Table 4: Survey on the technologies used; Institutions with medium and high expertise level (only technologies with more than 2 hits)
Organisms and cellular Systems - Survey
Human Cell Lines
Table 5: Survey on the areas of Lipidomics expertise; Institutions with medium and high expertise level (only organisms with more than 2 hits)
Beside this contact and expertise database the LEP contains databases for lipid standards (Fig. 4) and for methods (Fig. 5), which should improve methodology and standard material exchange.
Fig. 4: Methodology Database.
Fig. 5: Lipid Standard Database.
Currently, as one goal of the FP project LipidomicNet the Wikipedia software is being integrated into the LEP (LEP-Wiki, Fig. 6), which will provide information on lipids from basic information to advanced aspects like the biology and pathophysiology that lipids are involved in.
A major source for LEP-Wiki is a close link to other databases including LIPID MAPS (http://www.lipidmaps.org) for lipid nomenclature and lipid species data, Lipid Bank - Japan (http://www.lipidbank.jp) for lipid species data and KEGG PATHWAY Database for metabolic pathways (http://www.genome.jp/kegg/pathway.html). Moreover, information on lipid metabolic pathways will be linked to genomics information including databases like Ensembl (http://www.ensembl.org).
LEP-Wiki lives from the contribution of people interested in Lipidomics. All Lipidomics Expertise Platform (LEP) members can edit the content and add new data.
Fig. 6: LEP-Wiki
Appendix 1: Contact details and description of institutions registered in LEP ordered by country (as per 01.01.2008)
biochemistry and biophysics of lipids cell-surface membrane structure and dynamics lipid-protein interactions in nicotinic receptors lipids in embryonic development lipids in neuronal differentiation and survival lipids in retina lipids in plants lipids in reproductive system
Inst. Biophysics & X-ray Structure Research / Fct. Lipidomics
Our research aims at the elucidation of the molecular mode of action of host defence peptides that affect cells by interacting in a non-specific manner with their membranes and not via specific receptors. An understanding of how these peptides distinguish between bacterial and mammalian cell membranes will allow the design of novel peptide antibiotics, which can selectively kill bacteria. Bacterial resistance to such antimicrobial peptides is less likely to occur owing to the nature of their target and fast killing kinetics. However, there has been evidence that resistance to antibiotics may also arise due to changes in lipid composition of their membranes. Therefore, the design of novel and effective antimicrobial peptides will only be possible, if the entire lipid spectrum of its membrane has been identified, which nowadays owing to recent advances in analytical instrumentation can be addressed both at the qualitative and quantitative level. Experimental approach - membrane biophysics (structural, thermodynamic and spectroscopic techniques)- lipid analysis of target membranes - peptide libraries
BIOCRATES Life Sciences
BIOCRATES Life Sciences
Metabolomics, Lipid quantitation, Bioinformatics
Targeted metabolomics Mass spectrometry Quantitation of phospho- and glycolipids, eicosanoids etc. Bioinformatics and biostatistics Biomarker discovery and validation
The main subjects studied in our group are synthesis of lipids and their assembly into organelle membranes of the yeast Saccharomyces cerevisiae. The majority of yeast lipids are synthesized in the endoplasmic reticulum with some significant contributions of mitochondria, the Golgi and the so-called lipid particles. Other subcellular fractions, e.g. the plasma membrane, are devoid of lipid-synthesizing activities. Spatial separation of lipid biosynthetic steps and lack of lipid synthesis in several cellular membranes necessitate an efficient transfer of lipids from their site of synthesis to their proper destination(s). The maintenance of organelle lipid profiles requires strict coordination and regulation of biosynthetic and translocation processes. Specific aspects currently studied are the assembly of lipids into mitochondrial membranes and lipid homeostasis in this compartment, and dynamics of neutral lipid storage in lipid particles. Recently we started to extend our studies to organelles of Pichia pastoris as a basis for future research of protein expression in this biotechnologically important yeast. Enzymes and other proteins involved in the above mentioned processes are investigated using biochemical, cell biological and molecular biological methods.
Inst. of Chemistry
membrane protein, conjugation, T4SS
We are working on the characterization of a typ IV-like secretion system (T4SS) from Gram positive bacteria. The system is encoded on the resistance plasmid pIP501. The tra region shows a modular organization and contains 15 ORFs, of which several have been predicted to encode for transmembrane or membrane asociated proteins. Our aim is the structure elucidation of the components essential for the conjugative DNA transfer.
Institute of Medical Technologies and Health Mangement
acyl-coA, mass spectrometry, interstitial fluid analysis
analysis methods based on GC-MS, HPLC-MS^2 and nano-HPLC-MS^2 analysis of interstitial fluid of humans and animals method validation according to GLP guidelines
Novel and already identified genes involved in lipid homeaostasis of different organs including liver, intestine, endothelial cells, macrophages-foam cells. Cholesterol efflux and cholesteryl ester hydrolases. Pathophysiology of athersoclerosis. Lipid metabolism in gneral. Lipidome of human plasma in health and diseases. Lipidome of enterocytes and cardiomycytes .
IMB Biochemistry - Yeast Genetics Group
University of Graz
++43 316 380 5487
yeast, fatty acid, membrane and lipid imaging
Lipid metabolism and membrane assembly in yeast, yeast as a model of lipid-associated disorders, regulation of fatty acid, triglyceride and phospholipid metabolism, high-resolution microscopy, implementation of novel imaging methods to investigate membrane and organelle stucture and dynamics in yeast, yeast lipidomics
Institute of Chemical Technologies and Analytics, Bio and Polymer Analysis
Vienna University of Technology
++43 1 58801 15160
MALDi, ESI, multistage MS, plant lipids, human blood
Characterisation of lipid pattern in human blood during dietary treatment Characterisation of lipid pattern of industrial (as a renewable source of chemicals), pharamceutical and medical relevant plants Development of ultrafast and structurespecific MALDI and ESI mass spectrometric techniques for all classes of lipids
Core Facility for Mass Spectrometry
ZMF/Medical University Graz
++43 (316) 385-73005
Mass Spectrometry, FT-MS, Glycerolipids, Sphingolipids
Development of mass spectrometric tools for the analysis of lipids (neutral and polar glycerolipids, sphingolipids, cholesterols) and lipid derived second messengers (e.g. eicosanoids) is a key research interest of our facility. This is reflected by participation in center grants such as SFB Lipotox and the technology based initiative Lipidomic Research Center (LRC) Graz. Currently we develop an analytical platform based on UPLC-FT-MS/MS for differential quantitation of the lipidome at the level of molecular species. Finally these data should enable researchers to establish up- and down regulated metabolic pathways for different sets of samples. If it is needed to provide absolute quantitative data for single species or a limited set of them, we have the possibility to quantify them in a targeted approach with LC-MS/MS.
Breakdown of fatty acids/derivatives via alpha-oxidation and beta-oxidation, peroxisomal lipid metabolism, bioactive sphingolipid metabolism, mouse models related to peroxisomal disorders,
Katholieke Universiteit Leuven
++32 16 32 96 88
Kasteelpark Arenberg 20
yeast, sphingolipid, ESI-MS
We are interested in sphingolipidomics in yeast. Using ESI-MS, we have optimized a method to determine and relatively quantify the three different classes of complex inositolphosphoryl-containing sphingolipids [i.e. IPC (inositolphosphoryl ceramide), MIPC (mannosyl inositolphosphoryl ceramide) and M(IP)2C (mannosyl diinositolphosphoryl ceramide] in S. cerevisiae [Aerts et al., 2006, FEBS Letters, 580(7):1903-7]. We are interested in technologies enabling quantification of sphingoid bases and ceramides in yeast membranes.
Laboratory for Experimental Medicine and Endocrinology (LEGENDO)
Katholieke Universiteit Leuven
Herestraat 49 bus 902
cancer, lipid rafts, protein acylation
Our team is interested in the metabolic changes in cancer cells versus normal cells, and particularly in the marked increase in lipogenesis that is observed in nearly all cancer types. We 1. study the mechanisms that underly this increase (imvolvement of oncogenes, steroid hormones,...), 2. We examine the impact of these chnages on lipid profiles, lipid rafts and lipid-modified proteins, 3. We investigate the consequences of these changes for cancer cell biology (growth, metastasis,...), and 4. We explore the potential clinical applications (diagnosis, therapy).
Neuronal Differentiation Unit
VIB and Catholic University of Leuven
cholesterol lipid rafts senescence
We are interested in analysing the role of cholesterol in the cell senescence/survival process. We postulate that cholesterol reduction in membrane lipid rafts it might be a central effector in survival of senescent neurons, implying that brain cholesterol regulation could be crucial for death/survival equilibrium durin brain aging.
Laboratório de Bioquímica e Biologia Celular de Lipídios
Departamento de Bioquímica - ICBS- Universidade Federal do rio Grande do Sul
Structural organization of glycosphingolipids and effect of length of fatty acid chain and hydroxylation of fatty acid, Lipid rafts and membrane domains in myelin and oligodendrocytes and role in signalling, Trans interactions between glycosphingolipid head groups and formation of a glycosynapse between apposed cell membranes, Role of phosphatidylinositides.
CIHR Group in Molecular and Cell Biology of Lipids
Goals of our CIHR Group in Molecular and Cell Biology of Lipids (MCBL) * To enhance the knowledge and understanding of the metabolism, function and transport of mammalian lipids, lipid biosynthetic enzymes and transport proteins, and the regulation of the genes that encode these proteins * To facilitate the translation of discoveries into potential diagnostics and treatments of human diseases * To provide fundamental knowledge that will improve the health of Canadians and peoples throughout the world * To provide an environment that will enhance scholarly and scientific endeavors. The principal investigators * Luis B. Agellon, PhD, Associate Professor of Biochemistry * Gordon A. Francis, MD, Associate Professor of Medicine * Richard Lehner, PhD, Associate Professor of Pediatrics and Cell Biology * Dennis E. Vance, PhD, Professor of Biochemistry * Jean E. Vance, PhD, Professor of Medicine Our research program The MCBL Group research program is organized into four major themes: * molecular regulation of genes involved in lipid homeostasis * biochemistry of lipid-protein interactions * lipid compartmentalization and intracellular trafficking * lipid homeostasis in murine models The current major research projects are: * regulation of phosphatidylcholine metabolism * molecular and cell biology of phosphatidylserine metabolism * triacylglycerol synthesis * role of triacylglycerol hydrolase in triacylglycerol metabolism * function and metabolism of sterols in the liver * metabolism of lipids in the enterohepatic circulation * cellular lipid efflux and HDL formation * lipid homeostasis in neurons Our Core Resources Members of the MCBL Group contribute specific technical expertise and newly developed technologies which are shared with other projects and laboratories through our Core resources. * The Core Cell Culture Laboratory provides access to a variety of cell lines (including various derivatives of McArdle RH7777 cells expressing recombinant forms of enzymes important in the metabolism of lipids), and technical support for immunofluorescence and confocal microscopy studies. * The Core Metabolism and Physiology Laboratory provides access to genetically-modified mouse strains used by investigators in the MCBL Group. This laboratory also provides access to primary cell cultures, in conjunction with the Core Cell Culture Laboratory, and technical support for surgical procedures. * The Core Lipid Analysis Laboratory provides access to current, standardized and validated analytical procedures, and technical support for the detection and analysis of lipids and their metabolites. * The Core Training Program provides opportunities for qualified postdoctoral fellows and graduate students to participate in our integrated research program.