Executive Summary



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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

27

Mice

22

Blood

22

Biopsy

18

Human Primary

15

Mouse

15

Rats

14

Yeast

14

Urine

10

Eubacteria

5

Rabbits

4

Arabidopsis

4

Agricultural Crop

3

Stool

3

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)


Company

Organisation

Phone

ZIP

City

Street

Country

Keywords

Description

Type

UNESCO Chair Biophys. & Mol. Neurobiol

Universidad Nacional del Sur

054 2914861201

8000

Bahia Blanca

C.C. 857

Argentina

cell-surface receptors / lipid-protein interactions / membranes / structure / dynamics

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

scientific

Inst. Biophysics & X-ray Structure Research / Fct. Lipidomics

Austrian Academy of Sciences

++43-316-4120-323

A-8045

Graz

Schmiedlstrasse 6

Austria

lipid polymorphism, membrane biophysics, membrane mimetic, membranolytic peptides

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

scientific

BIOCRATES Life Sciences

BIOCRATES Life Sciences

++43-512-579823-4216

6020

Innsbruck

Innrain 66

Austria

Metabolomics, Lipid quantitation, Bioinformatics

Targeted metabolomics Mass spectrometry Quantitation of phospho- and glycolipids, eicosanoids etc. Bioinformatics and biostatistics Biomarker discovery and validation

industrial

Institute for Genomics and Bioinformatics

Graz University of Technology

++43-316-873-5345

8010

Graz

Petersgasse 14

Austria

transcriptional regulation, microarrays, adipogenesis, lipotoxicity

Transcriptional regulation of lipotoxic pathways. Gene expression analysis of mouse models of lipid-associated disorders.

scientific

Institute for Molecular Biotechnology

Graz University of Technology

++43-316-873-4089

A-8010

Graz

Petersgasse 14/I

Austria

yeast lipids, sterols

Lipid transport in yeast The roles of sterols in membrane transport in yeast Sterol homeostasis in yeast

scientific

Institute of Biochemistry, Cell Biology Group

Graz University of Technology

+43-316-873-6462

A-8010

Graz

Petersgasse 12/2

Austria

yeast, mitochondria, lipid particles, phospholipids, neutral lipids

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.

scientific

Structural biology

Inst. of Chemistry

+43-316-3805423

8010

Graz

Heinrichstr. 28

Austria

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.

scientific

Institute of Medical Technologies and Health Mangement

Joanneum Research

++433168762103

8036

Graz

Auenbruggerplatz 20/3

Austria

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

scientific

Molecular Biology and Biochemistry,

Medical University Graz

+433163804200

A-8010

Graz

Harrachgasse 21

Austria

cholesterol metabolism, nuclear receptors, atherosclerosis

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 .

scientific

IMB Biochemistry - Yeast Genetics Group

University of Graz

++43 316 380 5487

A8010

Graz

Schubertstr. 1

Austria

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

scientific

Institute of Chemical Technologies and Analytics, Bio and Polymer Analysis

Vienna University of Technology

++43 1 58801 15160

A-1060

Vienna

Getreidemarkt 9/164

Austria

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

scientific

Core Facility for Mass Spectrometry

ZMF/Medical University Graz

++43 (316) 385-73005

8010

Graz

Stiftingtalstrasse 24

Austria

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.

scientific

Div. Pharmacology - Dep. Mol. Cell Biology

K.U.Leuven

++32-16-345801

B-3000

Leuven

Campus Gasthuisberg, Herestraat

Belgium

phytanic, pristanic, ceramide, sphingosine-phosphate

Breakdown of fatty acids/derivatives via alpha-oxidation and beta-oxidation, peroxisomal lipid metabolism, bioactive sphingolipid metabolism, mouse models related to peroxisomal disorders,

scientific

CMPG-PFI

Katholieke Universiteit Leuven

++32 16 32 96 88

3001

Heverlee

Kasteelpark Arenberg 20

Belgium

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.

scientific

Laboratory for Experimental Medicine and Endocrinology (LEGENDO)

Katholieke Universiteit Leuven

++32-16-330533

3000

Leuven

Herestraat 49 bus 902

Belgium

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).

scientific

Neuronal Differentiation Unit

VIB and Catholic University of Leuven

+32-16-330526

3000

Leuven

Herestraat 49

Belgium

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.

scientific

Laboratório de Bioquímica e Biologia Celular de Lipídios

Departamento de Bioquímica - ICBS- Universidade Federal do rio Grande do Sul

55-51-33-16-55-50

90.035-003

Porto Alegre

Rua Ramiro Barcelos 2600- anexo

Brazil

shingolipids, gangliosides, adipogenesis, lipogenesis

- Sphingolipid metabolism and their cellular functions in central nervous system and hematopoietic differentiation. - Adipogenesis and lipogenesis.

scientific

Research Institute, Boggs Laboratory

Hospital for Sick Children

1-416-813-5919

M5G1X8

Toronto

555 University Ave.

Canada

sulfatide, galactosylceramide, glycosynapse

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.

scientific

CIHR Group in Molecular and Cell Biology of Lipids

University of Alberta

1-780-492-2963

T6G 2S2

Edmonton

328 Heritage Medical Research Centre

Canada

atherosclerosis, obesity, neurodegeneration, 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.


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