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Metabolomic analysis

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https://www.readbyqxmd.com/read/28100172/integrated-genomics-based-mapping-reveals-the-genetics-underlying-maize-flavonoid-biosynthesis
#1
Min Jin, Xuehai Zhang, Mingchao Zhao, Min Deng, Yuanhao Du, Yang Zhou, Shouchuang Wang, Takayuki Tohge, Alisdair R Fernie, Lothar Willmitzer, Yariv Brotman, Jianbing Yan, Weiwei Wen
BACKGROUND: Flavonoids constitute a diverse class of secondary metabolites which exhibit potent bioactivities for human health and have been indicated to play an important role in plant development and defense. However, accumulation and variation of flavonoid content in diverse maize lines and the genes responsible for their biosynthesis in this important crop remain largely unknown. In this study, we combine genetic mapping, metabolite profiling and gene regulatory network analysis to further enhance understanding of the maize flavonoid pathway...
January 18, 2017: BMC Plant Biology
https://www.readbyqxmd.com/read/28098892/metabolomics-study-on-primary-dysmenorrhea-patients-during-the-luteal-regression-stage-based-on-ultra-performance-liquid-chromatography-coupled-with-quadrupole%C3%A2-time%C3%A2-of%C3%A2-flight-mass-spectrometry
#2
Ling Fang, Caiyun Gu, Xinyu Liu, Jiabin Xie, Zhiguo Hou, Meng Tian, Jia Yin, Aizhu Li, Yubo Li
Primary dysmenorrhea (PD) is a common gynecological disorder which, while not life‑threatening, severely affects the quality of life of women. Most patients with PD suffer ovarian hormone imbalances caused by uterine contraction, which results in dysmenorrhea. PD patients may also suffer from increases in estrogen levels caused by increased levels of prostaglandin synthesis and release during luteal regression and early menstruation. Although PD pathogenesis has been previously reported on, these studies only examined the menstrual period and neglected the importance of the luteal regression stage...
January 13, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28098246/tryptophan-metabolite-activation-of-the-aryl-hydrocarbon-receptor-regulates-il-10-receptor-expression-on-intestinal-epithelia
#3
J M Lanis, E E Alexeev, V F Curtis, D A Kitzenberg, D J Kao, K D Battista, M E Gerich, L E Glover, D J Kominsky, S P Colgan
IL-10 is a potent anti-inflammatory cytokine that inhibits the production of proinflammatory mediators. Signaling by IL-10 occurs through the IL-10 receptor (IL-10R), which is expressed in numerous cell types, including intestinal epithelial cells (IECs), where it is associated with development and maintenance of barrier function. Guided by an unbiased metabolomics screen, we identified tryptophan (Trp) metabolism as a major modifying pathway in interferon-γ (IFNγ)-dominant murine colitis. In parallel, we demonstrated that IFNγ induction of indoleamine 2,3-dioxygenase 1, an enzyme that catalyzes the conversion of Trp to kynurenine (Kyn), induces IL-10R1 expression...
January 18, 2017: Mucosal Immunology
https://www.readbyqxmd.com/read/28097070/sponge-exhalent-seawater-contains-a-unique-chemical-profile-of-dissolved-organic-matter
#4
Cara L Fiore, Christopher J Freeman, Elizabeth B Kujawinski
Sponges are efficient filter feeders, removing significant portions of particulate and dissolved organic matter (POM, DOM) from the water column. While the assimilation and respiration of POM and DOM by sponges and their abundant microbial symbiont communities have received much attention, there is virtually no information on the impact of sponge holobiont metabolism on the composition of DOM at a molecular-level. We applied untargeted and targeted metabolomics techniques to characterize DOM in seawater samples prior to entering the sponge (inhalant reef water), in samples exiting the sponge (exhalent seawater), and in samples collected just outside the reef area (off reef seawater)...
2017: PeerJ
https://www.readbyqxmd.com/read/28096192/integrated-physiological-proteomic-and-metabolomic-analysis-of-uv-stress-responses-and-adaptation-mechanisms-in-pinus-radiata
#5
Jesus Pascual, Maria Jesus Canal, Monica Escandon, Monica Meijon, Wolfram Weckwerth, Luis Valledor
Globally expected changes in environmental conditions, especially the increase of UV irradiation, necessitate extending our knowledge of the mechanisms mediating tree species adaptation to this stress. This is crucial for designing new strategies to maintain future forest productivity. Studies focused on environmentally realistic dosages of UV irradiation in forest species are scarce. Pinus sp. are commercially relevant trees and not much is known about their adaptation to UV. In this work, UV treatment and recovery of Pinus radiata plants with dosages mimicking future scenarios, based on current models of UV radiation, were performed in a time-dependent manner...
January 17, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28095889/evolution-of-gut-microbiota-composition-from-birth-to-24-weeks-in-the-infantmet-cohort
#6
Cian J Hill, Denise B Lynch, Kiera Murphy, Marynka Ulaszewska, Ian B Jeffery, Carol Anne O'Shea, Claire Watkins, Eugene Dempsey, Fulvio Mattivi, Kieran Touhy, R Paul Ross, C Anthony Ryan, Paul W O' Toole, Catherine Stanton
BACKGROUND: The gut is the most extensively studied niche of the human microbiome. The aim of this study was to characterise the initial gut microbiota development of a cohort of breastfed infants (n = 192) from 1 to 24 weeks of age. METHODS: V4-V5 region 16S rRNA amplicon Illumina sequencing and, in parallel, bacteriological culture. The metabolomic profile of infant urine at 4 weeks of age was also examined by LC-MS. RESULTS: Full-term (FT), spontaneous vaginally delivered (SVD) infants' microbiota remained stable at both phylum and genus levels during the 24-week period examined...
January 17, 2017: Microbiome
https://www.readbyqxmd.com/read/28094560/systemic-metabolite-changes-in-wild-type-c57bl-6-mice-fed-black-raspberries
#7
Pan Pan, Chad W Skaer, Hsin-Tzu Wang, Michael A Kreiser, Steven M Stirdivant, Kiyoko Oshima, Yi-Wen Huang, Matthew R Young, Li-Shu Wang
INTRODUCTION: Freeze-dried black raspberries (BRBs) elicit chemopreventive effects against colorectal cancer in humans and in rodents. The objective of this study was to investigate potential BRB-caused metabolite changes using wild-type (WT) C57BL/6 mice. METHODS AND RESULTS: WT mice were fed either control diet or control diet supplemented with 5% BRBs for 8 wk. A nontargeted metabolomic analysis was conducted on colonic mucosa, liver, and fecal specimens collected from both diet groups...
January 17, 2017: Nutrition and Cancer
https://www.readbyqxmd.com/read/28093124/the-co-feature-ratio-a-novel-method-for-the-measurement-of-chromatographic-and-signal-selectivity-in-lc-ms-based-metabolomics
#8
Albert Elmsjö, Jakob Haglöf, Mikael K R Engskog, Marika Nestor, Torbjörn Arvidsson, Curt Pettersson
Evaluation of analytical procedures, especially in regards to measuring chromatographic and signal selectivity, is highly challenging in untargeted metabolomics. The aim of this study was to suggest a new straightforward approach for a systematic examination of chromatographic and signal selectivity in LC-MS-based metabolomics. By calculating the ratio between each feature and its co-eluting features (the co-features), a measurement of the chromatographic selectivity (i.e. extent of co-elution) as well as the signal selectivity (e...
March 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28093073/application-of-meta-omics-techniques-to-understand-greenhouse-gas-emissions-originating-from-ruminal-metabolism
#9
REVIEW
Robert J Wallace, Timothy J Snelling, Christine A McCartney, Ilma Tapio, Francesco Strozzi
Methane emissions from ruminal fermentation contribute significantly to total anthropological greenhouse gas (GHG) emissions. New meta-omics technologies are beginning to revolutionise our understanding of the rumen microbial community structure, metabolic potential and metabolic activity. Here we explore these developments in relation to GHG emissions. Microbial rumen community analyses based on small subunit ribosomal RNA sequence analysis are not yet predictive of methane emissions from individual animals or treatments...
January 16, 2017: Genetics, Selection, Evolution: GSE
https://www.readbyqxmd.com/read/28093044/changes-in-biosynthesis-of-exopolysaccharide-in-lactococcus-lactis-subspecies-cremoris-treated-by-moderate-pulsed-electric-field-treatment
#10
Tetsuro Ohba, Kunihiko Uemura, Hiroshi Nabetani
Metabolome analysis and physicochemical analyses were executed with cell extracts of a Lactococcus lactis subspecies cremoris strain treated by moderate pulsed electric field (PEF) to elucidate the mechanism of enhanced production of exopolysaccharide (EPS) by the treatment. Metabolome analysis by capillary electrophoresis time of flight mass spectrometry annotated 224 metabolites from the cytoplasmic extract of the strain, which, however, showed no significant changes in metabolites related to the EPS production...
January 17, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28092796/global-open-data-management-in-metabolomics
#11
REVIEW
Kenneth Haug, Reza M Salek, Christoph Steinbeck
Chemical Biology employs chemical synthesis, analytical chemistry and other tools to study biological systems. Recent advances in both molecular biology such as next generation sequencing (NGS) have led to unprecedented insights towards the evolution of organisms' biochemical repertoires. Because of the specific data sharing culture in Genomics, genomes from all kingdoms of life become readily available for further analysis by other researchers. While the genome expresses the potential of an organism to adapt to external influences, the Metabolome presents a molecular phenotype that allows us to asses the external influences under which an organism exists and develops in a dynamic way...
January 13, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/28092471/genomics-pipelines-and-data-integration-challenges-and-opportunities-in-the-research-setting
#12
Jeremy Davis-Turak, Sean M Courtney, E Starr Hazard, W Bailey Glen, Willian da Silveira, Timothy Wesselman, Larry P Harbin, Bethany J Wolf, Dongjun Chung, Gary Hardiman
The emergence and mass utilization of high-throughput (HT) technologies, including sequencing technologies (genomics) and mass spectrometry (proteomics, metabolomics, lipids), has allowed geneticists, biologists, and biostatisticians to bridge the gap between genotype and phenotype on a massive scale. These new technologies have brought rapid advances in our understanding of cell biology, evolutionary history, microbial environments, and are increasingly providing new insights and applications towards clinical care and personalized medicine...
January 16, 2017: Expert Review of Molecular Diagnostics
https://www.readbyqxmd.com/read/28090435/-13-c-metabolomics-nmr-and-iroa-for-unknown-identification
#13
Chaevien S Clendinen, Gregory S Stupp, Bing Wang, Timothy J Garrett, Arthur S Edison
ABSTRACT BACKGROUND: Isotopic Ratio Outlier Analysis (IROA) is an untargeted metabolomics method that uses stable isotopic labeling and LC-HRMS for identification and relative quantification of metabolites in a biological sample under varying experimental conditions. OBJECTIVE: We demonstrate a method using high-sensitivity (13)C NMR to identify an unknown metabolite isolated from fractionated material from an IROA LC-HRMS experiment. METHODS: IROA samples from the nematode Caenorhabditis elegans were fractionated using LC-HRMS using 5 repeated injections and collecting 30 sec fractions...
August 2016: Current Metabolomics
https://www.readbyqxmd.com/read/28090199/mastr-ms-a-web-based-collaborative-laboratory-information-management-system-lims-for-metabolomics
#14
Adam Hunter, Saravanan Dayalan, David De Souza, Brad Power, Rodney Lorrimar, Tamas Szabo, Thu Nguyen, Sean O'Callaghan, Jeremy Hack, James Pyke, Amsha Nahid, Roberto Barrero, Ute Roessner, Vladimir Likic, Dedreia Tull, Antony Bacic, Malcolm McConville, Matthew Bellgard
BACKGROUND: An increasing number of research laboratories and core analytical facilities around the world are developing high throughput metabolomic analytical and data processing pipelines that are capable of handling hundreds to thousands of individual samples per year, often over multiple projects, collaborations and sample types. At present, there are no Laboratory Information Management Systems (LIMS) that are specifically tailored for metabolomics laboratories that are capable of tracking samples and associated metadata from the beginning to the end of an experiment, including data processing and archiving, and which are also suitable for use in large institutional core facilities or multi-laboratory consortia as well as single laboratory environments...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/28089366/limited-reduction-in-uremic-solute-concentrations-with-increased-dialysis-frequency-and-time-in-the-frequent-hemodialysis-network-daily-trial
#15
Tammy L Sirich, Kara Fong, Brett Larive, Gerald J Beck, Glenn M Chertow, Nathan W Levin, Alan S Kliger, Natalie S Plummer, Timothy W Meyer
The Frequent Hemodialysis Network Daily Trial compared conventional three-times weekly treatment to more frequent treatment with a longer weekly treatment time in patients receiving in-center hemodialysis. Evaluation at one year showed favorable effects of more intensive treatment on left ventricular mass, blood pressure, and phosphate control, but modest or no effects on physical or cognitive performance. The current study compared plasma concentrations of uremic solutes in stored samples from 53 trial patients who received three-times weekly in-center hemodialysis for an average weekly time of 10...
January 12, 2017: Kidney International
https://www.readbyqxmd.com/read/28088898/metabolomic-shifts-following-play-based-activity-in-overweight-preadolescents
#16
Marco Meucci, Carlo Baldari, Laura Guidetti, Jessica Renee Alley, Caorl Cook, Collier Robert Scott
BACKGROUND: Play-based activities can be a positive intervention to increase participation of overweight children. Metabolomics can reveal elemental shifts in the metabolome, lending potential mechanistic explanations behind improvements in physiological systems. OBJECTIVES: To elucidate dose-response urinary metabolomic signature shifts in overweight preadolescents following four or eight weeks of supervised play-based activity versus a typical summer break control group...
January 13, 2017: Current Pediatric Reviews
https://www.readbyqxmd.com/read/28088662/metabolic-profiles-of-exudates-from-chronic-leg-ulcerations
#17
Adam Junka, Wojciech Wojtowicz, Adam Ząbek, Grzegorz Krasowski, Danuta Smutnicka, Barbara Bakalorz, Agnieszka Boruta, Mariusz Dziadas, Piotr Młynarz, Parish Paymon Sedghizadeh, Marzenna Bartoszewicz
Chronic leg ulceration is a disease usually associated with other comorbidities, and significantly reduces patient quality of life. Infected leg ulcers can lead to limb-threatening sequelae or mortality. Leg ulcerations are colonized by a number of microbes that are able to cause life-threating infections in susceptible patients. Wound exudate is a body fluid that collects metabolites from patient eukaryotic cells and from prokaryotic bacterial communities inhabiting the wound. This study aimed at identification of metabolites in exudates collected from chronic leg ulcers, and correlation of this metabolome with patient comorbidities and microbiological status of the wound...
January 10, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28088278/metabolomic-analysis-of-urine-samples-by-uhplc-qtof-ms-impact-of-normalization-strategies
#18
Yoric Gagnebin, David Tonoli, Pierre Lescuyer, Belen Ponte, Sophie de Seigneux, Pierre-Yves Martin, Julie Schappler, Julien Boccard, Serge Rudaz
Among the various biological matrices used in metabolomics, urine is a biofluid of major interest because of its non-invasive collection and its availability in large quantities. However, significant sources of variability in urine metabolomics based on UHPLC-MS are related to the analytical drift and variation of the sample concentration, thus requiring normalization. A sequential normalization strategy was developed to remove these detrimental effects, including: (i) pre-acquisition sample normalization by individual dilution factors to narrow the concentration range and to standardize the analytical conditions, (ii) post-acquisition data normalization by quality control-based robust LOESS signal correction (QC-RLSC) to correct for potential analytical drift, and (iii) post-acquisition data normalization by MS total useful signal (MSTUS) or probabilistic quotient normalization (PQN) to prevent the impact of concentration variability...
February 22, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28087984/challenges-in-detecting-substances-for-equine-anti-doping
#19
REVIEW
A G Fragkaki, N Kioukia-Fougia, P Kiousi, M Kioussi, M Tsivou
The artificial increase of the physical capability of horses using drugs is well-known in racing and in other equine sports. Both illicit and therapeutic substances are regarded as prohibited substances in competition in most countries. Some countries do make distinctions for a few, specific drugs which are, however, allowed for use in other countries. The primary objective in the case of doping control is the detection of any trace of drug exposure, either parent drug or any of its metabolites, using the most powerful analytical methods which generally are based on chromatographic/mass spectrometric techniques...
January 14, 2017: Drug Testing and Analysis
https://www.readbyqxmd.com/read/28086860/nicotiana-attenuata-data-hub-nadh-an-integrative-platform-for-exploring-genomic-transcriptomic-and-metabolomic-data-in-wild-tobacco
#20
Thomas Brockmöller, Zhihao Ling, Dapeng Li, Emmanuel Gaquerel, Ian T Baldwin, Shuqing Xu
BACKGROUND: Nicotiana attenuata (coyote tobacco) is an ecological model for studying plant-environment interactions and plant gene function under real-world conditions. During the last decade, large amounts of genomic, transcriptomic and metabolomic data have been generated with this plant which has provided new insights into how native plants interact with herbivores, pollinators and microbes. However, an integrative and open access platform that allows for the efficient mining of these -omics data remained unavailable until now...
January 13, 2017: BMC Genomics
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