toxins impaired mitochondrial dynamics and functions. Oncotarget. 2017 Sep 29;8(44):77722-77733 Authors: Sun CY, Cheng ML, Pan HC, Lee JH, Lee CC Abstract Protein-bound uremic toxins, indoxyl sulfate and p-cresol sulfate, increase oxidative stress and adversely affect chronic kidney disease progression and cardiovascular complications. In this study, we examined whether mitochondria are the target of indoxyl sulfate and p-cresol sulfate intoxication in vivo and in vitro. The kidneys of 10-week-old male B-6 mice with ½-nephrectomy treated with indoxyl sulfate and p-cresol sulfate were used for the animal study. Cultured human renal tubular cells were used for the in vitro study. Our results indicated that indoxyl sulfate and p-cresol sulfate impaired aerobic and anaerobic metabolism in vivo and in vitro. Indoxyl sulfate and p-cresol sulfate caused mitochondrial fission by modulating the expression of mitochondrial fission-fusion proteins. Mitochondrial dysfunction and impaired biogenesis could be protected by treatment with antioxidants. The in vitro study also demonstrated that indoxyl sulfate and p-cresol sulfate reduced mitochondrial mass by activating autophagic machinery. In summary, our study suggests that mitochondrial injury is one of the major pathological mechanisms for uremic intoxication, which is related to chronic kidney disease and its complications. PMID: 29100420 [PubMed]

24 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 2017/11/04PubMed 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.

24 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 2017/11/04PubMed 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 based predictive biomarker model of ARDS: A systemic measure of clinical hypoxemia. PLoS One. 2017;12(11):e0187545 Authors: Sinha N, Viswan A, Singh C, Rai RK, Azim A, Baronia AK Abstract Despite advancements in ventilator technologies, lung supportive and rescue therapies, the outcome and prognostication in acute respiratory distress syndrome (ARDS) remains incremental and ambiguous. Metabolomics is a potential insightful measure to the diagnostic approaches practiced in critical disease settings. In our study patients diagnosed with mild and moderate/severe ARDS clinically governed by hypoxemic P/F ratio between 100-300 but with indistinct molecular phenotype were discriminated employing nuclear magnetic resonance (NMR) based metabolomics of mini bronchoalveolar lavage fluid (mBALF). Resulting biomarker prototype comprising six metabolites was substantiated highlighting ARDS susceptibility/recovery. Both the groups (mild and moderate/severe ARDS) showed distinct biochemical profile based on 83.3% classification by discriminant function analysis and cross validated accuracy of 91% using partial least squares discriminant analysis as major classifier. The predictive performance of narrowed down six metabolites were found analogous with chemometrics. The proposed biomarker model consisting of six metabolites proline, lysine/arginine, taurine, threonine and glutamate were found characteristic of ARDS sub-stages with aberrant metabolism observed mainly in arginine, proline metabolism, lysine synthesis and so forth correlating to diseased metabotype. Thus NMR based metabolomics has provided new insight into ARDS sub-stages and conclusively a precise biomarker model proposed, reflecting underlying metabolic dysfunction aiding prior clinical decision making. PMID: 29095932 [PubMed - in process]

"Omic" investigations of protozoa and worms for a deeper understanding of the human gut "parasitome". PLoS Negl Trop Dis. 2017 Nov;11(11):e0005916 Authors: Marzano V, Mancinelli L, Bracaglia G, Del Chierico F, Vernocchi P, Di Girolamo F, Garrone S, Tchidjou Kuekou H, D'Argenio P, Dallapiccola B, Urbani A, Putignani L Abstract The human gut has been continuously exposed to a broad spectrum of intestinal organisms, including viruses, bacteria, fungi, and parasites (protozoa and worms), over millions of years of coevolution, and plays a central role in human health. The modern lifestyles of Western countries, such as the adoption of highly hygienic habits, the extensive use of antimicrobial drugs, and increasing globalisation, have dramatically altered the composition of the gut milieu, especially in terms of its eukaryotic "citizens." In the past few decades, numerous studies have highlighted the composition and role of human intestinal bacteria in physiological and pathological conditions, while few investigations exist on gut parasites and particularly on their coexistence and interaction with the intestinal microbiota. Studies of the gut "parasitome" through "omic" technologies, such as (meta)genomics, transcriptomics, proteomics, and metabolomics, are herein reviewed to better understand their role in the relationships between intestinal parasites, host, and resident prokaryotes, whether pathogens or commensals. Systems biology-based profiles of the gut "parasitome" under physiological and severe disease conditions can indeed contribute to the control of infectious diseases and offer a new perspective of omics-assisted tropical medicine. PMID: 29095820 [PubMed - in process]