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Walter Shaw - One of the best experts on this subject based on the ideXlab platform.
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a comprehensive classification system for Lipids
European Journal of Lipid Science and Technology, 2005Co-Authors: Eoin Fahy, Alfred H. Merrill, Christopher K Glass, David W. Russell, Shankar Subramaniam, Yousuke Seyama, Robert C. Murphy, Christian R H Raetz, Alex H Brown, Walter ShawAbstract:Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, “lipidomics,” in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about Lipids, a comprehensive classification of Lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide Lipids into eight categories (fatty acyls, glyceroLipids, glycerophosphoLipids, sphingoLipids, sterol Lipids, prenol Lipids, saccharoLipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual Lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of Lipids and their properties in a way that is compatible with other macromolecular databases.[Reprinted with copyright permission from the Journal of Lipid Research. 2005. 46: 839–861.]
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A comprehensive classification system for Lipids
Journal of Lipid Research, 2005Co-Authors: Edward Fahy, Alfred H. Merrill, H. Alex Brown, Christopher K Glass, David W. Russell, Shankar Subramaniam, Yousuke Seyama, Robert C. Murphy, Christian R H Raetz, Walter ShawAbstract:Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, "lipidomics," in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about Lipids, a comprehensive classification of Lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide Lipids into eight categories (fatty acyls, glyceroLipids, glycerophosphoLipids, sphingoLipids, sterol Lipids, prenol Lipids, saccharoLipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual Lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of Lipids and their properties in a way that is compatible with other macromolecular databases.
Robert C. Murphy - One of the best experts on this subject based on the ideXlab platform.
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spatial organization of Lipids in the human retina and optic nerve by maldi imaging mass spectrometry
Journal of Lipid Research, 2014Co-Authors: Karin Zemski A Berry, Robert C. Murphy, William C Gordon, Nicolas G BazanAbstract:MALDI imaging mass spectrometry (IMS) was used to characterize lipid species within sections of human eyes. Common phosphoLipids that are abundant in most tissues were not highly localized and observed throughout the accessory tissue, optic nerve, and retina. Triacylglycerols were highly localized in accessory tissue, whereas sulfatide and plasmalogen glycerophosphoethanolamine (PE) Lipids with a monounsaturated fatty acid were found enriched in the optic nerve. Additionally, several Lipids were associated solely with the inner retina, photoreceptors, or retinal pigment epithelium (RPE); a plasmalogen PE lipid containing DHA (22:6), PE(P-18:0/22:6), was present exclusively in the inner retina, and DHA-containing glycerophosphatidylcholine (PC) and PE Lipids were found solely in photoreceptors. PC Lipids containing very long chain (VLC)-PUFAs were detected in photoreceptors despite their low abundance in the retina. Ceramide Lipids and the bis-retinoid, N-retinylidene-N-retinylethanolamine, was tentatively identified and found only in the RPE. This MALDI IMS study readily revealed the location of many Lipids that have been associated with degenerative retinal diseases. Complex lipid localization within retinal tissue provides a global view of lipid organization and initial evidence for specific functions in localized regions, offering opportunities to assess their significance in retinal diseases, such as macular degeneration, where Lipids have been implicated in the disease process.
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a comprehensive classification system for Lipids
European Journal of Lipid Science and Technology, 2005Co-Authors: Eoin Fahy, Alfred H. Merrill, Christopher K Glass, David W. Russell, Shankar Subramaniam, Yousuke Seyama, Robert C. Murphy, Christian R H Raetz, Alex H Brown, Walter ShawAbstract:Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, “lipidomics,” in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about Lipids, a comprehensive classification of Lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide Lipids into eight categories (fatty acyls, glyceroLipids, glycerophosphoLipids, sphingoLipids, sterol Lipids, prenol Lipids, saccharoLipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual Lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of Lipids and their properties in a way that is compatible with other macromolecular databases.[Reprinted with copyright permission from the Journal of Lipid Research. 2005. 46: 839–861.]
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A comprehensive classification system for Lipids
Journal of Lipid Research, 2005Co-Authors: Edward Fahy, Alfred H. Merrill, H. Alex Brown, Christopher K Glass, David W. Russell, Shankar Subramaniam, Yousuke Seyama, Robert C. Murphy, Christian R H Raetz, Walter ShawAbstract:Lipids are produced, transported, and recognized by the concerted actions of numerous enzymes, binding proteins, and receptors. A comprehensive analysis of lipid molecules, "lipidomics," in the context of genomics and proteomics is crucial to understanding cellular physiology and pathology; consequently, lipid biology has become a major research target of the postgenomic revolution and systems biology. To facilitate international communication about Lipids, a comprehensive classification of Lipids with a common platform that is compatible with informatics requirements has been developed to deal with the massive amounts of data that will be generated by our lipid community. As an initial step in this development, we divide Lipids into eight categories (fatty acyls, glyceroLipids, glycerophosphoLipids, sphingoLipids, sterol Lipids, prenol Lipids, saccharoLipids, and polyketides) containing distinct classes and subclasses of molecules, devise a common manner of representing the chemical structures of individual Lipids and their derivatives, and provide a 12 digit identifier for each unique lipid molecule. The lipid classification scheme is chemically based and driven by the distinct hydrophobic and hydrophilic elements that compose the lipid. This structured vocabulary will facilitate the systematization of lipid biology and enable the cataloging of Lipids and their properties in a way that is compatible with other macromolecular databases.
Christoph Benning - One of the best experts on this subject based on the ideXlab platform.
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WITHDRAWN: Functional diversity of glycerolipid acylhydrolases in plant metabolism and physiology
Progress in Lipid Research, 2019Co-Authors: Kun Wang, Timothy P. Durrett, Christoph BenningAbstract:Abstract Most current knowledge about plant lipid metabolism has focused on the biosynthesis of Lipids and their transport between different organelles. However, lipid composition changes during development and in response to environmental cues often go beyond adjustments of lipid biosynthesis. When Lipids have to be removed to adjust the extent of membranes during down regulation of photosynthesis, or lipid composition has to be adjusted to alter the biophysical properties of membranes, or lipid derived chemical signals have to be produced, lipid-degrading enzymes come into play. This review focuses on glycerolipid acylhydrolases that remove acyl groups from glyceroLipids and will highlight their roles in lipid remodeling and lipid-derived signal generation. One emerging theme is that these enzymes are involved in the dynamic movement of acyl groups through different lipid pools, for example from polar membrane Lipids to neutral Lipids sequestered in lipid droplets during de novo triacylglycerol synthesis. Another example of acyl group sequestration in the form of triacylglycerols in lipid droplets is membrane lipid remodeling in response to abiotic stresses. Fatty acids released for membrane Lipids can also give rise to potent signaling molecules and acylhydrolases are therefore often the first step in initiating the formation of these lipid signals.
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functional diversity of glycerolipid acylhydrolases in plant metabolism and physiology
Progress in Lipid Research, 2019Co-Authors: Kun Wang, Timothy P. Durrett, Christoph BenningAbstract:Abstract Most current knowledge about plant lipid metabolism has focused on the biosynthesis of Lipids and their transport between different organelles. However, lipid composition changes during development and in response to environmental cues often go beyond adjustments of lipid biosynthesis. When Lipids have to be removed to adjust the extent of membranes during down regulation of photosynthesis, or lipid composition has to be adjusted to alter the biophysical properties of membranes, or lipid derived chemical signals have to be produced, lipid-degrading enzymes come into play. This review focuses on glycerolipid acylhydrolases that remove acyl groups from glyceroLipids and will highlight their roles in lipid remodeling and lipid-derived signal generation. One emerging theme is that these enzymes are involved in the dynamic movement of acyl groups through different lipid pools, for example from polar membrane Lipids to neutral Lipids sequestered in lipid droplets during de novo triacylglycerol synthesis. Another example of acyl group sequestration in the form of triacylglycerols in lipid droplets is membrane lipid remodeling in response to abiotic stresses. Fatty acids released for membrane Lipids can also give rise to potent signaling molecules and acylhydrolases are therefore often the first step in initiating the formation of these lipid signals.
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cellular organization and regulation of plant glycerolipid metabolism
Plant and Cell Physiology, 2019Co-Authors: Anastasiya Lavell, Christoph BenningAbstract:: Great strides have been made in understanding how membranes and lipid droplets are formed and maintained in land plants, yet much more is to be learned given the complexity of plant lipid metabolism. A complicating factor is the multi-organellar presence of biosynthetic enzymes and unique compositional requirements of different membrane systems. This necessitates a rich network of transporters and transport mechanisms that supply fatty acids, membrane Lipids and storage Lipids to their final cellular destination. Though we know a large number of the biosynthetic enzymes involved in lipid biosynthesis and a few transport proteins, the regulatory mechanisms, in particular, coordinating expression and/or activity of the majority remain yet to be described. Plants undergoing stress alter their membranes' compositions, and Lipids such as phosphatidic acid have been implicated in stress signaling. Additionally, lipid metabolism in chloroplasts supplies precursors for jasmonic acid (JA) biosynthesis, and perturbations in lipid homeostasis has consequences on JA signaling. In this review, several aspects of plant lipid metabolism are discussed that are currently under investigation: cellular transport of Lipids, regulation of lipid biosynthesis, roles of Lipids in stress signaling, and lastly the structural and oligomeric states of lipid enzymes.
Marqueño Bassols Anna - One of the best experts on this subject based on the ideXlab platform.
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Noves eines per a la detecció de disruptors lipídics i obesògens ambientals
'Edicions de la Universitat de Barcelona', 2021Co-Authors: Marqueño Bassols AnnaAbstract:La lipidòmica és una de les ciències òmiques més recents, que s’ha aplicat amb èxit en estudis mèdics per el descobriment de biomarcadors i d’alteracions en vies metabòliques associades a malalties. La seva aplicació en ciències ambientals està adquirint rellevància a causa de l’important paper dels lípids en el desenvolupament, creixement i reproducció dels metazous. A nivell cel·lular, els lípids estan implicats en l’emmagatzematge d’energia, la senyalització i presenten funcions estructurals. Els organismes contenen milers d'espècies de lípids diferents amb estructures bastant semblants. Els darrers avenços en l’espectrometria de masses han impulsat el camp de la lipidòmica, permetent una millor anotació de les espècies lipídiques de diferents matrius biològiques (cèl·lules, biofluids, teixits), però també la detecció d’alteracions com a resposta a l’exposició a contaminació química. En el marc d'aquesta tesi, s'han utilitzat tres tècniques analítiques diferents basades en espectrometria de masses d'alta resolució per a la caracterització del perfil lipídic de diferents models biològics. El primer mètode, anàlisi per injecció en flux acoblat a l’espectrometria de masses d'alta resolució, representa una eina molt potent ja que, en només dos minuts, proporciona el cribratge del perfil lipídic dels lípids cel·lulars. Els altres dos mètodes, que incorporen una cromatografia de líquids d’ultra alta eficàcia per a la separació prèvia dels lípids, han permès la detecció d’espècies minoritàries, i l’aplicació de l’espectrometria de masses en tàndem juntament amb un enfocament no dirigit per al processament de dades va proporcionar un perfil de lípids més exhaustiu, juntament amb la confirmació de la identitat dels lípids. Aquestes tècniques analítiques s’han utilitzat per a l’estudi de l’impacte de diversos contaminants ambientals, sobre el metabolisme de lípids tant en cèl·lules humanes com de peix. Entre els compostos químics estudiats s’inclouen additius de plàstics i els seus derivats (BPA, BPF, BADGE, BADGE·H2O, BADGE·2HCl), el compost obesogènic tributil d’estany, all- trans àcid retinoic, el progestagen sintètic drospirenona i una mescla complexa de contaminants ambientals (estudi de camp). Els models cel·lulars utilitzats en aquesta Tesi són cèl·lules de placenta humana (JEG-3), cèl·lules hepàtiques de peix zebra (ZFL) i/o en carcinoma hepatocel·lular de Poeciliopsis lucida (PLHC-1), mentre que per a la mescla complexa, es van mostrejar dues espècies de peixos sentinella en un riu seguint un gradent de contaminació. La lipidòmica, juntament amb la realització d'alguns assaigs toxicològics i l'ús de reacció en cadena de la polimerasa en temps real han permès traçar un escenari més complet dels efectes toxicològics dels productes químics estudiats. En general, aquesta Tesi pretén contribuir a la implementació de la lipidòmica en investigació mediambiental proposant models biològics útils i fluxos de treball per a la caracterització del mecanisme d’acció de contaminants ambientals amb la capacitat d’actuar com a disruptors lipídics.Lipidomics is one of the newest omics sciences, which has proven their utility in medical research for the discovery of biomarkers and altered metabolic pathways related to disease. Its application in environmental sciences is becoming relevant due to the important role of Lipids in development, maintenance, and reproduction of metazoans. At the cellular level, Lipids are involved in energy storage, signaling, and exhibit structural functions. Organisms contain thousands of different lipid species with rather similar structures. The latest advances in mass spectrometry have prompted the field of lipidomics, allowing a better annotation of the lipid species of different biological matrices (cells, biofluids, tissues), but also the detection of alterations as a response to chemical pollution exposure. Three analytical techniques based on high-resolution mass spectrometry have been used for the characterization of the lipid profile of different biological models. The first method, flow injection analysis coupled to high-resolution mass spectrometry represents a powerful tool since, just in two minutes, it provides a quick screening of the lipid profile of cellular Lipids. The other two methods, which incorporate ultra-high performance liquid chromatography for the previous separation of the Lipids, have allowed the detection of minority species, and the application of tandem mass spectrometry together with an untargeted approach for data processing provided a more comprehensive lipid profile, together with the confirmation of lipid identities. These analytical techniques have been used for the study of the impact of several widespread environmental pollutants on the lipid metabolism of both human and fish cell models, comprising plastic additives (BPA, BPF, BADGE, BADGE·H2O, BADGE·2HCl), the obesogenic compound tributyltin, all-trans retinoic acid, the synthetic progestin drospirenone and a complex mixture of environmental pollutants (field study). Lipidomics, together with some toxicological assays and the use of real-time polymerase chain reaction have allowed drawing a more complete scenario of the toxicological effects of the chemicals under study. Overall, this dissertation aims to contribute to the use of lipidomics in environmental research by proposing useful biological models and workflows for the characterization of the mode of action of environmental pollutants with the capability to act as lipid disruptor
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Noves eines per a la detecció de disruptors lipídics i obesògens ambientals
'Edicions de la Universitat de Barcelona', 2021Co-Authors: Marqueño Bassols AnnaAbstract:[cat] La lipidòmica és una de les ciències òmiques més recents, que s’ha aplicat amb èxit en estudis mèdics per el descobriment de biomarcadors i d’alteracions en vies metabòliques associades a malalties. La seva aplicació en ciències ambientals està adquirint rellevància a causa de l’important paper dels lípids en el desenvolupament, creixement i reproducció dels metazous. A nivell cel·lular, els lípids estan implicats en l’emmagatzematge d’energia, la senyalització i presenten funcions estructurals. Els organismes contenen milers d'espècies de lípids diferents amb estructures bastant semblants. Els darrers avenços en l’espectrometria de masses han impulsat el camp de la lipidòmica, permetent una millor anotació de les espècies lipídiques de diferents matrius biològiques (cèl·lules, biofluids, teixits), però també la detecció d’alteracions com a resposta a l’exposició a contaminació química. En el marc d'aquesta tesi, s'han utilitzat tres tècniques analítiques diferents basades en espectrometria de masses d'alta resolució per a la caracterització del perfil lipídic de diferents models biològics. El primer mètode, anàlisi per injecció en flux acoblat a l’espectrometria de masses d'alta resolució, representa una eina molt potent ja que, en només dos minuts, proporciona el cribratge del perfil lipídic dels lípids cel·lulars. Els altres dos mètodes, que incorporen una cromatografia de líquids d’ultra alta eficàcia per a la separació prèvia dels lípids, han permès la detecció d’espècies minoritàries, i l’aplicació de l’espectrometria de masses en tàndem juntament amb un enfocament no dirigit per al processament de dades va proporcionar un perfil de lípids més exhaustiu, juntament amb la confirmació de la identitat dels lípids. Aquestes tècniques analítiques s’han utilitzat per a l’estudi de l’impacte de diversos contaminants ambientals, sobre el metabolisme de lípids tant en cèl·lules humanes com de peix. Entre els compostos químics estudiats s’inclouen additius de plàstics i els seus derivats (BPA, BPF, BADGE, BADGE·H2O, BADGE·2HCl), el compost obesogènic tributil d’estany, all- trans àcid retinoic, el progestagen sintètic drospirenona i una mescla complexa de contaminants ambientals (estudi de camp). Els models cel·lulars utilitzats en aquesta Tesi són cèl·lules de placenta humana (JEG-3), cèl·lules hepàtiques de peix zebra (ZFL) i/o en carcinoma hepatocel·lular de Poeciliopsis lucida (PLHC-1), mentre que per a la mescla complexa, es van mostrejar dues espècies de peixos sentinella en un riu seguint un gradent de contaminació. La lipidòmica, juntament amb la realització d'alguns assaigs toxicològics i l'ús de reacció en cadena de la polimerasa en temps real han permès traçar un escenari més complet dels efectes toxicològics dels productes químics estudiats. En general, aquesta Tesi pretén contribuir a la implementació de la lipidòmica en investigació mediambiental proposant models biològics útils i fluxos de treball per a la caracterització del mecanisme d’acció de contaminants ambientals amb la capacitat d’actuar com a disruptors lipídics.[eng] Lipidomics is one of the newest omics sciences, which has proven their utility in medical research for the discovery of biomarkers and altered metabolic pathways related to disease. Its application in environmental sciences is becoming relevant due to the important role of Lipids in development, maintenance, and reproduction of metazoans. At the cellular level, Lipids are involved in energy storage, signaling, and exhibit structural functions. Organisms contain thousands of different lipid species with rather similar structures. The latest advances in mass spectrometry have prompted the field of lipidomics, allowing a better annotation of the lipid species of different biological matrices (cells, biofluids, tissues), but also the detection of alterations as a response to chemical pollution exposure. Three analytical techniques based on high-resolution mass spectrometry have been used for the characterization of the lipid profile of different biological models. The first method, flow injection analysis coupled to high-resolution mass spectrometry represents a powerful tool since, just in two minutes, it provides a quick screening of the lipid profile of cellular Lipids. The other two methods, which incorporate ultra-high performance liquid chromatography for the previous separation of the Lipids, have allowed the detection of minority species, and the application of tandem mass spectrometry together with an untargeted approach for data processing provided a more comprehensive lipid profile, together with the confirmation of lipid identities. These analytical techniques have been used for the study of the impact of several widespread environmental pollutants on the lipid metabolism of both human and fish cell models, comprising plastic additives (BPA, BPF, BADGE, BADGE·H2O, BADGE·2HCl), the obesogenic compound tributyltin, all-trans retinoic acid, the synthetic progestin drospirenone and a complex mixture of environmental pollutants (field study). Lipidomics, together with some toxicological assays and the use of real-time polymerase chain reaction have allowed drawing a more complete scenario of the toxicological effects of the chemicals under study. Overall, this dissertation aims to contribute to the use of lipidomics in environmental research by proposing useful biological models and workflows for the characterization of the mode of action of environmental pollutants with the capability to act as lipid disruptor
Derek Marsh - One of the best experts on this subject based on the ideXlab platform.
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Electron spin resonance in membrane research: protein–lipid interactions from challenging beginnings to state of the art
European Biophysics Journal, 2010Co-Authors: Derek MarshAbstract:Conventional electron paramagnetic resonance (EPR) spectra of Lipids that are spin-labelled close to the terminal methyl end of the acyl chains are able to resolve the Lipids directly contacting the protein from those in the fluid bilayer regions of the membrane. This allows determination of both the stoichiometry of lipid–protein interaction (i.e., number of lipid sites at the protein perimeter) and the selectivity of the protein for different lipid species (i.e., association constants relative to the background lipid). Spin-label EPR data are summarised for 20 or more different transmembrane peptides and proteins, and 7 distinct species of Lipids. Lineshape simulations of the two-component conventional spin-label EPR spectra allow estimation of the rate at which protein-associated Lipids exchange with those in the bulk fluid regions of the membrane. For Lipids that do not display a selectivity for the protein, the intrinsic off-rates for exchange are in the region of 10 MHz: less than 10× slower than the rates of diffusive exchange in fluid lipid membranes. Lipids with an affinity for the protein, relative to the background lipid, have off-rates for leaving the protein that are correspondingly slower. Non-linear EPR, which depends on saturation of the spectrum at high radiation intensities, is optimally sensitive to dynamics on the timescale of spin-lattice relaxation, i.e., the microsecond regime. Both progressive saturation and saturation transfer EPR experiments provide definitive evidence that Lipids at the protein interface are exchanging on this timescale. The sensitivity of non-linear EPR to low frequencies of spin exchange also allows the location of spin-labelled membrane protein residues relative to those of spin-labelled Lipids, in double-labelling experiments.
