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https://www.readbyqxmd.com/read/29050286/a-prospective-study-of-serum-metabolites-and-glioma-risk
#1
Jiaqi Huang, Stephanie J Weinstein, Cari M Kitahara, Edward D Karoly, Joshua N Sampson, Demetrius Albanes
Malignant glioma is one of the most lethal adult cancers, yet its etiology remains largely unknown. We conducted a prospective serum metabolomic analysis of glioma based on 64 cases and 64 matched controls selected from Alpha-Tocopherol, Beta-Carotene Cancer Prevention (ATBC) Study. Median time from collection of baseline fasting serum to diagnosis was nine years (inter-decile range 3-20 years). LC/MS-MS identified 730 known metabolites, and conditional logistic regression models estimated odds ratios for one-standard deviation differences in log-metabolite signals...
September 19, 2017: Oncotarget
https://www.readbyqxmd.com/read/29044433/pregnancy-induced-changes-in-metabolome-and-proteome-in-ovine-uterine-flushings
#2
Jared J Romero, Bethany E Liebig, Corey D Broeckling, Jessica E Prenni, Thomas R Hansen
Mass spectrometry (MS) approaches were used herein to identify metabolites and proteins in uterine flushings (UF) that may contribute to nourishing the conceptus. Ovine uteri collected on Day 12 of the estrous cycle (n = 5 ewes exposed to vasectomized ram) or Days 12 (n = 4), 14 (n = 5), or 16 (n = 5) of pregnancy (bred with fertile ram) were flushed using buffered saline. Metabolites were extracted using 80% methanol and profiled using ultraperformance liquid chromatography (LC) tandem mass spectrometry. The proteome was examined by digestion with trypsin, followed by the analysis of peptides with LC-MS/MS...
August 1, 2017: Biology of Reproduction
https://www.readbyqxmd.com/read/29044196/exercise-and-high-fat-feeding-remodel-transcript-metabolite-interactive-networks-in-mouse-skeletal-muscle
#3
Joaquín Pérez-Schindler, Aditi Kanhere, Lindsay Edwards, J William Allwood, Warwick B Dunn, Simon Schenk, Andrew Philp
Enhanced coverage and sensitivity of next-generation 'omic' platforms has allowed the characterization of gene, metabolite and protein responses in highly metabolic tissues, such as, skeletal muscle. A limitation, however, is the capability to determine interaction between dynamic biological networks. To address this limitation, we applied Weighted Analyte Correlation Network Analysis (WACNA) to RNA-seq and metabolomic datasets to identify correlated subnetworks of transcripts and metabolites in response to a high-fat diet (HFD)-induced obesity and/or exercise...
October 18, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29043062/the-future-of-metabolomics-in-elixir
#4
Merlijn van Rijswijk, Charlie Beirnaert, Christophe Caron, Marta Cascante, Victoria Dominguez, Warwick B Dunn, Timothy M D Ebbels, Franck Giacomoni, Alejandra Gonzalez-Beltran, Thomas Hankemeier, Kenneth Haug, Jose L Izquierdo-Garcia, Rafael C Jimenez, Fabien Jourdan, Namrata Kale, Maria I Klapa, Oliver Kohlbacher, Kairi Koort, Kim Kultima, Gildas Le Corguillé, Nicholas K Moschonas, Steffen Neumann, Claire O'Donovan, Martin Reczko, Philippe Rocca-Serra, Antonio Rosato, Reza M Salek, Susanna-Assunta Sansone, Venkata Satagopam, Daniel Schober, Ruth Shimmo, Rachel A Spicer, Ola Spjuth, Etienne A Thévenot, Mark R Viant, Ralf J M Weber, Egon L Willighagen, Gianluigi Zanetti, Christoph Steinbeck
Metabolomics, the youngest of the major omics technologies, is supported by an active community of researchers and infrastructure developers across Europe. To coordinate and focus efforts around infrastructure building for metabolomics within Europe, a workshop on the "Future of metabolomics in ELIXIR" was organised at Frankfurt Airport in Germany. This one-day strategic workshop involved representatives of ELIXIR Nodes, members of the PhenoMeNal consortium developing an e-infrastructure that supports workflow-based metabolomics analysis pipelines, and experts from the international metabolomics community...
2017: F1000Research
https://www.readbyqxmd.com/read/29042446/clinical-and-metabolic-consequences-of-l-serine-supplementation-in-hereditary-sensory-and-autonomic-neuropathy-type-1c
#5
Mari Auranen, Jussi Toppila, Saranya Suriyanarayanan, Museer A Lone, Anders Paetau, Henna Tyynismaa, Thorsten Hornemann, Emil Ylikallio
Hereditary sensory neuropathy type 1 (HSAN1) may be the first genetic neuropathy amenable to a specific mechanism-based treatment, as L-serine supplementation can be used to lower the neurotoxic levels of 1-deoxysphingolipids (1-deoxySL) that cause the neurodegeneration. The treatment is so far untested in HSAN1C caused by variants in the serine palmitoyl transferase subunit 2 (SPTLC2) gene. The aim of this study was to establish whether oral L-serine lowers 1-deoxySL in a patient with HSAN1C, to perform a dose escalation to find the minimal effective dose, and to assess the safety profile and global metabolic effects of the treatment...
October 17, 2017: Cold Spring Harbor Molecular Case Studies
https://www.readbyqxmd.com/read/29040586/plasma-nervonic-acid-is-a-potential-biomarker-for-major-depressive-disorder-a-pilot-study
#6
Yuki Kageyama, Takaoki Kasahara, Takemichi Nakamura, Kotaro Hattori, Yasuhiko Deguchi, Munehide Tani, Kenji Kuroda, Sumiko Yoshida, Yu-Ichi Goto, Koki Inoue, Tadafumi Kato
Background: Diagnostic biomarkers of major depressive disorder (MDD), bipolar disorder (BD), and schizophrenia (SZ) are urgently needed because none are currently available. Methods: We performed a comprehensive metabolome analysis of plasma samples from drug-free patients with MDD (n = 9), BD (n = 6), SZ (n = 17), and matched healthy controls (n = 19) (cohort 1), using liquid chromatography time-of-flight mass spectrometry. A significant effect of diagnosis was found for two metabolites: nervonic acid and cortisone, with nervonic acid being the most significantly altered...
October 6, 2017: International Journal of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29040577/metabolomics-of-postprandial-plasma-alterations-a-comprehensive-japanese-study
#7
Takeo Moriya, Yoshinori Satomi, Hiroyuki Kobayashi
While endogenous metabolites in plasma can be used as clinical biomarkers, intra-day variations should be carefully considered. The postprandial effect is a large contributing factor and is dependent on regional features (e.g., meals, ethnicity). Thus, for clinical application, regional-specific postprandial baseline data are required. In this study, 10 healthy Japanese volunteers of different ages and genders ate the same meal, and blood samples were taken 30 min before and one hour after the meal challenge...
October 4, 2017: Journal of Biochemistry
https://www.readbyqxmd.com/read/29040513/targeted-metabolomics-reveals-reduced-levels-of-polyunsaturated-choline-plasmalogens-and-a-smaller-dimethylarginine-arginine-ratio-in-the-follicular-fluid-of-patients-with-a-diminished-ovarian-reserve
#8
J M Chao de la Barca, T Boueilh, G Simard, L Boucret, V Ferré-L'Hotellier, L Tessier, C Gadras, P E Bouet, P Descamps, V Procaccio, P Reynier, P May-Panloup
STUDY QUESTION: Does the metabolomic profile of the follicular fluid (FF) of patients with a diminished ovarian reserve (DOR) differ from that of patients with a normal ovarian reserve (NOR)? SUMMARY ANSWER: The metabolomic signature of the FF reveals a significant decrease in polyunsaturated choline plasmalogens and methyl arginine transferase activity in DOR patients compared to NOR patients. WHAT IS KNOWN ALREADY: The composition of the FF reflects the exchanges between the oocyte and its microenvironment during its acquisition of gametic competence...
October 13, 2017: Human Reproduction
https://www.readbyqxmd.com/read/29039932/annotation-a-computational-solution-for-streamlining-metabolomics-analysis
#9
Xavier Domingo-Almenara, J Rafael Montenegro-Burke, H Paul Benton, Gary Siuzdak
The aim of any untargeted metabolomics experiment is to identify and quantify dysregulated compounds relevant to a particular disease or stressor. However, metabolite identification is still considered an imposing bottleneck in untargeted metabolomics. Untargeted data analysis workflows for liquid chromatography/electrospray ionization/mass spectrometry (LC/ESI/MS) usually consist in applying peak-picking algorithms, align those peaks across multiple samples to obtain the so-called peak features (defined as a peak, or a set of aligned peaks across samples with a unique \textit{m/z} and a specific retention time), and subsequently discover statistically significant variations between experimental groups or conditions...
October 17, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29039583/serum-metabolomic-profile-in-genetically-modified-cows-carrying-human-%C3%AE-%C3%A2-lactalbumin-gene
#10
Qin Wang, Wei Fu, Xiaofei Liu, Jianwu Wang, Chunyan Feng, Songyin Qiu, Xiaolin Li, Dandan Liu, Shuifang Zhu, Xiangmei Lin
The present study aimed to investigate the serum metabolomic profiles in genetically modified cows carrying and expressing human lactalbumin α (LALBA) and non‑LALBA cows, and identify altered metabolic characteristics following the genetic modification. Serum biochemistry indexes were measured according to protocols recommended by International Federation of Clinical Chemistry. The metabolomic profiles were determined using the serum samples collected from LALBA (n=6) and non‑LALBA cows (n=6). Welch's two‑sample t‑test was used to identify the metabolites that significantly differed between the LALBA and non‑LALBA groups (fold‑change ≠ 1 and P<0...
October 11, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/29037666/multi-class-analysis-for-simultaneous-determination-of-pesticides-mycotoxins-process-induced-toxicants-and-packaging-contaminants-in-tea
#11
Mathieu Cladière, Grégoire Delaporte, Even Le Roux, Valérie Camel
This study attempts at uniting the analysis of four different classes of contaminants for both liquid and solid tea samples. A total of 32 compounds, classified as pesticides, mycotoxins, process-induced toxicants or packaging contaminants, were carefully chosen for their diversity of structures and physicochemical properties. The proposed method combines a sample treatment strategy coming from metabolomics with liquid chromatography analysis using a silica bonded C18-pentafluorophenyl column coupled to high resolution mass spectrometry...
March 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29037587/lipidomic-analysis-of-biological-samples-comparison-of-liquid-chromatography-supercritical-fluid-chromatography-and-direct-infusion-mass-spectrometry-methods
#12
Miroslav Lísa, Eva Cífková, Maria Khalikova, Magdaléna Ovčačíková, Michal Holčapek
Lipidomic analysis of biological samples in a clinical research represents challenging task for analytical methods given by the large number of samples and their extreme complexity. In this work, we compare direct infusion (DI) and chromatography - mass spectrometry (MS) lipidomic approaches represented by three analytical methods in terms of comprehensiveness, sample throughput, and validation results for the lipidomic analysis of biological samples represented by tumor tissue, surrounding normal tissue, plasma, and erythrocytes of kidney cancer patients...
October 8, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/29036359/profia-a-data-preprocessing-workflow-for-flow-injection-analysis-coupled-to-high-resolution-mass-spectrometry
#13
Alexis Delabrière, Ulli M Hohenester, Benoit Colsch, Christophe Junot, François Fenaille, Etienne A Thévenot
Motivation: Flow Injection Analysis coupled to High-Resolution Mass Spectrometry (FIA-HRMS) is a promising approach for high-throughput metabolomics. FIA-HRMS data, however, cannot be preprocessed with current software tools which rely on liquid chromatography separation, or handle low resolution data only. Results: We thus developed the proFIA package, which implements a suite of innovative algorithms to preprocess FIA-HRMS raw files, and generates the table of peak intensities...
July 14, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29036204/metabolic-phenotyping-in-the-mouse-model-of-urinary-tract-infection-shows-that-3-hydroxybutyrate-in-plasma-is-associated-with-infection
#14
Pei Han, Yong Huang, Yumin Xie, Wu Yang, Yaoyao Wang, Wenying Xiang, Peter J Hylands, Cristina Legido-Quigley
Urinary tract infection is one of the most common bacterial infections worldwide. Current diagnosis of urinary tract infection chiefly relies on its clinical presentation, urine dipstick tests and urine culture. Small molecules found in bio-fluids related with both infection and recovery would facilitate diagnosis and management of UTI. Mass spectrometry-based fingerprinting of plasma and urine at 3 time points, pre-infection (t = -24h), infection (t = 24h) and post 3-day treatment (t = 112h), were acquired in the following four groups: mice which were healthy, infected but not treated, infected and treated with ciprofloxacin, and infected and treated with Relinqing® granules (n = 6 per group)...
2017: PloS One
https://www.readbyqxmd.com/read/29034954/intergenerational-environmental-effects-functional-signals-in-offspring-transcriptomes-and-metabolomes-after-parental-jasmonic-acid-treatment-in-apomictic-dandelion
#15
Koen J F Verhoeven, Eline H Verbon, Thomas P van Gurp, Carla Oplaat, Julie Ferreira de Carvalho, Alison M Morse, Mark Stahl, Mirka Macel, Lauren M McIntyre
Parental environments can influence offspring traits. However, the magnitude of the impact of parental environments on offspring molecular phenotypes is poorly understood. Here, we test the direct effects and intergenerational effects of jasmonic acid (JA) treatment, which is involved in herbivory-induced defense signaling, on transcriptomes and metabolomes in apomictic common dandelion (Taraxacum officinale). In a full factorial crossed design with parental and offspring JA and control treatments, we performed leaf RNA-seq gene expression analysis, LC-MS metabolomics and total phenolics assays in offspring plants...
October 16, 2017: New Phytologist
https://www.readbyqxmd.com/read/29034577/untargeted-gc-ms-metabolomics-reveals-changes-in-the-metabolite-dynamics-of-industrial-scale-batch-fermentations-of-streptoccoccus-thermophilus-broth
#16
Bekzod Khakimov, Lene D Christiansen, Anna-Lena Heins, Klavs M Sørensen, Charlotte Schöller, Anders Clausen, Thomas Skov, Krist V Gernaey, Søren B Engelsen
An industrial scale biomass production using batch or fed-batch fermentations usually optimized by selection of bacterial strains, tuning fermentation media, feeding strategy, and temperature. However, in-depth investigation of the biomass metabolome during the production may reveal new knowledge for better optimization. In this study, for the first time, the authors investigated seven fermentation batches performed on five Streptoccoccus thermophilus strains during the biomass production at Chr. Hansen (Denmark) in a real life large scale fermentation process...
October 16, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/29034330/perinatal-bisphenol-a-exposure-induces-chronic-inflammation-in-rabbit-offspring-via-modulation-of-gut-bacteria-and-their-metabolites
#17
Lavanya Reddivari, D N Rao Veeramachaneni, William A Walters, Catherine Lozupone, Jennifer Palmer, M K Kurundu Hewage, Rohil Bhatnagar, Amnon Amir, Mary J Kennett, Rob Knight, Jairam K P Vanamala
Bisphenol A (BPA) accumulates in the maturing gut and liver in utero and is known to alter gut bacterial profiles in offspring. Gut bacterial dysbiosis may contribute to chronic colonic and systemic inflammation. We hypothesized that perinatal BPA exposure-induced intestinal (and liver) inflammation in offspring is due to alterations in the microbiome and colonic metabolome. The 16S rRNA amplicon sequencing analysis revealed differences in beta diversity with a significant reduction in the relative abundances of short-chain fatty acid (SCFA) producers such as Oscillospira and Ruminococcaceae due to BPA exposure...
September 2017: MSystems
https://www.readbyqxmd.com/read/29034329/comparative-metabolomics-of-mycoplasma-bovis-and-mycoplasma-gallisepticum-reveals-fundamental-differences-in-active-metabolic-pathways-and-suggests-novel-gene-annotations
#18
Y Masukagami, D P De Souza, S Dayalan, C Bowen, S O'Callaghan, K Kouremenos, B Nijagal, D Tull, K A Tivendale, P F Markham, M J McConville, G F Browning, F M Sansom
Mycoplasmas are simple, but successful parasites that have the smallest genome of any free-living cell and are thought to have a highly streamlined cellular metabolism. Here, we have undertaken a detailed metabolomic analysis of two species, Mycoplasma bovis and Mycoplasma gallisepticum, which cause economically important diseases in cattle and poultry, respectively. Untargeted gas chromatography-mass spectrometry and liquid chromatography-mass spectrometry analyses of mycoplasma metabolite extracts revealed significant differences in the steady-state levels of many metabolites in central carbon metabolism, while (13)C stable isotope labeling studies revealed marked differences in carbon source utilization...
September 2017: MSystems
https://www.readbyqxmd.com/read/29032784/spent-culture-medium-analysis-from-individually-cultured-bovine-embryos-demonstrates-metabolomic-differences
#19
Kayla J Perkel, Pavneesh Madan
Spent culture medium can provide valuable information regarding the physiological state of a bovine preimplantation embryos through non-invasive analysis of the sum/depleted metabolite constituents. Metabolomics has become of great interest as an adjunct technique to morphological and cleavage-rate assessment, but more importantly, in improving our understanding of metabolism. In this study, in vitro produced bovine embryos developing at different rates were evaluated using proton nuclear magnetic resonance (1H NMR)...
October 16, 2017: Zygote: the Biology of Gametes and Early Embryos
https://www.readbyqxmd.com/read/29032502/gut-microbiota-changes-in-the-extreme-decades-of-human-life-a-focus-on-centenarians
#20
REVIEW
Aurelia Santoro, Rita Ostan, Marco Candela, Elena Biagi, Patrizia Brigidi, Miriam Capri, Claudio Franceschi
The gut microbiota (GM) is a complex, evolutionarily molded ecological system, which contributes to a variety of physiological functions. The GM is highly dynamic, being sensitive to environmental stimuli, and its composition changes over the host's entire lifespan. However, the basic question of how much these changes may be ascribed to variables such as population, diet, genetics and gender, and/or to the aging process per se is still largely unanswered. We argue that comparison among studies on centenarians-the best model of healthy aging and longevity-recruited from different geographical areas/populations (different genetics and dietary habits) can help to disentangle the contribution of aging and non-aging-related variables to GM remodeling with age...
October 14, 2017: Cellular and Molecular Life Sciences: CMLS
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