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Omics metabolism

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https://www.readbyqxmd.com/read/28650854/recent-developments-in-deuterium-oxide-tracer-approaches-to-measure-rates-of-substrate-turnover-implications-for-protein-lipid-and-nucleic-acid-research
#1
Matthew S Brook, Daniel J Wilkinson, Philip J Atherton, Ken Smith
PURPOSE OF REVIEW: Methods that inform on dynamic metabolism that can be applied to clinical populations to understand disease progression and responses to therapeutic interventions are of great importance. This review perspective will highlight recent advances, development, and applications of the multivalent stable isotope tracer deuterium oxide (D2O) to the study of substrate metabolism with particular reference to protein, lipids, and nucleic acids, and how these methods can be readily applied within clinical and pharmaceutical research...
June 24, 2017: Current Opinion in Clinical Nutrition and Metabolic Care
https://www.readbyqxmd.com/read/28649285/introduction-of-the-diagene-study-clinical-characteristics-pathophysiology-and-determinants-of-vascular-complications-of-type-2-diabetes
#2
Thijs T W van Herpt, Roosmarijn F H Lemmers, Mandy van Hoek, Janneke G Langendonk, Ronald J Erdtsieck, Bert Bravenboer, Annelies Lucas, Monique T Mulder, Harm R Haak, Aloysius G Lieverse, Eric J G Sijbrands
BACKGROUND: Type 2 diabetes is a major healthcare problem. Glucose-, lipid-, and blood pressure-lowering strategies decrease the risk of micro- and macrovascular complications. However, a substantial residual risk remains. To unravel the etiology of type 2 diabetes and its complications, large-scale, well-phenotyped studies with prospective follow-up are needed. This is the goal of the DiaGene study. In this manuscript, we describe the design and baseline characteristics of the study...
2017: Diabetology & Metabolic Syndrome
https://www.readbyqxmd.com/read/28647896/omics-based-hybrid-prediction-in-maize
#3
Matthias Westhues, Tobias A Schrag, Claas Heuer, Georg Thaller, H Friedrich Utz, Wolfgang Schipprack, Alexander Thiemann, Felix Seifert, Anita Ehret, Armin Schlereth, Mark Stitt, Zoran Nikoloski, Lothar Willmitzer, Chris C Schön, Stefan Scholten, Albrecht E Melchinger
Complementing genomic data with other "omics" predictors can increase the probability of success for predicting the best hybrid combinations using complex agronomic traits. Accurate prediction of traits with complex genetic architecture is crucial for selecting superior candidates in animal and plant breeding and for guiding decisions in personalized medicine. Whole-genome prediction has revolutionized these areas but has inherent limitations in incorporating intricate epistatic interactions. Downstream "omics" data are expected to integrate interactions within and between different biological strata and provide the opportunity to improve trait prediction...
June 24, 2017: TAG. Theoretical and Applied Genetics. Theoretische und Angewandte Genetik
https://www.readbyqxmd.com/read/28646205/comparative-nanouplc-ms-e-analysis-between-magainin-i-susceptible-and-resistant-escherichia-coli-strains
#4
Marlon H Cardoso, Keyla C de Almeida, Elizabete de S Cândido, André M Murad, Simoni C Dias, Octávio L Franco
In recent years the antimicrobial peptides (AMPs) have been prospected and designed as new alternatives to conventional antibiotics. Indeed, AMPs have presented great potential toward pathogenic bacterial strains by means of complex mechanisms of action. However, reports have increasingly emerged regarding the mechanisms by which bacteria resist AMP administration. In this context, we performed a comparative proteomic study by using the total bacterial lysate of magainin I-susceptible and -resistant E. coli strains...
June 23, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28646024/metabolic-reprogramming-via-ppar%C3%AE-signaling-in-cardiac-hypertrophy-and-failure-from-metabolomics-to-epigenetics
#5
Junco Shibayama Warren, Shin-Ichi Oka, Daniela Zablocki, Junichi Sadoshima
Studies using -omics-based approaches have advanced our knowledge of metabolic remodeling in cardiac hypertrophy and failure. Metabolomic analysis of the failing heart has revealed global changes in mitochondrial substrate metabolism. Peroxisome proliferator-activated receptor alpha (PPARα) plays a critical role in synergistic regulation of cardiac metabolism through transcriptional control. Metabolic reprogramming via PPARα signaling in heart failure ultimately propagates into myocardial energetics. However, emerging evidence suggests that the expression level of PPARα per se does not always explain the energetic state in the heart...
June 23, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28645581/improvement-of-isopropanol-tolerance-of-escherichia-coli-using-adaptive-laboratory-evolution-and-omics-technologies
#6
Takaaki Horinouchi, Aki Sakai, Hazuki Kotani, Kumi Tanabe, Chikara Furusawa
Isopropanol (IPA) is the secondary alcohol that can be dehydrated to yield propylene. To produce IPA using microorganisms, a significant issue is that the toxicity of IPA causes retardation or inhibition of cell growth, decreasing the yield. One possible strategy to overcome this problem is to improve IPA tolerance of production organisms. For the understanding of tolerance to IPA, we performed parallel adaptive laboratory evolution (ALE) of Escherichia coli under IPA stress. To identify the genotypic change during ALE, we performed genome re-sequencing analyses of obtained tolerant strains...
June 20, 2017: Journal of Biotechnology
https://www.readbyqxmd.com/read/28642845/metabolic-adaptations-of-uropathogenic-e-coli-in-the-urinary-tract
#7
REVIEW
Riti Mann, Daniel G Mediati, Iain G Duggin, Elizabeth J Harry, Amy L Bottomley
Escherichia coli ordinarily resides in the lower gastrointestinal tract in humans, but some strains, known as Uropathogenic E. coli (UPEC), are also adapted to the relatively harsh environment of the urinary tract. Infections of the urine, bladder and kidneys by UPEC may lead to potentially fatal bloodstream infections. To survive this range of conditions, UPEC strains must have broad and flexible metabolic capabilities and efficiently utilize scarce essential nutrients. Whole-organism (or "omics") methods have recently provided significant advances in our understanding of the importance of metabolic adaptation in the success of UPECs...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28636311/insights-into-integrated-lead-generation-and-target-identification-in-malaria-and-tuberculosis-drug-discovery
#8
John Okombo, Kelly Chibale
New, safe and effective drugs are urgently needed to treat and control malaria and tuberculosis, which affect millions of people annually. However, financial return on investment in the poor settings where these diseases are mostly prevalent is very minimal to support market-driven drug discovery and development. Moreover, the imminent loss of therapeutic lifespan of existing therapies due to evolution and spread of drug resistance further compounds the urgency to identify novel effective drugs. However, the advent of new public-private partnerships focused on tropical diseases and the recent release of large data sets by pharmaceutical companies on antimalarial and antituberculosis compounds derived from phenotypic whole cell high throughput screening have spurred renewed interest and opened new frontiers in malaria and tuberculosis drug discovery...
June 21, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28634240/leucine-biosynthesis-is-involved-in-regulating-high-lipid-accumulation-in-yarrowia-lipolytica
#9
Eduard J Kerkhoven, Young-Mo Kim, Siwei Wei, Carrie D Nicora, Thomas L Fillmore, Samuel O Purvine, Bobbie-Jo Webb-Robertson, Richard D Smith, Scott E Baker, Thomas O Metz, Jens Nielsen
The yeast Yarrowia lipolytica is a potent accumulator of lipids, and lipogenesis in this organism can be influenced by a variety of factors, such as genetics and environmental conditions. Using a multifactorial study, we elucidated the effects of both genetic and environmental factors on regulation of lipogenesis in Y. lipolytica and identified how two opposite regulatory states both result in lipid accumulation. This study involved comparison of a strain overexpressing diacylglycerol acyltransferase (DGA1) with a control strain grown under either nitrogen or carbon limitation conditions...
June 20, 2017: MBio
https://www.readbyqxmd.com/read/28632769/combining-omics-and-microscopy-to-visualize-interactions-between-the-asian-citrus-psyllid-vector-and-the-huanglongbing-pathogen-candidatus-liberibacter-asiaticus-in-the-insect-gut
#10
Angela Kruse, Somayeh Fattah-Hosseini, Surya Saha, Richard Johnson, EricaRose Warwick, Kasie Sturgeon, Lukas Mueller, Michael J MacCoss, Robert G Shatters, Michelle Cilia Heck
Huanglongbing, or citrus greening disease, is an economically devastating bacterial disease of citrus. It is associated with infection by the gram-negative bacterium Candidatus Liberibacter asiaticus (CLas). CLas is transmitted by Diaphorina citri, the Asian citrus psyllid (ACP). For insect transmission to occur, CLas must be ingested during feeding on infected phloem sap and cross the gut barrier to gain entry into the insect vector. To investigate the effects of CLas exposure at the gut-pathogen interface, we performed RNAseq and mass spectrometry-based proteomics to analyze the transcriptome and proteome, respectively, of ACP gut tissue...
2017: PloS One
https://www.readbyqxmd.com/read/28628359/the-genetic-basis-for-sex-differences-in-obesity-and-lipid-metabolism
#11
Jenny C Link, Karen Reue
Men and women exhibit significant differences in obesity, cardiovascular disease, and diabetes. To provide better diagnosis and treatment for both sexes, it is important to identify factors that underlie the observed sex differences. Traditionally, sex differences have been attributed to the differential effects of male and female gonadal secretions (commonly referred to as sex hormones), which substantially influence many aspects of metabolism and related diseases. Less appreciated as a contributor to sex differences are the fundamental genetic differences between males and females, which are ultimately determined by the presence of an XX or XY sex chromosome complement...
June 19, 2017: Annual Review of Nutrition
https://www.readbyqxmd.com/read/28627424/channeling-in-native-microbial-pathways-implications-and-challenges-for-metabolic-engineering
#12
REVIEW
Mary H Abernathy, Lian He, Yinjie J Tang
Intracellular enzymes can be organized into a variety of assemblies, shuttling intermediates from one active site to the next. Eukaryotic compartmentalization within mitochondrion and peroxisomes and substrate tunneling within multi-enzyme complexes have been well recognized. Intriguingly, the central pathways in prokaryotes may also form extensive channels, including the heavily branched glycolysis pathway. In vivo channeling through cascade enzymes is difficult to directly measure, but can be inferred from in vitro tests, reaction thermodynamics, transport/reaction modeling, analysis of molecular diffusion and protein interactions, or steady state/dynamic isotopic labeling...
June 13, 2017: Biotechnology Advances
https://www.readbyqxmd.com/read/28622780/-iron-metabolism
#13
S Vaulont
Iron is an essential trace element ensuring many functions in the body. However, excess iron can be toxic with deleterious consequences on function and tissue integrity. The understanding of the molecular and cellular mechanisms allowing iron level to be kept at physiological concentration has greatly progressed in recent years, in particular with the identification of the iron-regulatory hormone, hepcidin and its receptor ferroportin, the sole iron exporter known to date. This discovery has improved our ability to diagnose and manage iron disorders and offered new therapeutic perspectives for an important class of human diseases...
May 2017: Archives de Pédiatrie: Organe Officiel de la Sociéte Française de Pédiatrie
https://www.readbyqxmd.com/read/28618245/multi-omics-integrative-investigation-of-fatty-acid-metabolism-in-obese-and-lean-subcutaneous-tissue
#14
Flavia Badoud, Dyanne Brewer, Armen Charchoglyan, Daniel J Cuthbertson, David M Mutch
White adipose tissue (WAT) plays a central role in whole-body energy homeostasis through storage and release of fatty acids. A deeper understanding of the complex and highly integrated pathways regulating WAT fatty acid metabolism, and how they are altered with obesity, is necessary for diagnostic and therapeutic innovations in nutritional disorders. In this multi-omics study, we investigated the influence of obesity on fatty acid metabolism in human subcutaneous adipose tissue (SAT) using an approach that integrated transcriptomic, peptidomic, and fatty acid analyses...
June 15, 2017: Omics: a Journal of Integrative Biology
https://www.readbyqxmd.com/read/28618012/metabolomic-signature-of-brain-cancer
#15
Renu Pandey, Laura Caflisch, Alessia Lodi, Andrew J Brenner, Stefano Tiziani
Despite advances in surgery and adjuvant therapy, brain tumours represent one of the leading causes of cancer-related mortality and morbidity in both adults and children. Gliomas constitute about 60% of all cerebral tumours, showing varying degrees of malignancy. They are difficult to treat due to dismal prognosis and limited therapeutics. Metabolomics is the untargeted and targeted analyses of endogenous and exogenous small molecules, which characterizes the phenotype of an individual. This emerging "omics" science provides functional readouts of cellular activity that contribute greatly to the understanding of cancer biology including brain tumour biology...
June 15, 2017: Molecular Carcinogenesis
https://www.readbyqxmd.com/read/28617414/obesity
#16
REVIEW
Pedro González-Muniesa, Miguel-Angel Mártinez-González, Frank B Hu, Jean-Pierre Després, Yuji Matsuzawa, Ruth J F Loos, Luis A Moreno, George A Bray, J Alfredo Martinez
Excessive fat deposition in obesity has a multifactorial aetiology, but is widely considered the result of disequilibrium between energy intake and expenditure. Despite specific public health policies and individual treatment efforts to combat the obesity epidemic, >2 billion people worldwide are overweight or obese. The central nervous system circuitry, fuel turnover and metabolism as well as adipose tissue homeostasis are important to comprehend excessive weight gain and associated comorbidities. Obesity has a profound impact on quality of life, even in seemingly healthy individuals...
June 15, 2017: Nature Reviews. Disease Primers
https://www.readbyqxmd.com/read/28614363/rigid-geometry-solves-curse-of-dimensionality-effects-in-clustering-methods-an-application-to-omics-data
#17
Shun Adachi
The quality of samples preserved long term at ultralow temperatures has not been adequately studied. To improve our understanding, we need a strategy to analyze protein degradation and metabolism at subfreezing temperatures. To do this, we obtained liquid chromatography-mass spectrometry (LC/MS) data of calculated protein signal intensities in HEK-293 cells. Our first attempt at directly clustering the values failed, most likely due to the so-called "curse of dimensionality". The clusters were not reproducible, and the outputs differed with different methods...
2017: PloS One
https://www.readbyqxmd.com/read/28602082/linking-genes-to-microbial-biogeochemical-cycling-lessons-from-arsenic
#18
Yong-Guan Zhu, Xi-Mei Xue, Andreas Kappler, Barry P Rosen, Andrew A Meharg
The biotransformation of arsenic is highly relevant to the arsenic biogeochemical cycle. Identification of the molecular details of microbial pathways of arsenic biotransformation coupled with analyses of microbial communities by meta-omics can provide insights into detailed aspects of the complexities of this biocycle. Arsenic transformations couple to other biogeochemical cycles, and to the fate of both nutrients and other toxic environmental contaminants. Microbial redox metabolism of iron, carbon, sulfur and nitrogen affects the redox and bioavailability of arsenic species...
June 11, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28596717/integration-of-metabolomic-and-transcriptomic-networks-in-pregnant-women-reveals-biological-pathways-and-predictive-signatures-associated-with-preeclampsia
#19
Rachel S Kelly, Damien C Croteau-Chonka, Amber Dahlin, Hooman Mirzakhani, Ann C Wu, Emily S Wan, Michael J McGeachie, Weiliang Qiu, Joanne E Sordillo, Amal Al-Garawi, Kathryn J Gray, Thomas F McElrath, Vincent J Carey, Clary B Clish, Augusto A Litonjua, Scott T Weiss, Jessica A Lasky-Su
INTRODUCTION: Preeclampsia is a leading cause of maternal and fetal mortality worldwide, yet its exact pathogenesis remains elusive. OBJECTIVES: This study, nested within the Vitamin D Antenatal Asthma Reduction Trial (VDAART), aimed to develop integrated omics models of preeclampsia that have utility in both prediction and in the elucidation of underlying biological mechanisms. METHODS: Metabolomic profiling was performed on first trimester plasma samples of 47 pregnant women from VDAART who subsequently developed preeclampsia and 62 controls with healthy pregnancies, using liquid-chromatography tandem mass-spectrometry...
January 2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/28591626/multi-level-omics-analysis-provides-insight-to-the-ignicoccus-hospitalis-nanoarchaeum-equitans-association
#20
Rachel A Rawle, Timothy Hamerly, Brian P Tripet, Richard J Giannone, Louie Wurch, Robert L Hettich, Mircea Podar, Valerie Copié, Brian Bothner
BACKGROUND: Studies of interspecies interactions are inherently difficult due to the complex mechanisms which enable these relationships. A model system for studying interspecies interactions is the marine hyperthermophiles Ignicoccus hospitalis and Nanoarchaeum equitans. Recent independently-conducted 'omics' analyses have generated insights into the molecular factors modulating this association. However, significant questions remain about the nature of the interactions between these archaea...
June 4, 2017: Biochimica et Biophysica Acta
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