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https://www.readbyqxmd.com/read/28330265/isolation-and-characterization-of-plant-synergistic-bacteria-capable-of-degrading-xenobiotics-from-oil-spillage-sites
#1
Indranil De, Sarika Gupta
Oil spillage sites primarily contain various types of hydrocarbons, such as linear chain, polycyclic, and aromatic compounds, posing several detrimental effects on plants. Results from our previous study showed an alteration of various metabolomic parameters, indirectly resulting in an observable decline of growth in the mung seedlings upon incubation with phenol, toluene, xylene, and hexane. This study evaluates the role of these compounds upon plant growth and focusses to mitigate the effect of the same, using some isolated plant synergistic bacteria...
December 2016: 3 Biotech
https://www.readbyqxmd.com/read/28329151/caloric-restriction-and-rapamycin-differentially-alter-energy-metabolism-in-yeast
#2
Kyung-Mi Choi, Seok-Jin Hong, Jan M van Deursen, Sooah Kim, Kyoung Heon Kim, Cheol-Koo Lee
Rapamycin (RM), a drug that inhibits the mechanistic target of rapamycin (mTOR) pathway and responds to nutrient availability, seemingly mimics the effects of caloric restriction (CR) on healthy life span. However, the extent of the mechanistic overlap between RM and CR remains incompletely understood. Here, we compared the impact of CR and RM on cellular metabolic status. Both regimens maintained intracellular ATP through the chronological aging process and showed enhanced mitochondrial capacity. Comparative transcriptome analysis showed that CR had a stronger impact on global gene expression than RM...
March 8, 2017: Journals of Gerontology. Series A, Biological Sciences and Medical Sciences
https://www.readbyqxmd.com/read/28328083/oral-iron-supplementation-potential-implications-for-the-gut-microbiome-and-metabolome-in-patients-with-ckd
#3
Guus A M Kortman, Dorien Reijnders, Dorine W Swinkels
Patients with chronic kidney disease (CKD) and loss of kidney function are at increased risk for morbidity and mortality. The risks of CKD are attributed to "uremia," an increased concentration of uremic retention solutes (toxins) in the plasma. Recently, a colo-renal axis became clearly apparent and uremia has been associated with an altered gut microbiome composition and metabolism. There is a high prevalence of anemia in patients with CKD, for which patients are often treated with oral or intravenous iron...
March 22, 2017: Hemodialysis International
https://www.readbyqxmd.com/read/28328075/role-of-amino-acids-in-rheumatoid-arthritis-studied-by-metabolomics
#4
Min He, Amy C Harms, Eduard van Wijk, Mei Wang, Ruud Berger, Slavik Koval, Thomas Hankemeier, Jan van der Greef
BACKGROUND: Rheumatoid arthritis (RA) is a complex, chronic autoimmune disease characterized by various inflammatory symptoms, including joint swelling, joint pain, and both structural and functional joint damage. The most commonly used animal model for studying RA is mice with collagen-induced arthritis (CIA); the wide use of this model is due primarily to many similarities with RA in human patients. Metabolomics is used increasingly in biological studies for diagnosing disease and for predicting and evaluating drug interventions, as a large number of disease-associated metabolites can be analyzed and interpreted from a biological perspective...
March 22, 2017: International Journal of Rheumatic Diseases
https://www.readbyqxmd.com/read/28327092/metax-a-flexible-and-comprehensive-software-for-processing-metabolomics-data
#5
Bo Wen, Zhanlong Mei, Chunwei Zeng, Siqi Liu
BACKGROUND: Non-targeted metabolomics based on mass spectrometry enables high-throughput profiling of the metabolites in a biological sample. The large amount of data generated from mass spectrometry requires intensive computational processing for annotation of mass spectra and identification of metabolites. Computational analysis tools that are fully integrated with multiple functions and are easily operated by users who lack extensive knowledge in programing are needed in this research field...
March 21, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28327077/regional-muscle-tissue-saturation-is-an-indicator-of-global-inadequate-circulation-during-cardiopulmonary-bypass-a-randomized-porcine-study-using-muscle-intestinal-and-brain-tissue-metabolomics
#6
Sisse Anette Thomassen, Benedict Kjærgaard, Preben Sørensen, Jan Jesper Andreasen, Anders Larsson, Bodil Steen Rasmussen
BACKGROUND: Muscle tissue saturation (StO2) measured with near-infrared spectroscopy has generally been considered a measurement of the tissue microcirculatory condition. However, we hypothesized that StO2 could be more regarded as a fast and reliable measure of global than of regional circulatory adequacy and tested this with muscle, intestinal and brain metabolomics at normal and two levels of low cardiopulmonary bypass blood flow rates in a porcine model. METHODS: Twelve 80 kg pigs were connected to normothermic cardiopulmonary bypass with a blood flow of 60 mL/kg/min for one hour, reduced randomly to 47...
April 2017: Perfusion
https://www.readbyqxmd.com/read/28325553/metabolomics-through-the-lens-of-precision-cardiovascular-medicine
#7
REVIEW
Sin Man Lam, Yuan Wang, Bowen Li, Jie Du, Guanghou Shui
Metabolomics, which targets at the extensive characterization and quantitation of global metabolites from both endogenous and exogenous sources, has emerged as a novel technological avenue to advance the field of precision medicine principally driven by genomics-oriented approaches. In particular, metabolomics has revealed the cardinal roles that the environment exerts in driving the progression of major diseases threatening public health. Herein, the existent and potential applications of metabolomics in two key areas of precision cardiovascular medicine will be critically discussed: 1) the use of metabolomics in unveiling novel disease biomarkers and pathological pathways; 2) the contribution of metabolomics in cardiovascular drug development...
March 8, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28323936/the-steroid-metabolome-in-the-isolated-ovarian-follicle-and-its-response-to-androgen-exposure-and-antagonism
#8
Marie Lebbe, Angela E Taylor, Jenny A Visser, Jackson Kirkman-Brown, Teresa K Woodruff, Wiebke Arlt
The ovarian follicle is a major site of steroidogenesis, crucially required for normal ovarian function and female reproduction. Our understanding of androgen synthesis and metabolism in the developing follicle has been limited by sensitivity and specificity issues of previously used assays. Here we used liquid chromatography-tandem mass spectrometry to map the stage-dependent endogenous steroid metabolome in an encapsulated in vitro follicle growth system, from murine secondary through antral follicles. Furthermore, follicles were cultured in the presence of androgen precursors, non-aromatizable active androgen and androgen receptor (AR) antagonist to assess effects on steroidogenesis and follicle development...
February 23, 2017: Endocrinology
https://www.readbyqxmd.com/read/28323825/association-between-fatty-acid-metabolism-in-the-brain-and-alzheimer-disease-neuropathology-and-cognitive-performance-a-nontargeted-metabolomic-study
#9
Stuart G Snowden, Amera A Ebshiana, Abdul Hye, Yang An, Olga Pletnikova, Richard O'Brien, John Troncoso, Cristina Legido-Quigley, Madhav Thambisetty
BACKGROUND: The metabolic basis of Alzheimer disease (AD) pathology and expression of AD symptoms is poorly understood. Omega-3 and -6 fatty acids have previously been linked to both protective and pathogenic effects in AD. However, to date little is known about how the abundance of these species is affected by differing levels of disease pathology in the brain. METHODS AND FINDINGS: We performed metabolic profiling on brain tissue samples from 43 individuals ranging in age from 57 to 95 y old who were stratified into three groups: AD (N = 14), controls (N = 14) and "asymptomatic Alzheimer's disease" (ASYMAD), i...
March 2017: PLoS Medicine
https://www.readbyqxmd.com/read/28323243/proteomics-of-facs-sorted-heterogeneous-corynebacterium-glutamicum-populations
#10
Andreas Harst, Stefan P Albaum, Tanja Bojarzyn, Christian Trötschel, Ansgar Poetsch
The metabolic status of individual cells in microbial cultures can differ, being relevant for biotechnology, environmental and medical microbiology. However, it is hardly understood in molecular detail due to limitations of current analytical tools. Here, we demonstrate that FACS in combination with proteomics can be used to sort and analyze cell populations based on their metabolic state. A previously established GFP reporter system was used to detect and sort single Corynebacterium glutamicum cells based on the concentration of branched chain amino acids (BCAA) using FACS...
March 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28323032/metabolic-re-wiring-of-isogenic-breast-epithelial-cell-lines-following-epithelial-to-mesenchymal-transition
#11
Skarphedinn Halldorsson, Neha Rohatgi, Manuela Magnusdottir, Kumari Sonal Choudhary, Thorarinn Guðjónsson, Erik Knutsen, Anna Barkovskaya, Bylgja Hilmarsdottir, Maria Perander, Gunhild M Mælandsmo, Steinn Gudmundsson, Óttar Rolfsson
Epithelial to mesenchymal transition (EMT) has implications in tumor progression and metastasis. Metabolic alterations have been described in cancer development but studies focused on the metabolic re-wiring that takes place during EMT are still limited. We performed metabolomics profiling of a breast epithelial cell line and its EMT derived mesenchymal phenotype to create genome-scale metabolic models descriptive of both cell lines. Glycolysis and OXPHOS were higher in the epithelial phenotype while amino acid anaplerosis and fatty acid oxidation fueled the mesenchymal phenotype...
March 16, 2017: Cancer Letters
https://www.readbyqxmd.com/read/28322828/metabolic-characterization-of-human-aqueous-humor-in-relation-to-high-myopia
#12
Yinghong Ji, Jun Rao, Xianfang Rong, Shang Lou, Zhi Zheng, Yi Lu
High myopia is the common eye disorder worldwide, which may contribute to increase the risk of serious disorders including glaucoma and cataract. Although various studies including genomics, transcriptomics, and proteomics have been implicated to identify potential biomarkers (genes or proteins) for predicting high myopia and to reveal the underlying mechanisms, the comprehensive metabolomics in relation to high myopia is very limited. In this study, we identified 242 metabolites in aqueous humor (AH) from a set of 40 patients (including 20 with high myopia and 20 for controls), using a non-targeted metabolomic technology, gas chromatography coupled to time-of-flight mass spectrometer (GC/TOF MS)...
March 17, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/28322544/graphene-oxide-quantum-dots-as-novel-nanozymes-for-alcohol-intoxication
#13
Anqi Sun, Li Mu, Xiangang Hu
Alcohol overconsumption as a worldwide issue results in alcoholic liver disease (ALD), such as steatosis, alcoholic hepatitis and cirrhosis. The treatment of ALD has been widely investigated but remains challenging. In this work, the protective effects of graphene oxide quantum dots (GOQDs) as novel nanozymes against alcohol overconsumption are discovered, and the specific mechanisms underlying these effects are elucidated via omics analysis. GOQDs dramatically alleviate the reduction of cell viability induced by ethanol and can act as nanozymes to accelerate ethanol metabolism and avoid the accumulation of toxic intermediates in cells...
March 21, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28322027/rapid-differentiating-colorectal-cancer-and-colorectal-polyp-using-dried-blood-spot-mass-spectrometry-metabolomic-approach
#14
Yu Jing, Xue Wu, Peng Gao, Zhongze Fang, Jingjing Wu, Qingjun Wang, Chen Li, Zhitu Zhu, Yunfeng Cao
Colorectal cancer (CRC) is the third leading causes of cancer mortality, and the early-stage detection could significantly enhance survival rates. Cancer influences the important metabolic pathways and the changes in metabolite levels had been used in many studies as the potential biomarkers. This study is aimed at screening metabolite biomarkers with CRC diagnosis potentials. The direct infusion mass spectrometry (MS) metabolomic analysis based on dried blood spot was used to distinguish CRC from polyp. The target metabolites were composed of 23 amino acids and 26 acylcarnitines...
March 20, 2017: IUBMB Life
https://www.readbyqxmd.com/read/28321390/metabonomics-research-progress-on-liver-diseases
#15
REVIEW
Mengqian Yu, Ying Zhu, Qingwei Cong, Chunyan Wu
Metabolomics as the new omics technique develops after genomics, transcriptomics, and proteomics and has rapid development at present. Liver diseases are worldwide public health problems. In China, chronic hepatitis B and its secondary diseases are the common liver diseases. They can be diagnosed by the combination of history, virology, liver function, and medical imaging. However, some patients seldom have relevant physical examination, so the diagnosis may be delayed. Many other liver diseases, such as drug-induced liver injury (DILI), alcoholic liver disease (ALD) and nonalcoholic fatty liver disease (NAFLD), and autoimmune liver diseases, still do not have definite diagnostic markers; the diagnosis consists of history, medical imaging, and the relevant score...
2017: Canadian Journal of Gastroenterology & Hepatology
https://www.readbyqxmd.com/read/28321369/developmental-and-loco-like-effects-of-a-swainsonine-induced-inhibition-of-%C3%AE-mannosidase-in-the-honey-bee-apis-mellifera
#16
Laura Wedd, Regan Ashby, Sylvain Foret, Ryszard Maleszka
BACKGROUND: Deficiencies in lysosomal a-mannosidase (LAM) activity in animals, caused either by mutations or by consuming toxic alkaloids, lead to severe phenotypic and behavioural consequences. Yet, epialleles adversely affecting LAM expression exist in the honey bee population suggesting that they might be beneficial in certain contexts and cannot be eliminated by natural selection. METHODS: We have used a combination of enzymology, molecular biology and metabolomics to characterise the catalytic properties of honey bee LAM (AmLAM) and then used an indolizidine alkaloid swainsonine to inhibit its activity in vitro and in vivo...
2017: PeerJ
https://www.readbyqxmd.com/read/28321230/integrated-transcriptome-and-metabolic-analyses-reveals-novel-insights-into-free-amino-acid-metabolism-in-huangjinya-tea-cultivar
#17
Qunfeng Zhang, Meiya Liu, Jianyun Ruan
The chlorotic tea variety Huangjinya, a natural mutant, contains enhanced levels of free amino acids in its leaves, which improves the drinking quality of its brewed tea. Consequently, this chlorotic mutant has a higher economic value than the non-chlorotic varieties. However, the molecular mechanisms behind the increased levels of free amino acids in this mutant are mostly unknown, as are the possible effects of this mutation on the overall metabolome and biosynthetic pathways in tea leaves. To gain further insight into the effects of chlorosis on the global metabolome and biosynthetic pathways in this mutant, Huangjinya plants were grown under normal and reduced sunlight, resulting in chlorotic and non-chlorotic leaves, respectively; their leaves were analyzed using transcriptomics as well as targeted and untargeted metabolomics...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28321214/exogenous-l-valine-promotes-phagocytosis-to-kill-multidrug-resistant-bacterial-pathogens
#18
Xin-Hai Chen, Shi-Rao Liu, Bo Peng, Dan Li, Zhi-Xue Cheng, Jia-Xin Zhu, Song Zhang, Yu-Ming Peng, Hui Li, Tian-Tuo Zhang, Xuan-Xian Peng
The emergence of multidrug-resistant bacteria presents a severe threat to public health and causes extensive losses in livestock husbandry and aquaculture. Effective strategies to control such infections are in high demand. Enhancing host immunity is an ideal strategy with fewer side effects than antibiotics. To explore metabolite candidates, we applied a metabolomics approach to investigate the metabolic profiles of mice after Klebsiella pneumoniae infection. Compared with the mice that died from K. pneumoniae infection, mice that survived the infection displayed elevated levels of l-valine...
2017: Frontiers in Immunology
https://www.readbyqxmd.com/read/28320949/discovery-of-scmr-as-a-global-regulator-of-secondary-metabolism-and-virulence-in-burkholderia-thailandensis-e264
#19
Dainan Mao, Leah B Bushin, Kyuho Moon, Yihan Wu, Mohammad R Seyedsayamdost
Bacteria produce a diverse array of secondary metabolites that have been invaluable in the clinic and in research. These metabolites are synthesized by dedicated biosynthetic gene clusters (BGCs), which assemble architecturally complex molecules from simple building blocks. The majority of BGCs in a given bacterium are not expressed under normal laboratory growth conditions, and our understanding of how they are silenced is in its infancy. Here, we have addressed this question in the Gram-negative model bacterium Burkholderia thailandensis E264 using genetic, transcriptomic, metabolomic, and chemical approaches...
March 20, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28320327/metabolomics-analysis-reveals-the-metabolic-and-functional-roles-of-flavonoids-in-light-sensitive-tea-leaves
#20
Qunfeng Zhang, Meiya Liu, Jianyun Ruan
BACKGROUND: As the predominant secondary metabolic pathway in tea plants, flavonoid biosynthesis increases with increasing temperature and illumination. However, the concentration of most flavonoids decreases greatly in light-sensitive tea leaves when they are exposed to light, which further improves tea quality. To reveal the metabolism and potential functions of flavonoids in tea leaves, a natural light-sensitive tea mutant (Huangjinya) cultivated under different light conditions was subjected to metabolomics analysis...
March 20, 2017: BMC Plant Biology
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