Nomenclature Of Lipids Research Articles

Pilot Lipidomics Study of Copepods: Investigation of Potential Lipid-Based Biomarkers for the Early Detection and Quantification of the Biological Effects of Climate Change on the Oceanic Food Chain.

Maintenance of the health of our oceans is critical for the survival of the oceanic food chain upon which humanity is dependent. Zooplanktonic copepods are among the most numerous multicellular organisms on earth. As the base of the primary consumer food web, they constitute a major biomass in oceans, being an important food source for fish and functioning in the carbon cycle. The potential impact of climate change on copepod populations is an area of intense study. Omics technologies offer the potential to detect early metabolic alterations induced by the stresses of climate change. One such omics approach is lipidomics, which can accurately quantify changes in lipid pools serving structural, signal transduction, and energy roles. We utilized high-resolution mass spectrometry (≤2 ppm mass error) to characterize the lipidome of three different species of copepods in an effort to identify lipid-based biomarkers of copepod health and viability which are more sensitive than observational tools. With the establishment of such a lipid database, we will have an analytical platform useful for prospectively monitoring the lipidome of copepods in a planned long-term five-year ecological study of climate change on this oceanic sentinel species. The copepods examined in this pilot study included a North Atlantic species (Calanus finmarchicus) and two species from the Gulf of Mexico, one a filter feeder (Acartia tonsa) and one a hunter (Labidocerca aestiva). Our findings clearly indicate that the lipidomes of copepod species can vary greatly, supporting the need to obtain a broad snapshot of each unique lipidome in a long-term multigeneration prospective study of climate change. This is critical, since there may well be species-specific responses to the stressors of climate change and co-stressors such as pollution. While lipid nomenclature and biochemistry are extremely complex, it is not essential for all readers interested in climate change to understand all of the various lipid classes presented in this study. The clear message from this research is that we can monitor key copepod lipid families with high accuracy, and therefore potentially monitor lipid families that respond to environmental perturbations evoked by climate change.

LORA, Lipid Over-Representation Analysis Based on Structural Information.

With the increasing number of lipidomic studies, there is a need for an efficient and automated analysis of lipidomic data. One of the challenges faced by most existing approaches to lipidomic data analysis is lipid nomenclature. The systematic nomenclature of lipids contains all available information about the molecule, including its hierarchical representation, which can be used for statistical evaluation. The Lipid Over-Representation Analysis (LORA) web application (https://lora.metabolomics.fgu.cas.cz) analyzes this information using the Java-based Goslin framework, which translates lipid names into a standardized nomenclature. Goslin provides the level of lipid hierarchy, including information on headgroups, acyl chains, and their modifications, up to the "complete structure" level. LORA allows the user to upload the experimental query and reference data sets, select a grammar for lipid name normalization, and then process the data. The user can then interactively explore the results and perform lipid over-representation analysis based on selected criteria. The results are graphically visualized according to the lipidome hierarchy. The lipids present in the most over-represented terms (lipids with the highest number of enriched shared structural features) are defined as Very Important Lipids (VILs). For example, the main result of a demo data set is the information that the query is significantly enriched with "glycerophospholipids" containing "acyl 20:4" at the "sn-2 position". These terms define a set of VILs (e.g., PC 18:2/20:4;O and PE 16:0/20:4(5,8,10,14);OH). All results, graphs, and visualizations are summarized in a report. LORA is a tool focused on the smart mining of epilipidomics data sets to facilitate their interpretation at the molecular level.

Elucidation of Gut Microbiota-Associated Lipids Using LC-MS/MS and 16S rRNA Sequence Analyses.

SummaryHost-microbiota interactions create a unique metabolic milieu that modulates intestinal environments. Integration of 16S ribosomal RNA (rRNA) sequences and mass spectrometry (MS)-based lipidomics has a great potential to reveal the relationship between bacterial composition and the complex metabolic network in the gut. In this study, we conducted untargeted lipidomics followed by a feature-based molecular MS/MS spectral networking to characterize gut bacteria-dependent lipid subclasses in mice. An estimated 24.8% of lipid molecules in feces were microbiota-dependent, as judged by > 10-fold decrease in antibiotic-treated mice. Among these, there was a series of unique and microbiota-related lipid structures, including acyl alpha-hydroxyl fatty acid (AAHFA) that was newly identified in this study. Based on the integrated analysis of 985 lipid profiles and 16S rRNA sequence data providing 2,494 operational taxonomic units, we could successfully predict the bacterial species responsible for the biosynthesis of these unique lipids, including AAHFA.

Supercritical fluid chromatography for lipid analysis in foodstuffs.

The task of lipid analysis has always challenged separation scientists, and new techniques in chromatography were often developed for the separation of lipids; however, no single technique or methodology is yet capable of affording a comprehensive screening of all lipid species and classes. This review acquaints the role of supercritical fluid chromatography within the field of lipid analysis, from the early developed capillary separations based on pure CO2 , to the most recent techniques employing packed columns under subcritical conditions, including the niche multidimensional techniques using supercritical fluids in at least one of the separation dimensions. A short history of supercritical fluid chromatography will be introduced first, from its early popularity in the late 1980s, to the sudden fall and oblivion until the last decade, experiencing a regain of interest within the chromatographic community. Afterwards, the subject of lipid nomenclature and classification will be briefly dealt with, before discussing the main applications of supercritical fluid chromatography for food analysis, according to the specific class of lipids.

Characteristics of lipids and their feeding value in swine diets.

In livestock diets, energy is one of the most expensive nutritional components of feed formulation. Because lipids are a concentrated energy source, inclusion of lipids are known to affect growth rate and feed efficiency, but are also known to affect diet palatability, feed dustiness, and pellet quality. In reviewing the literature, the majority of research studies conducted on the subject of lipids have focused mainly on the effects of feeding presumably high quality lipids on growth performance, digestion, and metabolism in young animals. There is, however, the wide array of composition and quality differences among lipid sources available to the animal industry making it essential to understand differences in lipid composition and quality factors affecting their digestion and metabolism more fully. In addition there is often confusion in lipid nomenclature, measuring lipid content and composition, and evaluating quality factors necessary to understand the true feeding value to animals. Lastly, advances in understanding lipid digestion, post-absorption metabolism, and physiological processes (e.g., cell division and differentiation, immune function and inflammation); and in metabolic oxidative stress in the animal and lipid peroxidation, necessitates a more compressive assessment of factors affecting the value of lipid supplementation to livestock diets. The following review provides insight into lipid classification, digestion and absorption, lipid peroxidation indices, lipid quality and nutritional value, and antioxidants in growing pigs.

Spatial and temporal alterations of phospholipids determined by mass spectrometry during mouse embryo implantation

Molecular events involved in successful embryo implantation are not well understood. In this study, we used MALDI imaging mass spectrometry (IMS) technologies to characterize the spatial and temporal distribution of phospholipid species associated with mouse embryo implantation. Molecular images showing phospholipid distribution within implantation sites changed markedly between distinct cellular areas during days 4-8 of pregnancy. For example, by day 8, linoleate- and docosahexaenoate-containing phospholipids localized to regions destined to undergo cell death, whereas oleate-containing phospholipids localized to angiogenic regions. Arachidonate-containing phospholipids showed different segregation patterns depending on the lipid class, revealing a strong correlation of phosphatidylethanolamines and phosphatidylinositols with cytosolic phospholipase A(2alpha) and cyclooxygenase-2 during embryo implantation. LC-ESI-MS/MS was used to validate MALDI IMS phospholipid distribution patterns. Overall, molecular images revealed the dynamic complexity of lipid distributions in early pregnancy, signifying the importance of complex interplay of lipid molecules in uterine biology and implantation.

An editor for pathway drawing and data visualization in the Biopathways Workbench

BackgroundPathway models serve as the basis for much of systems biology. They are often built using programs designed for the purpose. Constructing new models generally requires simultaneous access to experimental data of diverse types, to databases of well-characterized biological compounds and molecular intermediates, and to reference model pathways. However, few if any software applications provide all such capabilities within a single user interface.ResultsThe Pathway Editor is a program written in the Java programming language that allows de-novo pathway creation and downloading of LIPID MAPS (Lipid Metabolites and Pathways Strategy) and KEGG lipid metabolic pathways, and of measured time-dependent changes to lipid components of metabolism. Accessed through Java Web Start, the program downloads pathways from the LIPID MAPS Pathway database (Pathway) as well as from the LIPID MAPS web server . Data arises from metabolomic (lipidomic), microarray, and protein array experiments performed by the LIPID MAPS consortium of laboratories and is arranged by experiment. Facility is provided to create, connect, and annotate nodes and processes on a drawing panel with reference to database objects and time course data. Node and interaction layout as well as data display may be configured in pathway diagrams as desired. Users may extend diagrams, and may also read and write data and non-lipidomic KEGG pathways to and from files. Pathway diagrams in XML format, containing database identifiers referencing specific compounds and experiments, can be saved to a local file for subsequent use. The program is built upon a library of classes, referred to as the Biopathways Workbench, that convert between different file formats and database objects. An example of this feature is provided in the form of read/construct/write access to models in SBML (Systems Biology Markup Language) contained in the local file system.ConclusionInclusion of access to multiple experimental data types and of pathway diagrams within a single interface, automatic updating through connectivity to an online database, and a focus on annotation, including reference to standardized lipid nomenclature as well as common lipid names, supports the view that the Pathway Editor represents a significant, practicable contribution to current pathway modeling tools.

An OWL-DL Ontology for Classification of Lipids

Lipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.

An OWL-DL Ontology for Classification of Lipids

AbstractLipids can be systematically classified according to functional properties, structural features, biochemical origin or biological system. However Lipid nomenclature has yet to become a robust research tool since no rigorous definitions exist for membership of specific lipid classes. Lipids need to be defined in a manner that is systematic yet at the same time semantically explicit. We report on the reuse of existing lipid nomenclature, ontology describing chemical structure and the extension of the OWL-DL Lipid Ontology to support the classification of lipid molecules. We applied definitions, DL-axioms, to describe lipids classes and illustrate suitability of the ontology for the classification of Fatty Acyl lipids and Mycolic acids.

Update of the LIPID MAPS comprehensive classification system for lipids

In 2005, the International Lipid Classification and Nomenclature Committee under the sponsorship of the LIPID MAPS Consortium developed and established a "Comprehensive Classification System for Lipids" based on well-defined chemical and biochemical principles and using an ontology that is extensible, flexible, and scalable. This classification system, which is compatible with contemporary databasing and informatics needs, has now been accepted internationally and widely adopted. In response to considerable attention and requests from lipid researchers from around the globe and in a variety of fields, the comprehensive classification system has undergone significant revisions over the last few years to more fully represent lipid structures from a wider variety of sources and to provide additional levels of detail as necessary. The details of this classification system are reviewed and updated and are presented here, along with revisions to its suggested nomenclature and structure-drawing recommendations for lipids.

Towards ontology-driven navigation of the lipid bibliosphere

BackgroundThe indexing of scientific literature and content is a relevant and contemporary requirement within life science information systems. Navigating information available in legacy formats continues to be a challenge both in enterprise and academic domains. The emergence of semantic web technologies and their fusion with artificial intelligence techniques has provided a new toolkit with which to address these data integration challenges. In the emerging field of lipidomics such navigation challenges are barriers to the translation of scientific results into actionable knowledge, critical to the treatment of diseases such as Alzheimer's syndrome, Mycobacterium infections and cancer.ResultsWe present a literature-driven workflow involving document delivery and natural language processing steps generating tagged sentences containing lipid, protein and disease names, which are instantiated to custom designed lipid ontology. We describe the design challenges in capturing lipid nomenclature, the mandate of the ontology and its role as query model in the navigation of the lipid bibliosphere. We illustrate the extent of the description logic-based A-box query capability provided by the instantiated ontology using a graphical query composer to query sentences describing lipid-protein and lipid-disease correlations.ConclusionAs scientists accept the need to readjust the manner in which we search for information and derive knowledge we illustrate a system that can constrain the literature explosion and knowledge navigation problems. Specifically we have focussed on solving this challenge for lipidomics researchers who have to deal with the lack of standardized vocabulary, differing classification schemes, and a wide array of synonyms before being able to derive scientific insights. The use of the OWL-DL variant of the Web Ontology Language (OWL) and description logic reasoning is pivotal in this regard, providing the lipid scientist with advanced query access to the results of text mining algorithms instantiated into the ontology. The visual query paradigm assists in the adoption of this technology.

A comprehensive classification system for lipids

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.

The 1st Congress of the International Society for the Study of Fatty Acids and Lipids (ISSFAL): fatty acids and lipids from cell biology to human disease.

The ISSFAL held its first congress on “Fatty Acids and Lipids from Cell Biology to Human Disease” in Lugano, Switzerland, June 30-July 3, 1993. Four hundred and fifty persons from 35 countries attended, and a total of 332 abstracts consisting of state-of-the:art reviews, critiques, and new data were presented at 13 plenary lectures, 10 major symposia, 10 oral communications sessions, and 14 poster sessions, covering topics such as Intracellular Communication; A New Look at Fatty Acids as Signal Transducing Molecules; Omega-3 Polyunsaturated Fatty Acids (PUFA) in the Rigulation of Cytokine Synthesis; The Role of Fatty Acids During Pregnancy and Lactation; Fatty Acids and Human Physiology; Cardiovascular System; Hypertension; Diabetes; Cancer; Inflammation and Immunology; PUFA and Antioxidants; a round table discussion on The Future of Fatty Acids in Human Nutrition; Health and Policy Implications; and a final session, chaired by Dr. A. P. Simopoulos, in which summary statements were presented by the session chairmen for general discussion. During this final session it was recommended that tram fatty acids should be labeled as such and should not be included with other fatty acids, such as saturates or PUFA. The need for standardization of fatty acid and lipid nomenclature was recognized, and at the Board meeting of ISSFAL, a scientific committee was appointed by the President, Dr. A. Leaf, to develop a position paper. The summary statements of the symposia appear below in an abbreviated form. The full statements are included in the Congress proceedings.

A database of lipid-phase transition temperatures and enthalpy changes

The systematic study of the mesomorphic phase properties of synthetic and biologically derived lipids began some 30 years ago. In the past decade, interest in this area has grown enormously. As a result, there exists a wealth of information on lipid phase behavior, but unfortunately, these data have, until now, been scattered throughout the literature in a variety of books, proceedings, and journals. The data have recently been compiled in a centralized database with a view to providing ready access to the same and to the appropriate literature. The compilation facilitates review of what has thus far been accomplished and highlights what remains to be done in this active research area. As such, it represents a convenient summary of the existing data which, when evaluated, will enable us to identify where deficits exist in the data, to reveal the fundamental physicochemical principles upon which lipid phase behavior is based, and to understand more completely lipid phase relations in biological, reconstituted, and formulated systems. The compilation consists of a tabulation of all known mesomorphic and polymorphic phase transition temperatures and enthalpy changes for synthetic and biologically derived lipids in the dry and in the partially and fully hydrated states. Also included is the effect on these thermodynamic values of pH, and of salt and metal ion concentration and other additives such as proteins, drugs, etc. The methods used in making the measurements and the experimental conditions are reported. Bibliographic information includes complete literature referencing and list of authors. As of this writing, the database is current through June 1990 and contains 9500 records. Each record contains 28 fields. Here, we describe how the database originated, its scope and contents, data abstraction procedures, and issues relating to mesophase and lipid nomenclature, data analysis, and evaluation, and database maintenance and distribution.

A database of lipid phase transition temperatures and enthalpy changes

The systematic study of the mesomorphic phase properties of synthetic and biologically derived lipids began some 30 years ago. In the past decade, interest in this area has grown enormously. As a result, there exists a wealth of information on lipid phase behavior, but unfortunately these data have, until now, been scattered throughout the literature in a variety of books, proceedings and journals, The data have recently been compiled in a centralized database with a view to providing ready access to same and to the appropriate literature. The compilation facilitates review of what has thus far been accomplished and highlights what remains to be done in this active research area. As such, it represents a convenient summary of the existing data which, when evaluated, will enable us to identify where deficits exist in the data, to reveal the fundamental physicochemical principles upon which lipid phase behavior is based and to understand more completely lipid phase relations in biological, reconstituted and formulated systems. The compilation consists of a tabulation of all known mesomorphic and polymorphic phase transition temperatures and enthalpy changes, for synthetic and biologically-derived lipids in the dry and in the partially and fully hydrated states. Also included is the effect on these thermodynamic values of pH, and of salt and metal ion concentration and other additives such as proteins, drugs, etc. The methods used in making the measurements and the experimental conditions are reported. Bibliographic information includes complete literature referencing and list of authors. As of this writing, the database is current through June, 1990 and contains in excess of 9500 records. Each record contains 28 fields. Here, we describe how the database originated, its scope and contents, data abstraction procedures, and issues relating to mesophase and lipid nomenclature, data analysis and evaluation, and database maintenance and distribution.

Numbering of atoms in myo‐inositol

A relaxation of previous recommendations on the numbering of the atoms of myo‐inositol is suggested: substituents need not necessarily be numbered so that the smallest possible locant is used. This allows an alternative designation to be used, when authors wish, to bring out structural relationships.

The Nomenclature of Lipids

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The nomenclature of lipids

LipidsVolume 12, Issue 6 p. 455-468 Article The nomenclature of lipids† Recommendations (1976)† IUPAC-IUB Commission on Biochemical Nomenclature, IUPAC-IUB Commission on Biochemical Nomenclature Members of CBN are: O. Hoffmann-Ostenhof (Chairman), W.E. Cohn (Secretary), A.E. Braunstein, H.B.F. Dixon, B.L. Horecker, W.B. Jakoby, P. Karlson, W. Klyne, C. Liébecq, E.C. Webb.Search for more papers by this author IUPAC-IUB Commission on Biochemical Nomenclature, IUPAC-IUB Commission on Biochemical Nomenclature Members of CBN are: O. Hoffmann-Ostenhof (Chairman), W.E. Cohn (Secretary), A.E. Braunstein, H.B.F. Dixon, B.L. Horecker, W.B. Jakoby, P. Karlson, W. Klyne, C. Liébecq, E.C. Webb.Search for more papers by this author First published: 01 June 1977 https://doi.org/10.1007/BF02535443Citations: 266 Reprints of this document, supplied by the publishing journals, may be obtained from W.E. Cohn (Director of the NAS-NRC Office of Biochemical Nomenclature), Biology Division, Oak Ridge National Laboratory, Box Y, Oak Ridge, Tennessee, U.S.A. 37830. † Document2 of the IUPAC-IUB Commission on Biochemical Nomenclature (CBN) approved by IUPAC and IUB in 1976, and published with the cooperation of the IUB Commission of Editors of Biochemical Journals.3 Comments on these Recommendations and suggestions for future revisions may be sent to any member of CBN.4 ‡ These Recommendations are a revision and extension of “The Nomenclature of Lipids,” which appeared in 1967, as amended in 1970 (1). AboutPDF ToolsRequest permissionExport citationAdd to favoritesTrack citation ShareShare Give accessShare full text accessShare full-text accessPlease review our Terms and Conditions of Use and check box below to share full-text version of article.I have read and accept the Wiley Online Library Terms and Conditions of UseShareable LinkUse the link below to share a full-text version of this article with your friends and colleagues. Learn more.Copy URL Share a linkShare onFacebookTwitterLinked InRedditWechat Citing Literature Volume12, Issue6June 1977Pages 455-468 RelatedInformation

Acyl-chloro-deoxyglycerophosphorylcholines: Structure of the so-called cyclic lysolecithins

The reaction between sn-glycero-3-phosphorylcholine and fatty acid chloride for the synthesis of 1,2-diacyl- sn-glycero-3-phosphorylcholines † † Also called lecithins and l-α-phosphatidylcholines; the recommendations of the IUPAC-IUB Commission on the nomenclature of lipids have been followed in this paper (see Biochim. Biophys. Acta, 152 (1968) 1). can lead to several by-products. One of these was originally considered to be 2-monoacyl- sn-glycero-3-phosphorylcholine but cyclic phosphotriester structures were proposed later and the material has been referred to as cyclic lysolecithin. The compound is difficult to separate from 1,2-diacyl- sn-glycero-3-phosphorylcholine and has been considered to be responsible for the poor yield of 1,2-diacyl- sn-glycero-3-phosphorylcholine. It is now shown to be a mixture of isomeric acyl-chloro-deoxy-glycero-phosphorylcholines.

The Phosphatides.

The publishers of this monograph state that this is the first complete work on phosphatides in over 20 years. During this period much information has been made available on their chemical structure, purification, analysis, occurrence in nature, biochemical and physiological roles, and industrial applications. The author deals with each of these aspects in turn. He covers the literature through 1949 thoroughly and incorporates the most important 1950 developments. A valuable feature of the work is his discussion of lipid nomenclature in various parts of the world and his careful usage of one system, that adopted by the American Chemical Society. The bibliographies and indexes are good. The printing and binding are up to the high standard of American Chemical Society monographs.