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Omics metabolism

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https://www.readbyqxmd.com/read/28548658/distinctive-microbiomes-and-metabolites-linked-with-weight-loss-after-gastric-bypass-but-not-gastric-banding
#1
Zehra Esra Ilhan, John K DiBaise, Nancy G Isern, David W Hoyt, Andrew K Marcus, Dae-Wook Kang, Michael D Crowell, Bruce E Rittmann, Rosa Krajmalnik-Brown
Roux-en-Y gastric bypass (RYGB) and laparoscopic adjustable gastric banding (LAGB) are anatomically different bariatric operations. RYGB achieves greater weight loss compared with LAGB. Changes in the gut microbiome have been documented after RYGB, but not LAGB, and the microbial contribution to sustainable surgical weight loss warrants further evaluation. We hypothesized that RYGB imposes greater changes on the microbiota and its metabolism than LAGB, and that the altered microbiota may contribute to greater weight loss...
May 26, 2017: ISME Journal
https://www.readbyqxmd.com/read/28544881/mammalian-systems-biotechnology-reveals-global-cellular-adaptations-in-a-recombinant-cho-cell-line
#2
Faraaz Noor Khan Yusufi, Meiyappan Lakshmanan, Ying Swan Ho, Bernard Liat Wen Loo, Pramila Ariyaratne, Yuansheng Yang, Say Kong Ng, Tessa Rui Min Tan, Hock Chuan Yeo, Hsueh Lee Lim, Sze Wai Ng, Ai Ping Hiu, Chung Ping Chow, Corrine Wan, Shuwen Chen, Gavin Teo, Gao Song, Ju Xin Chin, Xiaoan Ruan, Ken Wing Kin Sung, Wei-Shou Hu, Miranda Gek Sim Yap, Muriel Bardor, Niranjan Nagarajan, Dong-Yup Lee
Effective development of host cells for therapeutic protein production is hampered by the poor characterization of cellular transfection. Here, we employed a multi-omics-based systems biotechnology approach to elucidate the genotypic and phenotypic differences between a wild-type and recombinant antibody-producing Chinese hamster ovary (CHO) cell line. At the genomic level, we observed extensive rearrangements in specific targeted loci linked to transgene integration sites. Transcriptional re-wiring of DNA damage repair and cellular metabolism in the antibody producer, via changes in gene copy numbers, was also detected...
May 24, 2017: Cell Systems
https://www.readbyqxmd.com/read/28539364/integrative-proteomics-and-biochemical-analyses-define-ptc6p-as-the-saccharomyces-cerevisiae-pyruvate-dehydrogenase-phosphatase
#3
Xiao Guo, Natalie M Niemi, Joshua J Coon, Dave J Pagliarini
The pyruvate dehydrogenase complex (PDC) is the primary metabolic checkpoint connecting glycolysis and mitochondrial oxidative phosphorylation, and is important for maintaining cellular and organismal glucose homeostasis. Phosphorylation of the PDC E1 subunit was identified as a key inhibitory modification in bovine tissue approximately 50 years ago, and this regulatory process is now known to be conserved throughout evolution. Although Saccharomyces cerevisiae is a pervasive model organism for investigating cellular metabolism and its regulation by signaling processes, the phosphatase(s) responsible for activating the PDC in S...
May 24, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28531195/livestock-metabolomics-and-the-livestock-metabolome-a-systematic-review
#4
Seyed Ali Goldansaz, An Chi Guo, Tanvir Sajed, Michael A Steele, Graham S Plastow, David S Wishart
Metabolomics uses advanced analytical chemistry techniques to comprehensively measure large numbers of small molecule metabolites in cells, tissues and biofluids. The ability to rapidly detect and quantify hundreds or even thousands of metabolites within a single sample is helping scientists paint a far more complete picture of system-wide metabolism and biology. Metabolomics is also allowing researchers to focus on measuring the end-products of complex, hard-to-decipher genetic, epigenetic and environmental interactions...
2017: PloS One
https://www.readbyqxmd.com/read/28530140/associations-of-nasopharyngeal-metabolome-and-microbiome-with-severity-among-infants-with-bronchiolitis-a-multi-omic-analysis
#5
Christopher J Stewart, Jonathan M Mansbach, Matthew C Wong, Nadim J Ajami, Joseph F Petrosino, Carlos A Camargo, Kohei Hasegawa
RATIONALE: Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, while emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity. OBJECTIVES: To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis...
May 21, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28521733/nfpscanner-a-webtool-for-knowledge-based-deciphering-of-biomedical-networks
#6
Wenjian Xu, Yang Cao, Ziwei Xie, Haochen He, Song He, Hao Hong, Xiaochen Bo, Fei Li
BACKGROUND: Many biological pathways have been created to represent different types of knowledge, such as genetic interactions, metabolic reactions, and gene-regulating and physical-binding relationships. Biologists are using a wide range of omics data to elaborately construct various context-specific differential molecular networks. However, they cannot easily gain insight into unfamiliar gene networks with the tools that are currently available for pathways resource and network analysis...
May 18, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28503089/anticancer-chemodiversity-of-ranunculaceae-medicinal-plants-molecular-mechanisms-and-functions
#7
REVIEW
Da-Cheng Hao, Chun-Nian He, Jie Shen, Pei-Gen Xiao
The buttercup family, Ranunculaceae, comprising more than 2,200 species in at least 62 genera, mostly herbs, has long been used in folk medicine and worldwide ethnomedicine since the beginning of human civilization. Various medicinal phytometabolites have been found in Ranunculaceae plants, many of which, such as alkaloids, terpenoids, saponins, and polysaccharides, have shown anti-cancer activities in vitro and in vivo. Most concerns have been raised for two epiphany molecules, the monoterpene thymoquinone and the isoquinoline alkaloid berberine...
February 2017: Current Genomics
https://www.readbyqxmd.com/read/28500387/thermal-adaptation-strategies-of-the-extremophile-bacterium-thermus-filiformis-based-on-multi-omics-analysis
#8
F Mandelli, M B Couger, D A A Paixão, C B Machado, C M Carnielli, J A Aricetti, I Polikarpov, R Prade, C Caldana, A F Paes Leme, A Z Mercadante, D M Riaño-Pachón, Fabio Marcio Squina
Thermus filiformis is an aerobic thermophilic bacterium isolated from a hot spring in New Zealand. The experimental study of the mechanisms of thermal adaptation is important to unveil response strategies of the microorganism to stress. In this study, the main pathways involved on T. filiformis thermoadaptation, as well as, thermozymes with potential biotechnological applications were revealed based on omics approaches. The strategy adopted in this study disclosed that pathways related to the carbohydrate metabolism were affected in response to thermoadaptation...
May 12, 2017: Extremophiles: Life Under Extreme Conditions
https://www.readbyqxmd.com/read/28491041/describing-the-diapause-preparatory-proteome-of-the-beetle-colaphellus-bowringi-and-identifying-candidates-affecting-lipid-accumulation-using-isobaric-tags-for-mass-spectrometry-based-proteome-quantification-itraq
#9
Qian-Qian Tan, Wen Liu, Fen Zhu, Chao-Liang Lei, Daniel A Hahn, Xiao-Ping Wang
Prior to entering diapause, insects must prepare themselves physiologically to withstand the stresses of arresting their development for a lengthy period. While studies describing the biochemical and cellular milieu of the maintenance phase of diapause are accumulating, few studies have taken an "omics" approach to describing molecular events during the diapause preparatory phase. We used isobaric tags and mass spectrometry (iTRAQ) to quantitatively compare the expression profiles of proteins identified during the onset of diapause preparation phase in the heads of adult female cabbage beetles, Colaphellus bowringi...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28482123/integrative-analysis-of-transcriptomic-and-metabolomic-data-via-sparse-canonical-correlation-analysis-with-incorporation-of-biological-information
#10
Sandra E Safo, Shuzhao Li, Qi Long
Integrative analysis of high dimensional omics data is becoming increasingly popular. At the same time, incorporating known functional relationships among variables in analysis of omics data has been shown to help elucidate underlying mechanisms for complex diseases. In this article, our goal is to assess association between transcriptomic and metabolomic data from a Predictive Health Institute (PHI) study that includes healthy adults at a high risk of developing cardiovascular diseases. Adopting a strategy that is both data-driven and knowledge-based, we develop statistical methods for sparse canonical correlation analysis (CCA) with incorporation of known biological information...
May 8, 2017: Biometrics
https://www.readbyqxmd.com/read/28467922/metabolic-flexibility-in-health-and-disease
#11
REVIEW
Bret H Goodpaster, Lauren M Sparks
Metabolic flexibility is the ability to respond or adapt to conditional changes in metabolic demand. This broad concept has been propagated to explain insulin resistance and mechanisms governing fuel selection between glucose and fatty acids, highlighting the metabolic inflexibility of obesity and type 2 diabetes. In parallel, contemporary exercise physiology research has helped to identify potential mechanisms underlying altered fuel metabolism in obesity and diabetes. Advances in "omics" technologies have further stimulated additional basic and clinical-translational research to further interrogate mechanisms for improved metabolic flexibility in skeletal muscle and adipose tissue with the goal of preventing and treating metabolic disease...
May 2, 2017: Cell Metabolism
https://www.readbyqxmd.com/read/28467501/metabolomic-profiling-of-ascending-thoracic-aortic-aneurysms-and-dissections-implications-for-pathophysiology-and-biomarker-discovery
#12
Christian Doppler, Kathrin Arnhard, Julia Dumfarth, Katharina Heinz, Barbara Messner, Christian Stern, Therese Koal, Kristaps Klavins, Katarina Danzl, Florian Pitterl, Michael Grimm, Herbert Oberacher, David Bernhard
OBJECTIVE: Our basic understanding of ascending thoracic aortic aneurysm (ATAA) pathogenesis is still very limited, hampering early diagnosis, risk prediction, and development of treatment options. "Omics"-technologies, ideal to reveal tissue alterations from the normal physiological state due to disease have hardly been applied in the field. Using a metabolomic approach, with this study the authors seek to define tissue differences between controls and various forms of ATAAs. METHODS: Using a targeted FIA-MS/MS metabolomics approach, we analysed and compared the metabolic profiles of ascending thoracic aortic wall tissue of age-matched controls (n = 8), bicuspid aortic valve-associated aneurysms (BAV-A; n = 9), tricuspid aortic valve-associated aneurysms (TAV-A; n = 14), and tricuspid aortic valve-associated aortic dissections (TAV-Diss; n = 6)...
2017: PloS One
https://www.readbyqxmd.com/read/28467092/metabolomics-proteomics-combined-approach-identifies-differential-metabolism-associated-molecular-events-between-senescence-and-apoptosis
#13
Mengqiu Wu, Hui Ye, Chang Shao, Xiao Zheng, Qingran Li, Lin Wang, Min Zhao, Gaoyuan Lu, Baoqiang Chen, Jun Zhang, Yun Wang, Guangji Wang, Haiping Hao
Apoptosis and senescence are two types of cell fates in response to chemotherapy. Besides canonical pathways that mediate cell fates, cancer cell metabolism has been revealed as a crucial factor affecting cell fate decisions and thus represents a new target for antitumor therapy. Therefore, a comprehensive description of metabolic pathways underlying cell senescence and apoptosis in response to chemotherapy is highly demanded for therapeutic exploitation of both processes. Herein we employed a metabolomics-proteomics combined approach to identify metabolism-associated molecular events that mediate cellular responses to senescence and apoptosis using doxorubicin-treated human breast cancer cells MCF7 as models...
May 10, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28466490/local-and-regional-control-of-calcium-dynamics-in-the-pancreatic-islet
#14
REVIEW
Guy A Rutter, David J Hodson, Pauline Chabosseau, Elizabeth Haythorne, Timothy J Pullen, Isabelle Leclerc
Ca(2+) is the key intracellular regulator of insulin secretion, acting in the beta cell as the ultimate trigger for exocytosis. In response to high glucose, ATP-sensitive K(+) channel closure and plasma membrane depolarisation engage a sophisticated machinery to drive pulsatile cytosolic Ca(2+) changes. Voltage-gated Ca(2+) channels, Ca(2+) -activated K(+) channels and Na(+) /Ca(2+) exchange all play important roles. The use of targeted Ca(2+) probes has revealed that during each cytosolic Ca(2+) pulse, uptake of Ca(2+) by mitochondria, endoplasmic reticulum (ER), secretory granules and lysosomes fine-tune cytosolic Ca(2+) dynamics and control organellar function...
May 3, 2017: Diabetes, Obesity & Metabolism
https://www.readbyqxmd.com/read/28454561/a-comprehensive-multi-omics-approach-uncovers-adaptations-for-growth-and-survival-of-pseudomonas-aeruginosa-on-n-alkanes
#15
Sarah L Grady, Stephanie A Malfatti, Thusitha S Gunasekera, Brian K Dalley, Matt G Lyman, Richard C Striebich, Michael B Mayhew, Carol L Zhou, Oscar N Ruiz, Larry C Dugan
BACKGROUND: Examination of complex biological systems has long been achieved through methodical investigation of the system's individual components. While informative, this strategy often leads to inappropriate conclusions about the system as a whole. With the advent of high-throughput "omic" technologies, however, researchers can now simultaneously analyze an entire system at the level of molecule (DNA, RNA, protein, metabolite) and process (transcription, translation, enzyme catalysis)...
April 28, 2017: BMC Genomics
https://www.readbyqxmd.com/read/28454513/mycbase-a-database-of-functional-sites-and-biochemical-properties-of-myc-in-both-normal-and-cancer-cells
#16
Debangana Chakravorty, Tanmoy Jana, Sukhen Das Mandal, Anuradha Seth, Anubrata Bhattacharya, Sudipto Saha
BACKGROUND: Myc is an essential gene having multiple functions such as in cell growth, differentiation, apoptosis, genomic stability, angiogenesis, and disease biology. A large number of researchers dedicated to Myc biology are generating a substantial amount of data in normal and cancer cells/tissues including Burkitt's lymphoma and ovarian cancer. RESULTS: MYCbase ( http://bicresources.jcbose.ac.in/ssaha4/mycbase ) is a collection of experimentally supported functional sites in Myc that can influence the biological cellular processes...
April 28, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28450578/integrated-assessment-of-diclofenac-biotransformation-pharmacokinetics-and-omics-based-toxicity-in-a-3d-human-liver-immunocompetent-co-culture-system
#17
Ujjal Sarkar, Kodihalli C Ravindra, Emma Large, Carissa L Young, Dinelia Rivera-Burgos, Jiajie Yu, Murat Cirit, David J Hughes, John S Wishnok, Douglas A Lauffenburger, Linda G Griffith, Steven R Tannenbaum
In vitro hepatocyte culture systems have inherent limitations in capturing known human drug toxicities that arise from complex immune responses. Therefore, we established and characterized a liver immuno-competent co-culture model and evaluated diclofenac (DCF) metabolic profiles, in vitro-in vivo clearance correlations, toxicological responses, and acute phase responses using liquid chromatography tandem mass spectrometry. DCF biotransformation was assessed after 48 h of culture, and the major phase I and II metabolites were similar to the in vivo DCF metabolism profile in humans...
April 27, 2017: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/28450497/integrating-3-omics-data-analyze-rat-lung-tissue-of-copd-states-and-medical-intervention-by-delineation-of-molecular-and-pathway-alterations
#18
Jiansheng Li, Peng Zhao, Liping Yang, Ya Li, Yange Tian, Suyun Li
Chronic obstructive pulmonary disease (COPD) is a serious health problem. However, molecular pathogenesis of COPD remains unknown. Here, we explored the molecular effects of cigarette smoke and bacterial infection in lung tissues of COPD rats. We also investigated therapeutic effects of aminophylline (APL) on the COPD rats, and integrated transcriptome, proteome, and metabolome data for a global view of molecular mechanisms of COPD progression. Using molecular function and pathway analyses, the genes and proteins regulated in COPD and APL-treated rats were mainly attributed to oxidoreductase, antioxidant activity, energy and fatty acid metabolism...
April 27, 2017: Bioscience Reports
https://www.readbyqxmd.com/read/28450214/omics-analysis-of-human-bone-to-identify-genes-and-molecular-networks-regulating-skeletal-remodeling-in-health-and-disease
#19
REVIEW
Sjur Reppe, Harish K Datta, Kaare M Gautvik
The skeleton is a metabolically active organ throughout life where specific bone cell activity and paracrine/endocrine factors regulate its morphogenesis and remodeling. In recent years, an increasing number of reports have used multi-omics technologies to characterize subsets of bone biological molecular networks. The skeleton is affected by primary and secondary disease, lifestyle and many drugs. Therefore, to obtain relevant and reliable data from well characterized patient and control cohorts are vital...
April 24, 2017: Bone
https://www.readbyqxmd.com/read/28449662/an-integrated-rnaseq-1-h-nmr-metabolomics-approach-to-understand-soybean-primary-metabolism-regulation-in-response-to-rhizoctonia-foliar-blight-disease
#20
Tanya R Copley, Konstantinos A Aliferis, Daniel J Kliebenstein, Suha H Jabaji
BACKGROUND: Rhizoctonia solani AG1-IA is a devastating phytopathogen causing Rhizoctonia foliar blight (RFB) of soybean worldwide with yield losses reaching 60%. Plant defense mechanisms are complex and information from different metabolic pathways is required to thoroughly understand plant defense regulation and function. Combining information from different "omics" levels such as transcriptomics, metabolomics, and proteomics is required to gain insights into plant metabolism and its regulation...
April 27, 2017: BMC Plant Biology
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