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Lipidomics

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https://www.readbyqxmd.com/read/29138692/transcriptomics-driven-lipidomics-tdl-identifies-the-microbiome-regulated-targets-of-ileal-lipid-metabolism
#1
Anirikh Chakrabarti, Mathieu Membrez, Delphine Morin-Rivron, Jay Siddharth, Chieh Jason Chou, Hugues Henry, Stephen Bruce, Sylviane Metairon, Frederic Raymond, Bertrand Betrisey, Carole Loyer, Scott J Parkinson, Mojgan Masoodi
The gut microbiome and lipid metabolism are both recognized as essential components in the maintenance of metabolic health. The mechanisms involved are multifactorial and (especially for microbiome) poorly defined. A strategic approach to investigate the complexity of the microbial influence on lipid metabolism would facilitate determination of relevant molecular mechanisms for microbiome-targeted therapeutics. E. coli is associated with obesity and metabolic syndrome and we used this association in conjunction with gnotobiotic models to investigate the impact of E...
2017: NPJ Systems Biology and Applications
https://www.readbyqxmd.com/read/29138414/potential-application-of-1-h-nmr-for-routine-serum-lipidome-analysis-evaluation-of-effects-of-bariatric-surgery
#2
Adriana Mika, Zbigniew Kaczynski, Piotr Stepnowski, Maciej Kaczor, Monika Proczko-Stepaniak, Lukasz Kaska, Tomasz Sledzinski
Routine laboratory lipid assays include simple measurements of total cholesterol, triacylglycerols and HDL. However, lipids are a large group of compounds involved in many metabolic pathways, and their alterations may have serious health consequences. In this study, we used (1)H NMR to analyze lipids extracted from sera of 16 obese patients prior to and after bariatric surgeries. We observed a post-surgery decrease in serum concentrations of lipids from various groups. The hereby presented findings imply that (1)H NMR is suitable for rapid, simple and non-invasive detection of lipids from 30 structural groups, among them triacylglycerols, phosphatidylcholine, phosphatidylethanolamine, sphingomyelin, total phospholipids, total, free and esterified cholesterol, total and unsaturated fatty acids...
November 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29136824/assessment-of-potential-false-positives-via-orbitrap-based-untargeted-lipidomics-from-rat-tissues
#3
Lina Xu, Xueying Wang, Yupei Jiao, Xiaohui Liu
Untargeted lipidomics is increasingly popular due to the broad coverage of lipid species. Data dependent MS/MS acquisition is commonly used in order to acquire sufficient information for confident lipid assignment. However, although lipids are identified based on MS/MS confirmation, a number of false positives are still observed. Here, we discuss several causes of introducing lipid false identifications in untargeted analysis. Phosphotidylcholines and cholesteryl esters generate in-source fragmentation to produce dimethylated phosphotidylethanolamine and free cholesterol...
February 1, 2018: Talanta
https://www.readbyqxmd.com/read/29136580/advancing-the-large-scale-ccs-database-for-metabolomics-and-lipidomics-at-the-machine-learning-era
#4
REVIEW
Zhiwei Zhou, Jia Tu, Zheng-Jiang Zhu
Metabolomics and lipidomics aim to comprehensively measure the dynamic changes of all metabolites and lipids that are present in biological systems. The use of ion mobility-mass spectrometry (IM-MS) for metabolomics and lipidomics has facilitated the separation and the identification of metabolites and lipids in complex biological samples. The collision cross-section (CCS) value derived from IM-MS is a valuable physiochemical property for the unambiguous identification of metabolites and lipids. However, CCS values obtained from experimental measurement and computational modeling are limited available, which significantly restricts the application of IM-MS...
November 11, 2017: Current Opinion in Chemical Biology
https://www.readbyqxmd.com/read/29136239/changes-in-membrane-lipid-composition-and-function-accompanying-chilling-injury-in-bell-peppers
#5
Ximan Kong, Baodong Wei, Zhu Gao, Ying Zhou, Fei Shi, Xin Zhou, Qian Zhou, Shujuan Ji
Bell peppers are vulnerable to low temperature (below 7 °C) and subject to chilling injury (CI). To elucidate the relationship between cell membrane lipid composition and CI, a membrane lipidomic approach was carried out. In addition, we performed microstructural analysis and low-field nuclear magnetic resonance to better understand CI. We also monitored primary physiological metabolism parameters to explain lipidomics. Our study indicated that cellular structure damage was more serious at 4 °C, mostly represented by plasmalemma damage and plastid degradation...
November 9, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/29134469/erratum-to-mechanism-of-phospholipid-hydrolysis-for-oyster-crassostrea-plicatula-phospholipids-during-storage-using-shotgun-lipidomics
#6
Qinsheng Chen, Xincen Wang, Peixu Cong, Yanjun Liu, Yuming Wang, Jie Xu, Changhu Xue
Erratum to: Lipids https://doi.org/10.1007/s11745-017-4305-7.
November 13, 2017: Lipids
https://www.readbyqxmd.com/read/29134198/%C3%AF-3-polyunsaturated-fatty-acids-direct-differentiation-of-the-membrane-phenotype-in-mesenchymal-stem-cells-to-potentiate-osteogenesis
#7
Kandice R Levental, Michal A Surma, Allison D Skinkle, Joseph H Lorent, Yong Zhou, Christian Klose, Jeffrey T Chang, John F Hancock, Ilya Levental
Mammalian cells produce hundreds of dynamically regulated lipid species that are actively turned over and trafficked to produce functional membranes. These lipid repertoires are susceptible to perturbations from dietary sources, with potentially profound physiological consequences. However, neither the lipid repertoires of various cellular membranes, their modulation by dietary fats, nor their effects on cellular phenotypes have been widely explored. We report that differentiation of human mesenchymal stem cells (MSCs) into osteoblasts or adipocytes results in extensive remodeling of the plasma membrane (PM), producing cell-specific membrane compositions and biophysical properties...
November 2017: Science Advances
https://www.readbyqxmd.com/read/29132429/characterization-of-skin-function-associated-with-obesity-and-specific-correlation-to-local-systemic-parameters-in-american-women
#8
Shinobu Mori, Akiko Shiraishi, Karen Epplen, Desiree Butcher, Daiki Murase, Yuka Yasuda, Takatoshi Murase
BACKGROUND: Obesity is considered problematic not only as a major cause of diabetes, hypertension, and dyslipidemia, but also as a risk of intractable dermatosis; however influence of obesity on skin function has not been clarified. To clarify the mechanism of obesity-associated skin disorders, we aimed to characterize the skin function of subjects with obesity, and identify possible influencing factors. METHODS: Complex analyses including instrumental measurement, biochemical and lipidomics were performed for facial skin and physical evaluation in 93 Caucasian women with obesity (OB) and non-obesity (NOB)...
November 13, 2017: Lipids in Health and Disease
https://www.readbyqxmd.com/read/29130149/is-lipidomic-the-answer-to-the-search-of-a-biomarker-for-organ-preservation-protocol-in-head-and-neck-squamous-cell-carcinoma
#9
Ana Carolina Laus, Ismael Dale Cotrim Guerreiro da Silva, Fernanda Bertuccez Cordeiro, Edson Guimarães Lo Turco, Luciano de Souza Viana, André Lopes Carvalho
In the last decade organ preservation protocols based on chemoradiotherapy (CRT) has been showing the possibility of preserving function without jeopardizing survival for locally advanced head and neck squamous cell carcinoma (HNSCC). Still, only a percentage of the patients will benefit from this approach and, to date, no biomarkers are known to correctly predict these patients. More recently, modern mass spectrometry method has been used to determine metabolic profiles, and lipidomics, in particular, emerged as a new field of study in oncology and other diseases...
November 13, 2017: Pathology Oncology Research: POR
https://www.readbyqxmd.com/read/29129753/nitrogen-mustard-induced-corneal-injury-involves-the-sphingomyelin-ceramide-pathway
#10
Georgia Charkoftaki, James Jester, David Thompson, Vasilis Vasiliou
PURPOSE: Nitrogen mustard (NM), which simulates the effects of sulfur mustard (SM), is a potent vesicant known to cause irreversible corneal damage. This study investigates the mechanisms by which NM induces corneal damage by examining the impact of NM exposure on the morphology and lipidome of the cornea. METHODS: Intact ex vivo rabbit eyes were placed in serum-free DMEM organ culture. NM (0, 1, 2.5, 5 or 10 mg/ml) was applied to the central cornea for 5, 10 or 15 min using a 5 mm filter disk and subsequently rinsed with DMEM...
November 9, 2017: Ocular Surface
https://www.readbyqxmd.com/read/29126481/quantum-chemical-fragment-precursor-tests-accelerating-de-novo-annotation-of-tandem-mass-spectra
#11
Benjamin G Janesko, Li Li, Rodger Mensing
Tandem mass spectrometry is widely used to assign and distinguish chemical structures in proteomics, metabolomics, lipidomics, and many other areas. Spectral annotation remains a major bottleneck. Our "Quantum Chemical Fragment Precursor Tests" (QC-FPT) approach brings the accuracy and generality of modern quantum chemistry to combinatorial-search-based computer-aided spectral annotation. QC-FPT takes as input the dominant fragment peaks from a particular experiment, and one or more chemically reasonable hypotheses for the precursor ion's three-dimensional structure...
December 1, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29124854/thermoacclimation-and-genome-adaptation-of-the-membrane-lipidome-in-marine-synechococcus
#12
Justine Pittera, Juliette Jouhet, Solène Breton, Laurence Garczarek, Frédéric Partensky, Éric Maréchal, Ngoc An Nguyen, Hugo Doré, Morgane Ratin, Frances D Pitt, David J Scanlan, Christophe Six
The marine cyanobacteria of the genus Synechococcus are important primary producers, displaying a wide latitudinal distribution that is underpinned by diversification into temperature ecotypes. The physiological basis underlying these ecotypes is poorly known. In many organisms, regulation of membrane fluidity is crucial for acclimating to variations in temperature. Here, we reveal the detailed composition of the membrane lipidome of the model strain Synechococcus sp. WH7803 and its response to temperature variation...
November 10, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29123162/lpptiger-software-for-lipidome-specific-prediction-and-identification-of-oxidized-phospholipids-from-lc-ms-datasets
#13
Zhixu Ni, Georgia Angelidou, Ralf Hoffmann, Maria Fedorova
Oxidized phospholipids (oxPLs) have been recently recognized as important mediators of various and often controversial cellular functions and stress responses. Due to the low concentrations in vivo, oxPL detection is mostly performed by targeted mass spectrometry. Although significantly improving the sensitivity, this approach does not provide a comprehensive view on oxPLs required for understanding oxPL functional activities. While capable of providing information on the diversity of oxPLs, the main challenge of untargeted lipidomics is the absence of bioinformatics tools to support high-throughput identification of previously unconsidered, oxidized lipids...
November 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/29123078/high-performance-liquid-chromatography-mass-spectrometry-lc-ms-based-quantitative-lipidomics-study-of-ganglioside-nana-3-plasma-to-establish-its-association-with-parkinson-s-disease-patients
#14
Jinzhi Zhang, Xiao Zhang, Lijuan Wang, Caidi Yang
BACKGROUND It is well known that, pathologically, Parkinson's disease is a common neurodegenerative disorder. In Parkinson's disease, the protein which is abundant in the human brain, alpha-synuclein, accumulates inside the nerve cells. In this situation, dysregulation of lipid metabolism performs a crucial role; however, its association with Parkinson's disease is has not yet been explored. MATERIAL AND METHODS We performed a high-performance liquid chromatography-mass spectrometry-derived quantitative lipidomics study to analyze the profile of lipidomic plasma obtained from 170 PD patients and 120 controls, taken from our hospital...
November 10, 2017: Medical Science Monitor: International Medical Journal of Experimental and Clinical Research
https://www.readbyqxmd.com/read/29122727/gender-related-metabolomics-and-lipidomics-from-experimental-animal-models-to-clinical-evidence
#15
Matteo Audano, Mariateresa Maldini, Emma De Fabiani, Nico Mitro, Donatella Caruso
Lipidomics and metabolomics have emerged as important tools for the characterization of specific physiological and pathological traits. The selection of the analytical approaches and the choice of a targeted rather than an untargeted strategy in metabolomics find their reasons in the driving hypothesis of the study, sample features and instrumental availability. Moreover, in the last years, -omics approaches have found their application in the study of sex-related dimorphism. In this review, lipidomic and metabolomic analyses are presented in a biomedical perspective...
November 6, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/29117646/lipids-from-yeasts-and-fungi-physiology-production-and-analytical-considerations
#16
REVIEW
Maria Athenaki, Chryssavgi Gardeli, Panagiota Diamantopoulou, Sidoine Sadjeu Tchakouteu, Dimitris Sarris, Antonios Philippoussis, Seraphim Papanikolaou
The last years there has been a significant rise in the number of publications in the international literature that deal with the production lipids by microbial sources (the "single cell oils; SCOs" that are produced by the so-called "oleaginous" microorganisms). In the first part of the present review-article, a general overview of the oleaginous microorganisms (mostly yeasts, algae and fungi) and their potential upon the production of SCOs is presented. Thereafter, physiological and kinetic events related with the production of, mostly, yeast and fungal lipids when sugars and related substrates like polysaccharides, glycerol, etc (the "de novo" lipid accumulation process) or hydrophobic substrates like oils and fats (the "ex novo" lipid accumulation process) were employed as microbial carbon sources, are presented and critically discussed...
November 8, 2017: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/29113676/computational-lipidomics-of-the-neuronal-plasma-membrane
#17
Helgi I Ingólfsson, Timothy S Carpenter, Harsh Bhatia, Peer-Timo Bremer, Siewert J Marrink, Felice C Lightstone
Membrane lipid composition varies greatly within submembrane compartments, different organelle membranes, and also between cells of different cell stage, cell and tissue types, and organisms. Environmental factors (such as diet) also influence membrane composition. The membrane lipid composition is tightly regulated by the cell, maintaining a homeostasis that, if disrupted, can impair cell function and lead to disease. This is especially pronounced in the brain, where defects in lipid regulation are linked to various neurological diseases...
November 4, 2017: Biophysical Journal
https://www.readbyqxmd.com/read/29111762/metabolomics-and-lipidomics-profiling-of-a-combined-mitochondrial-plus-endoplasmic-reticulum-fraction-of-human-fibroblasts-a-robust-tool-for-clinical-studies
#18
Charlotte Veyrat-Durebex, Cinzia Bocca, Stéphanie Chupin, Judith Kouassi Nzoughet, Gilles Simard, Guy Lenaers, Pascal Reynier, Hélène Blasco
Mitochondria and endoplasmic reticulum (ER) are physically and functionally connected. This close interaction, via mitochondria-associated membranes, is increasingly explored and supports the importance of studying these two organelles as a whole. Metabolomics and lipidomics are powerful approaches for the exploration of metabolic pathways that may be useful to provide deeper information on these organelles' functions, dysfunctions, and interactions. We developed a quick and simple experimental procedure for the purification of a mitochondria-ER fraction from human fibroblasts...
November 14, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/29111682/monitoring-membrane-lipidome-turnover-by-metabolic-15-n-labeling-and-shotgun-ultra-high-resolution-orbitrap-ft-ms
#19
Kai Schuhmann, Kristina Srzentić, Konstantin O Nagornov, Henrik Thomas, Theresia Gutmann, Ünal Coskun, Yury O Tsybin, Andrej Shevchenko
Lipidomes undergo permanent extensive re-modelling, but how the turnover rate differs between lipid classes and molecular species is poorly understood. We employed metabolic (15)N-labeling and shotgun ultra-high resolution mass spectrometry (sUHR) to quantify the absolute (molar) abundance and determine the turnover rate of glycerophospho- and sphingolipids by the direct analysis of total lipid extracts. sUHR performed on a commercial Orbitrap Elite instrument at the mass resolution of 1.35×10(6) (m/z200) baseline resolved peaks of (13)C isotopes of unlabeled and monoisotopic peaks of (15)N-labeled lipids (Δm = 0...
November 7, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/29109428/serial-omics-of-p53-brca1-mouse-breast-tumor-and-normal-mammary-gland
#20
Susanne B Breitkopf, Mateus De Oliveira Taveira, Min Yuan, Gerburg M Wulf, John M Asara
This study demonstrates a liquid-liquid extraction for the sequential tandem mass spectrometry (LC-MS/MS) analysis of non-polar lipids, polar metabolites, proteins and phosphorylation sites from a single piece of tissue. Extraction of 10 mg BRCA-/-, p53-/- breast tumor tissue or normal mammary gland tissue with methyl-tert-butyl ether (MTBE) results in three phases: an upper non-polar phase containing 1,382 lipids, a lower polar phase with 805 metabolites and a precipitated protein pellet with 4,792 proteins with 1,072 phosphorylation sites...
November 6, 2017: Scientific Reports
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