Read by QxMD icon Read

Metabolomic analysis

Xin Hu, Joshua D Chandler, Jolyn Fernandes, Michael L Orr, Li Hao, Karan Uppal, David C Neujahr, Dean P Jones, Young-Mi Go
BACKGROUND: The protective effect of selenium (Se) on cadmium (Cd) toxicity is well documented, but underlying mechanisms are unclear. METHODS: Male mice fed standard diet were given Cd (CdCl2 , 18 μmol/L) in drinking water with or without Se (Na2 SeO4, 20 μmol/L) for 16 weeks. Lungs were analyzed for Cd concentration, transcriptomics and metabolomics. Data were analyzed with biostatistics, bioinformatics, pathway enrichment analysis, and combined transcriptome-metabolome-wide association study...
April 12, 2018: Biochimica et Biophysica Acta
Satoru Tomita, Toshihide Nakamura, Sanae Okada
This study revealed the compositional characteristics of sunki, a traditional, unsalted, lactic acid-fermented pickle produced using turnip leaf in Kiso district, Japan. Comprehensive compositional analysis by two metabolomic approaches based on NMR and solid-phase microextraction-GC/MS methods was used to determine its chemical composition by annotating 54 water-soluble and 62 volatile compounds. Principal component analysis showed that samples had different compositions, depending on the agricultural processing factory and production year...
August 30, 2018: Food Chemistry
Anne-Charlotte Dubbelman, Filip Cuyckens, Lieve Dillen, Gerhard Gross, Rob J Vreeken, Thomas Hankemeier
BACKGROUND: High-throughput simultaneous quantitative and qualitative (Quan/Qual) analysis is attractive to combine targeted with non-targeted analysis, e.g. in pharmacometabolomics and drug metabolism studies. This study aimed to investigate the possibilities and limitations of high-throughput Quan/Qual analysis by ultra-high performance liquid chromatography (UHPLC) coupled with high-resolution mass spectrometry (HRMS), to develop a widely applicable Quan/Qual UHPLC-HRMS method and to provide recommendations for Quan/Qual method development...
August 22, 2018: Analytica Chimica Acta
Yue Liu, Shan Lu, Liang Zhao, Xin Dong, Zhenyu Zhu, Yongsheng Jin, Haisheng Chen, Feng Lu, Zhanying Hong, Yifeng Chai
Studies have documented the potential antitumor activities of glaucocalyxin A (GLA), an ent-kaurene diterpenoid isolated from Rabdosia japonica. However, the metabolic mechanism underlying the antitumor activity of GLA remains largely unknown. The effects of GLA on the metabolome of human liver cancer cells using GC/MS- and LC/MS-based metabolic profiling have been investigated. An untargeted metabolomics approach in conjunction with orthogonal projection to latent structures-discriminant analysis (OPLS-DA) has been developed to characterize the metabolic modifications induced by GLA treatment in human hepatoma cell line SMMC7721...
April 13, 2018: Analytical and Bioanalytical Chemistry
Lihua Zuo, Lin Zhou, Tanye Xu, Zhuolun Li, Liwei Liu, Yingying Shi, Jian Kang, Guanmin Gao, Shuzhang Du, Zhi Sun, Xiaojian Zhang
Xuebijing (XBJ) injection is an ethnomedicinal formula that has been widely used in the therapy of sepsis in China. However, the underlying theraputic mechanisms remain uninvestigated. In this research, a metabolomic method based on UHPLC-Q-Orbitrap HRMS was applied to make a holistic evaluation of XBJ on septic rats which were induced by the classical cecal ligation and puncture (CLP) operation. The plasma metabolic changes were profiled and evaluated by multivariate analytical (MVA) methods. In the results, a total of 41 differential metabolites were identified between CLP-operated group and sham-operated group, which were mainly involved in amino acid metabolism and lipid metabolism...
2018: Frontiers in Pharmacology
G Yücel, M Behnes, C Barth, A Wenke, B Sartorius, K Mashayekhi, B Yazdani, T Bertsch, J Rusnak, A Saleh, U Hoffmann, C Fastner, S Lang, X Zhou, K Sattler, M Borggrefe, I Akin
Patients with non-valvular atrial fibrillation (AF) and a high risk for oral anticoagulation can be treated by percutaneous implantation of left atrial appendage occlusion devices (LAAC) to reduce the risk of cardio-embolic stroke. This study evaluates whether LAAC may influence lipid metabolism, which has never been investigated before. Patients with successful LAAC were included consecutively. Venous peripheral blood samples of patients were collected immediately before (T0, baseline) and 6 months after (T1, mid-term) LAAC...
April 12, 2018: Scientific Reports
Reika Kawabata-Iwakawa, Masahiko Nishiyama
Comprehensive genomic and transcriptome analyses using next-generation sequencing(NGS)analysis has lead a discovery of a variety of novel driver gene mutations and new therapeutic targets for cancer patients, and has remarkably improved outcome of the patients through the development novel molecular targeting drugs. Even so, in so-called intractable or refractory cancers, those "druggable"alterations common to the diseases are rarely found due to the high diversity of the tumor. Furthermore, most of molecular target therapy is known to acquire the resistance to the drug by means of multiple factors such as up-regulation of the partially inhibited pathway, mutation of the target, activation of alternative pathways, histological translocation, and oncogene de-addiction...
March 2018: Gan to Kagaku Ryoho. Cancer & Chemotherapy
S P Mudau, P A Steenkamp, L A Piater, M De Palma, M Tucci, N E Madala, I A Dubery
Chlorogenic acids (CGAs) are phenolic compounds biosynthesized in the phenylpropanoid pathway, with hydroxycinnamoyl quinate hydroxycinnamoyltransferase (HQT) as the key enzyme. Variation of CGAs has been noted in different plants, with globe artichoke (Cynara cardunculus var. scolymus L.) producing high amounts and a diverse spectrum of CGAs in its leaves. In the current study, the effect of overexpression of the hqt1 transgene from globe artichoke in tobacco was evaluated at the metabolome level. Here, metabolomic approaches based on ultra-high performance liquid chromatography coupled to mass spectrometry, together with chemometric models such as principal component analysis and orthogonal partial least square discriminant analysis, were employed to evaluate altered metabolic changes due to hqt1 overexpression...
April 5, 2018: Plant Physiology and Biochemistry: PPB
Nikolaos Evangelatos, Kapaettu Satyamoorthy, Georgia Levidou, Pia Bauer, Helmut Brand, Christina Kouskouti, Hans Lehrach, Angela Brand
"-Omics" research is in transition with the recent rise of multi-omics technology platforms. Integration of "-omics" and multi-omics research is of high priority in sepsis, a heterogeneous syndrome that is widely recognized as a global health burden and a priority biomedical funding field. We report here an original study on bibliometric trends in the use of "-omics" technologies, and multi-omics approaches in particular, in sepsis research in three (supra)national settings, the United States, the European Union 28 Member States (EU-28), and China...
March 2018: Omics: a Journal of Integrative Biology
Lieven Van Meulebroek, Jella Wauters, Beata Pomian, Julie Vanden Bussche, Philippe Delahaut, Eric Fichant, Lynn Vanhaecke
In the European Union, the use of thyreostats for animal fattening purposes has been banned and monitoring plans have been established to detect potential abuse. However, this is not always straightforward as thyreostats such as thiouracil may also have a semi-endogenous origin. Therefore, this study aimed at defining urinary metabolites, which may aid in defining the origin of detected thiouracil. Hereto, a parallel-like randomized in vivo study was conducted in which calves (n = 8) and cows (n = 8) were subjected to either a control treatment, rapeseed-enriched diet to induce semi-endogenous formation, or thiouracil treatment...
2018: PloS One
Shinji Ishikawa, Yuki Ono, Norikuni Ohtake, Kuni Sueyoshi, Sayuri Tanabata, Takuji Ohyama
Leguminous plants form root nodules with rhizobia that fix atmospheric dinitrogen (N₂) for the nitrogen (N) nutrient. Combined nitrogen sources, particular nitrate, severely repress nodule growth and nitrogen fixation activity in soybeans ( Glycine max [L.] Merr.). A microarray-based transcriptome analysis and the metabolome analysis were carried out for the roots and nodules of hydroponically grown soybean plants treated with 5 mM of nitrate for 24 h and compared with control without nitrate. Gene expression ratios of nitrate vs...
April 12, 2018: Plants (Basel, Switzerland)
Nishith Kumar, Md Aminul Hoque, Masahiro Sugimoto
BACKGROUND: The identification of differential metabolites in metabolomics is still a big challenge and plays a prominent role in metabolomics data analyses. Metabolomics datasets often contain outliers because of analytical, experimental, and biological ambiguity, but the currently available differential metabolite identification techniques are sensitive to outliers. RESULTS: We propose a kernel weight based outlier-robust volcano plot for identifying differential metabolites from noisy metabolomics datasets...
April 11, 2018: BMC Bioinformatics
Tom F O'Callaghan, Rosa Vázquez-Fresno, Arnau Serra-Cayuela, Edison Dong, Rupasri Mandal, Deirdre Hennessy, Stephen McAuliffe, Pat Dillon, David S Wishart, Catherine Stanton, R Paul Ross
The purpose of this study was to examine the effects of two pasture feeding systems-perennial ryegrass (GRS) and perennial ryegrass and white clover (CLV)-and an indoor total mixed ration (TMR) system on the (a) rumen microbiome; (b) rumen fluid and milk metabolome; and (c) to assess the potential to distinguish milk from different feeding systems by their respective metabolomes. Rumen fluid was collected from nine rumen cannulated cows under the different feeding systems in early, mid and late lactation, and raw milk samples were collected from ten non-cannulated cows in mid-lactation from each of the feeding systems...
April 6, 2018: Metabolites
Daqiang Pan, Caroline Lindau, Simon Lagies, Nils Wiedemann, Bernd Kammerer
Introduction: Subcellular compartmentalization enables eukaryotic cells to carry out different reactions at the same time, resulting in different metabolite pools in the subcellular compartments. Thus, mutations affecting the mitochondrial energy metabolism could cause different metabolic alterations in mitochondria compared to the cytoplasm. Given that the metabolite pool in the cytosol is larger than that of other subcellular compartments, metabolic profiling of total cells could miss these compartment-specific metabolic alterations...
2018: Metabolomics: Official Journal of the Metabolomic Society
Kenshi Watanabe, Kim Hazel V Arafiles, Risa Higashi, Yoshiko Okamura, Takahisa Tajima, Yukihiko Matsumura, Yutaka Nakashimada, Keisuke Matsuyama, Tsunehiro Aki
The marine eukaryotic microheterotroph thraustochytrid genus Aurantiochytrium is a known producer of polyunsaturated fatty acids, carotenoids, and squalene. We previously constructed a lipid fermentation system for Aurantiochytrium sp. strains using underutilized biomass, such as canned syrup and brown macroalgae. To improve the productivity, in this study, Aurantiochytrium sp. RH-7A and RH-7A-7 that produced high levels of carotenoids, such as astaxanthin and canthaxanthin, were isolated through chemical mutagenesis...
April 9, 2018: Journal of Oleo Science
Elizabeth M Llufrio, Lingjue Wang, Fuad J Naser, Gary J Patti
A growing appreciation of the metabolic artifacts of cell culture has generated heightened enthusiasm for performing metabolomics on populations of cells purified from tissues and biofluids. Fluorescence activated cell sorting, or FACS, is a widely used experimental approach to purify specific cell types from complex heterogeneous samples. Here we show that FACS introduces oxidative stress and alters the metabolic state of cells. Compared to unsorted controls, astrocytes subjected to FACS prior to metabolomic analysis showed altered ratios of GSSG to GSH, NADPH to NADP+ , and NAD+ to NADH...
March 9, 2018: Redox Biology
T R Sutton, M Minnion, F Barbarino, G Koster, B O Fernandez, A F Cumpstey, P Wischmann, M Madhani, M P Frenneaux, A D Postle, M M Cortese-Krott, M Feelisch
Several diseases are associated with perturbations in redox signaling and aberrant hydrogen sulfide metabolism, and numerous analytical methods exist for the measurement of the sulfur-containing species affected. However, uncertainty remains about their concentrations and speciation in cells/biofluids, perhaps in part due to differences in sample processing and detection principles. Using ultrahigh-performance liquid chromatography in combination with electrospray-ionization tandem mass spectrometry we here outline a specific and sensitive platform for the simultaneous measurement of 12 analytes, including total and free thiols, their disulfides and sulfide in complex biological matrices such as blood, saliva and urine...
February 19, 2018: Redox Biology
Caixia Ren, Jia Liu, Juntuo Zhou, Hui Liang, Yizhang Zhu, Qingqing Wang, Yinglin Leng, Zhe Zhang, Yun Yuan, Zhaoxia Wang, Yuxin Yin
Mitochondrial disease (MD) is a rare mitochondrial respiratory chain disorder with a high mortality and extremely challenging to treat. Although genomic, transcriptomic, and proteomic analyses have been performed to investigate the pathogenesis of MD, the role of metabolomics in MD, particularly of lipidomics remains unclear. This study was undertaken to identify potential lipid biomarkers of MD. An untargeted lipidomic approach was used to compare the plasma lipid metabolites in 20 MD patients and 20 controls through Liquid Chromatography coupled to Mass Spectrometry...
April 5, 2018: Biochemical and Biophysical Research Communications
Soad Al Jaouni, Ahmed M Saleh, Mohammed A M Wadaan, Wael N Hozzein, Samy Selim, Hamada AbdElgawad
Many studies have discussed the influence of elevated carbon dioxide (eCO2 ) on modeling and crop plants. However, much less effort has been dedicated to herbal plants. In this study, a robust monitoring for the levels of 94 primary and secondary metabolites and minerals in two medicinal herbs, basil (Ocimum basilicum L.) and peppermint (Mentha piperita L.), grwon under both ambient (aCO2 , 360 ppm) and eCO2 (620 ppm) was performed. We also assessed how the changes in herbal tissue chemistry affected their biological activity...
March 29, 2018: Journal of Plant Physiology
Jeong-Eun Park, HyeRin Lim, Jun Woo Kim, Kwang-Hee Shin
AIMS: Fasting plasma glucose, oral glucose tolerance test, and glycated hemoglobin are diagnostic markers for type 2 diabetes mellitus (T2DM). However, it is necessary to detect physiological changes in T2DM rapidly and stratify diabetic stage using other biomarkers. We performed a systematic review and meta-analysis to contribute to the development of objective and sensitive diagnostic indicators by integrating metabolite biomarkers derived from large-scale cohort studies. METHODS: We searched for metabolomics studies of T2DM cohort in PubMed, Scopus, and Web of Science for studies published within the last 10 years from January 2008 to February 2017...
April 4, 2018: Diabetes Research and Clinical Practice
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"