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https://www.readbyqxmd.com/read/28729385/pyqms-enables-universal-and-accurate-quantification-of-mass-spectrometry-data
#1
Johannes Leufken, Anna Niehues, Peter Sarin, Florian Wessel, Michael Hippler, Sebastian A Leidel, Christian Fufezan
Quantitative mass spectrometry (MS) is a key technique in many research areas (1), including proteomics, metabolomics, glycomics, and lipidomics. Because all of the corresponding molecules can be described by chemical formulas, universal quantification tools are highly desirable. Here we present pyQms, an open-source software for accurate quantification of all types of molecules measurable by MS. pyQms uses isotope pattern matching which offers an accurate quality assessment of all quantifications and the ability to directly incorporate mass spectrometer accuracy...
July 20, 2017: Molecular & Cellular Proteomics: MCP
https://www.readbyqxmd.com/read/28728066/baseline-serum-phosphatidylcholine-plasmalogen-concentrations-are-inversely-associated-with-incident-myocardial-infarction-in-patients-with-mixed-peripheral-artery-disease-presentations
#2
Joseph V Moxon, Rhondda E Jones, Gerard Wong, Jacquelyn M Weir, Natalie A Mellett, Bronwyn A Kingwell, Peter J Meikle, Jonathan Golledge
BACKGROUND AND AIMS: Despite current best care, patients with peripheral artery disease (PAD) remain at high risk of myocardial infarction, and biomarkers to more accurately assess cardiovascular risk are needed. This study assessed the relationship between the serum lipidome and incident myocardial infarction in a cohort of PAD patients. METHODS: 265 PAD patients were followed up for a median of 23 months, during which 18 people suffered a myocardial infarction...
June 29, 2017: Atherosclerosis
https://www.readbyqxmd.com/read/28725670/fatty-acid-and-lipidomic-data-in-normal-and-tumor-colon-tissues-of-rats-fed-diets-with-and-without-fish-oil
#3
Zora Djuric, Muhammad Nadeem Aslam, Becky R Simon, Ananda Sen, Yan Jiang, Jianwei Ren, Rena Chan, Tanu Soni, Thekkelnaycke M Rajendiran, William L Smith, Dean E Brenner
Data is provided to show the detailed fatty acid and lipidomic composition of normal and tumor rat colon tissues. Rats were fed either a Western fat diet or a fish oil diet, and half the rats from each diet group were treated with chemical carcinogens that induce colon cancer (azoxymethane and dextran sodium sulfate). The data show total fatty acid profiles of sera and of all the colon tissues, namely normal tissue from control rats and both normal and tumor tissues from carcinogen-treated rats, as obtained by gas chromatography with mass spectral detection...
August 2017: Data in Brief
https://www.readbyqxmd.com/read/28724694/role-of-long-chain-acyl-coas-in-the-regulation-of-mycolic-acid-biosynthesis-in-mycobacteria
#4
Yi Ting Tsai, Valentina Salzman, Matías Cabruja, Gabriela Gago, Hugo Gramajo
One of the dominant features of the biology of Mycobacterium tuberculosis, and other mycobacteria, is the mycobacterial cell envelope with its exceptional complex composition. Mycolic acids are major and very specific components of the cell envelope and play a key role in its architecture and impermeability. Biosynthesis of mycolic acid (MA) precursors requires two types of fatty acid synthases, FAS I and FAS II, which should work in concert in order to keep lipid homeostasis tightly regulated. Both FAS systems are regulated at their transcriptional level by specific regulatory proteins...
July 2017: Open Biology
https://www.readbyqxmd.com/read/28717896/optimization-of-lipid-extraction-and-analytical-protocols-for-uhplc-esi-hrms-based-lipidomic-analysis-of-adherent-mammalian-cancer-cells
#5
Huizhen Zhang, Yue Gao, Jiahong Sun, Shicheng Fan, Xinpeng Yao, Xiaorong Ran, Chuanqi Zheng, Min Huang, Huichang Bi
Lipidomics, which reveals comprehensive characterization of molecular lipids, is a rapidly growing technology used in biomedical research. Lipid extraction is a critical step in lipidomic analysis. However, the effectiveness of different lipid extract solvent systems from cellular samples still remains unclear. In the current study, the protocol of reverse-phase liquid chromatography mass spectrometry (LC/MS)-based lipidomics was optimized for extraction and detection of lipids from human pancreatic cancer cell line PANC-1...
July 17, 2017: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/28710072/circulating-acylcarnitine-profile-in-human-heart-failure-a-surrogate-of-fatty-acid-metabolic-dysregulation-in-mitochondria-and-beyond
#6
Matthieu Ruiz, Francois Labarthe, Annik Fortier, Bertrand Bouchard, Julie Thompson Legault, Virginie Bolduc, Odile Rigal, Jane Chen, Anique Ducharme, Peter A Crawford, Jean-Claude Tardif, Christine Des Rosiers
Heart failure (HF) is associated with metabolic perturbations, particularly of fatty acids (FA), which remain to be better understood in humans. This study aimed at testing the hypothesis that HF patients with reduced ejection fraction, display systemic perturbations in levels of energy-related metabolites, especially those reflecting dysregulation of FA metabolism, namely acylcarnitines (ACs). Circulating metabolites were assessed using mass spectrometry (MS)-based methods in two cohorts. The main cohort consisted of 72 controls and 68 HF patients, exhibiting depressed left ventricular ejection fraction (25...
July 14, 2017: American Journal of Physiology. Heart and Circulatory Physiology
https://www.readbyqxmd.com/read/28708380/a-novel-strategy-for-quantitative-analysis-of-isomeric-bis-monoacylglycero-phosphate-and-phosphatidylglycerol-species-by-shotgun-lipidomics-after-one-step-methylation
#7
Miao Wang, Juan Pablo Palavicini, Adam Cseresznye, Xianlin Han
Understanding the cellular function and metabolism of bis(monoacylglycero)phosphate (BMP), an important but low abundance class of phospholipids, has been hindered due to its difficulties to be resolved from its structural isomer (i.e., phosphatidylglycerol, PG, another low abundance class of phospholipids). A novel strategy for quantitative analysis of BMP and PG species was developed after one-step methylation of lipid extracts in combination with high mass accuracy/resolution mass spectrometry after direct infusion (i...
July 14, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28706218/patch-clamp-assisted-single-neuron-lipidomics
#8
Collin B Merrill, Abdul Basit, Andrea Armirotti, Yousheng Jia, Christine M Gall, Gary Lynch, Daniele Piomelli
Our understanding of the physiological and pathological functions of brain lipids is limited by the inability to analyze these molecules at cellular resolution. Here, we present a method that enables the detection of lipids in identified single neurons from live mammalian brains. Neuronal cell bodies are captured from perfused mouse brain slices by patch clamping, and lipids are analyzed using an optimized nanoflow liquid chromatography/mass spectrometry protocol. In a first application of the method, we identified more than 40 lipid species from dentate gyrus granule cells and CA1 pyramidal neurons of the hippocampus...
July 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28702319/grandpaternal-induced-transgenerational-dietary-reprogramming-of-the-unfolded-protein-response-in-skeletal-muscle
#9
Petter S Alm, Thais de Castro Barbosa, Romain Barrès, Anna Krook, Juleen R Zierath
OBJECTIVE: Parental nutrition and lifestyle impact the metabolic phenotype of the offspring. We have reported that grandpaternal chronic high-fat diet (HFD) transgenerationally impairs glucose metabolism in subsequent generations. Here we determined whether grandpaternal diet transgenerationally impacts the transcriptome and lipidome in skeletal muscle. Our aim was to identify tissue-specific pathways involved in transgenerational inheritance of environmental-induced phenotypes. METHODS: F0 male Sprague-Dawley rats were fed a HFD or chow for 12 weeks before breeding with chow-fed females to generate the F1 generation...
July 2017: Molecular Metabolism
https://www.readbyqxmd.com/read/28698403/identifying-mitotane-induced-mitochondria-associated-membranes-dysfunctions-metabolomic-and-lipidomic-approaches
#10
Ségolène Hescot, Larbi Amazit, Marie Lhomme, Simon Travers, Anais DuBow, Stéphanie Battini, Geoffrey Boulate, Izzie Jacques Namer, Anne Lombès, Anatol Kontush, Alessio Imperiale, Eric Baudin, Marc Lombès
Mitotane (o,p'DDD), the most effective drug in adrenocortical carcinoma, concentrates into the mitochondria and impacts mitochondrial functions. To address the molecular mechanisms of mitotane action and to identify its potential target, metabolomic and lipidomic approaches as well as imaging analyses were employed in human adrenocortical H295R cells allowing identification of Mitochondria-Associated Membranes dysfunction as a critical impact of mitotane. Study of intracellular energetic metabolites by NMR spectroscopy showed that mitotane significantly decreased aspartate while concomitantly increased glutamate content in a time- and concentration-dependent manner...
July 4, 2017: Oncotarget
https://www.readbyqxmd.com/read/28697812/imaging-and-lipidomics-methods-for-lipid-analysis-in-metabolic-and-cardiovascular-disease
#11
K G Stevens, C A Bader, A Sorvina, D A Brooks, S E Plush, J L Morrison
Cardiometabolic diseases exhibit changes in lipid biology, which is important as lipids have critical roles in membrane architecture, signalling, hormone synthesis, homoeostasis and metabolism. However, Developmental Origins of Health and Disease studies of cardiometabolic disease rarely include analysis of lipids. This short review highlights some examples of lipid pathology and then explores the technology available for analysing lipids, focussing on the need to develop imaging modalities for intracellular lipids...
July 12, 2017: Journal of Developmental Origins of Health and Disease
https://www.readbyqxmd.com/read/28694404/-the-role-of-omics-technology-in-the-pathophysiology-diagnosis-and-treatment-of-cardiovascular-diseases
#12
Ümit Yaşar Sinan, Serkan Unlu
Although evident improvement has occurred in the diagnosis and treatment of cardiovascular disease (CVD), it is still the most important cause of mortality worldwide. The majority of the CVDs are multifactorial and polygenic. Therefore, it is logical to use genomics, proteomics, lipidomics, and metabolomics together for diagnosis and effective treatment of CVD. "Genome" is the combination of the words "gene" and "chromosome," and includes all protein-coding genes and intergenic spaces (as well as intragenic regions, or introns, within genes) in an organism...
July 2017: Türk Kardiyoloji Derneği Arşivi: Türk Kardiyoloji Derneğinin Yayın Organıdır
https://www.readbyqxmd.com/read/28694327/efficacy-of-nutritional-interventions-to-lower-circulating-ceramides-in-young-adults-fruvedomic-pilot-study
#13
Alice T Mathews, Oluremi A Famodu, Melissa D Olfert, Pamela J Murray, Christopher F Cuff, Marianne T Downes, Norman J Haughey, Sarah E Colby, Paul D Chantler, I Mark Olfert, Joseph W McFadden
The 2010 USDA Dietary Guidelines for Americans (DGA) recommends a diet largely composed of fruit and vegetables. Consuming a diet high in fruit and vegetables and low in refined carbohydrates and saturated fat may reduce an individual's risk for type 2 diabetes, nonalcoholic fatty liver disease, low-grade chronic inflammation, and metabolic syndrome (MetS). Several recent studies have implicated the bioactive sphingolipid ceramide as an associative and causative biomarker for the development of these conditions...
July 2017: Physiological Reports
https://www.readbyqxmd.com/read/28693421/lipidmatch-an-automated-workflow-for-rule-based-lipid-identification-using-untargeted-high-resolution-tandem-mass-spectrometry-data
#14
Jeremy P Koelmel, Nicholas M Kroeger, Candice Z Ulmer, John A Bowden, Rainey E Patterson, Jason A Cochran, Christopher W W Beecher, Timothy J Garrett, Richard A Yost
BACKGROUND: Lipids are ubiquitous and serve numerous biological functions; thus lipids have been shown to have great potential as candidates for elucidating biomarkers and pathway perturbations associated with disease. Methods expanding coverage of the lipidome increase the likelihood of biomarker discovery and could lead to more comprehensive understanding of disease etiology. RESULTS: We introduce LipidMatch, an R-based tool for lipid identification for liquid chromatography tandem mass spectrometry workflows...
July 10, 2017: BMC Bioinformatics
https://www.readbyqxmd.com/read/28689763/remodeling-of-brain-lipidome-in-methamphetamine-sensitized-mice
#15
Linhong Jiang, Hui Gu, Yiyun Lin, Wei Xu, Ruiming Zhu, Jueying Kong, Li Luo, Hailei Long, Bing Liu, Bo Chen, Yinglan Zhao, Xiaobo Cen
Lipids are predominant components of the brain and key regulators for neural structure and function. The effect of methamphetamine (METH) on behavior, cognition as well as memory has been intensively investigated; however, the impact of METH on brain lipid profiles is largely unknown. Here, we used a global lipidomic approach to investigate brain lipidome of METH-sensitized mice. We found that repeated METH significantly modified the lipidome in the hippocampus, prefrontal cortex (PFC) and striatum. Interestingly, nucleus accumbens showed no obvious alteration in lipidomic profiling...
July 6, 2017: Toxicology Letters
https://www.readbyqxmd.com/read/28688796/fatty-acid-based-lipidomics-and-membrane-remodeling-induced-by-apoe3-and-apoe4-in-human-neuroblastoma-cells
#16
Paraskevi Prasinou, Ioannis Dafnis, Giorgia Giacometti, Carla Ferreri, Angeliki Chroni, Chryssostomos Chatgilialoglu
Apolipoprotein E (apoE) is a major lipid carrier of the lipoprotein transport system that plays critical roles in various pathologies. Human apoE has three common isoforms, the apoE4 being associated with Alzheimer's disease. This is the first study in the literature investigating the effects of apoE (apoE3 and apoE4 isoforms) on membrane fatty acid profile in neuroblastoma SK-N-SH cells. Fatty acid analyses were carried out by gas chromatography of the corresponding methyl esters (FAME). We observed the occurrence of membrane fatty acid remodeling in the presence of each of the two apoE isoforms...
July 6, 2017: Biochimica et Biophysica Acta
https://www.readbyqxmd.com/read/28687674/anti-inflammatory-%C3%AF-3-endocannabinoid-epoxides
#17
Daniel R McDougle, Josephine E Watson, Amr A Abdeen, Reheman Adili, Megan P Caputo, John E Krapf, Rodney W Johnson, Kristopher A Kilian, Michael Holinstat, Aditi Das
Clinical studies suggest that diets rich in ω-3 polyunsaturated fatty acids (PUFAs) provide beneficial anti-inflammatory effects, in part through their conversion to bioactive metabolites. Here we report on the endogenous production of a previously unknown class of ω-3 PUFA-derived lipid metabolites that originate from the crosstalk between endocannabinoid and cytochrome P450 (CYP) epoxygenase metabolic pathways. The ω-3 endocannabinoid epoxides are derived from docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA) to form epoxyeicosatetraenoic acid-ethanolamide (EEQ-EA) and epoxydocosapentaenoic acid-ethanolamide (EDP-EA), respectively...
July 7, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28687611/vitamin-a-regulates-akt-signaling-through-the-phospholipid-fatty-acid-composition
#18
Helmut Pein, Solveigh C Koeberle, Maria Voelkel, Freya Schneider, Antonietta Rossi, Maria Thürmer, Konstantin Loeser, Lidia Sautebin, Helen Morrison, Oliver Werz, Andreas Koeberle
Protein kinases, including the serine/threonine kinase Akt, mediate manifold bioactivities of vitamin A, although the mechanisms behind the sustained kinase activation are diffuse. To investigate the role of cellular lipids as targetable factors in Akt signaling, we combined mass spectrometry-based lipidomics with immunologic detection of Akt (Ser473) phosphorylation. A screening campaign revealed retinol (vitamin A alcohol) and all-trans retinoic acid (vitamin A acid) (RA) as hits that time-dependently (≥24 h) deplete phosphatidylcholine-bound polyunsaturated fatty acids (PUFA-PCs) from NIH-3T3 mouse fibroblasts while inducing Akt activation (EC50 ≈ 0...
July 7, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
https://www.readbyqxmd.com/read/28683964/detrimental-effect-of-hypercholesterolemia-on-high-density-lipoprotein-particle-remodeling%C3%A2-in%C3%A2-pigs
#19
Teresa Padró, Judit Cubedo, Sandra Camino, Maria Teresa Béjar, Soumaya Ben-Aicha, Guiomar Mendieta, Joan Carles Escolà-Gil, Rafael Escate, Manuel Gutiérrez, Laura Casani, Lina Badimon, Gemma Vilahur
BACKGROUND: Beneficial effects of high-density lipoproteins (HDL) seem altered in patients with symptomatic cardiovascular disease. We recently demonstrated in a swine model of ischemia-reperfusion (IR) that hypercholesterolemia abolishes HDL-related cardioprotection. OBJECTIVES: This study sought to investigate, using the same animal model, whether the reported impairment of HDL cardioprotective function was associated with alterations in HDL remodeling and functionality...
July 11, 2017: Journal of the American College of Cardiology
https://www.readbyqxmd.com/read/28679548/zebrafish-lipid-droplets-regulate-embryonic-atp-homeostasis-to-power-early-development
#20
Asmita Dutta, Deepak Kumar Sinha
In zebrafish embryos, the maternally supplied pool of ATP is insufficient to power even the earliest of developmental events (0-3 hpf) such as oocyte-to-embryo transition (OET). The embryos generate an additional pulse (2.5 h long) of ATP (1.25-4 hpf) to achieve the embryonic ATP homeostasis. We demonstrate that the additional pulse of ATP is needed for successful execution of OET. The maternally supplied yolk lipids play a crucial role in maintaining the embryonic ATP homeostasis. In this paper, we identify the source and trafficking routes of free fatty acids (FFAs) that feed the mitochondria for synthesis of ATP...
July 2017: Open Biology
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