P02 UU

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{{Infobox_Institution
{{Infobox_Institution
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|myInstitutionname=Protagen AG - Stefan Müllner, Protagen AG, Dortmund
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|myInstitutionname=[http://www.uu.nl/uupublish/homeuu/1main.html Utrecht University - Bernd Helms, Department of Biochemistry and Cell Biology]
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|myLogo=
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|myLogo=[[Image:UniUtrechtlogo.gif]]
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|myCountry=Germany
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|myPrincipal_investigator=[[User:Bernd_Helms|Prof. Dr. Bernd Helms]]
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|myBenefitnr=P20
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EMail: [mailto:j.b.helms@vet.uu.nl Bernd Helms]
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|myAbout=
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Telephone: +31 30 2535375
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|myContribution=
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|myCountry=Netherland
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Protagen AG provides a unique technology platform addressing all aspects in modern protein
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|myBenefitnr=P02
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science including:
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|myAbout=Our research is focused on understanding the molecular principles of membrane dynamics in
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# 2-dimensional electrophoresis of lipid binding proteins
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animal cells. In the cell, membranes are continuously transported between organelles. This
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A highly reproducible method for the differential display of membrane and plasma membrane
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process includes protein and lipid sorting during transport to maintain the unique membrane
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proteins, i.e. lipid associated proteins, based on the Large Gel 2-dimensional gel
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composition of each organelle. Within membranes, a select group of lipids and proteins can
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electrophoresis method (2DE) developed by Joachim Klose a method for highly reproducible
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dynamically segregate into microdomains or so-called lipid rafts to regulate cellular
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differential display of membrane proteins was developed.
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processes. The dynamic properties of biological membranes appear to play a crucial role in
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# Identification of high affinity protein binders and binding proteins
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many normal cellular functions and many diseases result from dysfunction of membrane
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In order to identify high affinity protein ligands and other high-affinity binding molecules, e.g.
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dynamics. We study (dys)functions of membrane dynamics in tissue repair in the liver, hostpathogen
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lipids, aptamers, small molecules and nucleic acids Protagen employs a high content protein
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interactions, and in reproduction.
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macroarray. The macroarrays contain His-tagged > 37.000 DNA sequenced human protein
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The role of lipids in the pathogenesis of these disorders is a main focus of our Department.
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expression products produced in E.coli.
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We previously described the purification and detailed characterisation of microdomains from
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# Protein Microarrays and Fast Selection of the best Antibody
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Golgi membranes (GICs). Characterisation of its protein constituents show that these
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The set of binders used in the project for pull downs and other methods will be tested for
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domains play a role in maintenance of Golgi structure and function. In addition, the data
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specificity on protein Microarrays - UNIchip® - in order to significantly reduce the false
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suggest that the Golgi complex plays a role in innate immunity. In line with these
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positive rate. This technology allows the quantitative analysis of the off-target binding
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observations, it has been found by others that several intracellular pathogens target the Golgi
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partners and sensitivity/affinity testing.Specialised Microarrays for quantitative and statistical
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complex for their intracellular survival and replication. With the development of lipidomics
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significant studies of protein lipid interaction will be produced employing the high-throughput
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techniques, it now becomes evident that pathogens also take full advantage of the
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capabilities at Protagen.
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complexity of the host lipidome. Pathogens have devised ingenious ways to interfere with the
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# Posttranslational Modifications of Target Proteins
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host cell lipidome. Since early 2006 we have made a strong commitment to lipid research by
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Modiro® - a new software tool developed by Protagen allows the precise identification of all
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implementation of a lipidomics "core" facility at our Department, fully dedicated to the
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known and even hitherto unknown posttranslational protein modifications (PTM) in proteins
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analysis of lipids by mass spectrometry. Our research is supported by several grants from
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and peptides. MS/MS spectra generated by machines from all manufactures can be
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the Netherlands Research Organisation (NWO) and by support from Industry.
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analysed.
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The available technologies include MS based lipidomics techniques (three mass
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# Automated Protein Identification Platform
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spectrometers, all equipped with ion sources (turbo-)ESI, nano-ESI, and APCI,
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The latest generation of mass spectrometers by Bruker Daltonics were acquired in
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autosamplers, micropumps, and UV detectors, HPLC, Evaporative Light Scattering Detectors
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December 2006 – Ultraflex III, HCT Ultra and MicroTOF-Q - by Protagen. In addition, a highthroughput
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wavelength UV detector, and variable wavelength Fluorescence detector), assays for lipid
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and robotised workflow for proteome analysis is established and functional at
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metabolism using heavy isotope labeld precursors, lipid isolation and separation techniques,
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Protagen. This platform is accessible for all project partners.
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isolation of primary liver cells, fractionation studies and isolation of subcellular organelles,
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|myTaskforces=
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and biochemical and biophysical analysis of protein-lipid interactions. The department also
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|myWorkpackages=
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houses "The Center for Cell Imaging" that contains state of the art imaging equipment
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}}
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including a confocal and multi-photon microscope as well as a transmission electron
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microscope and carries shared responsibility for a FACS facility. The department is
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integrated into the Academic Biomedical centre of Utrecht University, allowing access to
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various facilities including 'the Netherlands Proteomics Centre' , state of the art electron
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microscopy and tomography facilities, and microarray facilities.
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|myContribution=The partner will be responsible for studying the mechanism and relevance of vitamin A deposition during hepatic stellate cell proliferation and differentiation for the known interaction with hepatocytes.
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|myTaskforces=[[Task_Force_I|Task Force I]], [[Task_Force_V|Task Force V]], and [[Task_Force_IX|Task Force IX]]
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|myWorkpackages=[[WP2|WP2]] and [[WP3|WP3]]
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}}<br> <br>
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[[Category:Project_organisation]]

Current revision

InstitutionUtrecht University - Bernd Helms, Department of Biochemistry and Cell BiologyImage:UniUtrechtlogo.gif
Principal investigator Prof. Dr. Bernd Helms

EMail: Bernd Helms

Telephone: +31 30 2535375
Country Netherland
Beneficiary NumberP02
About usOur research is focused on understanding the molecular principles of membrane dynamics in

animal cells. In the cell, membranes are continuously transported between organelles. This process includes protein and lipid sorting during transport to maintain the unique membrane composition of each organelle. Within membranes, a select group of lipids and proteins can dynamically segregate into microdomains or so-called lipid rafts to regulate cellular processes. The dynamic properties of biological membranes appear to play a crucial role in many normal cellular functions and many diseases result from dysfunction of membrane dynamics. We study (dys)functions of membrane dynamics in tissue repair in the liver, hostpathogen interactions, and in reproduction. The role of lipids in the pathogenesis of these disorders is a main focus of our Department. We previously described the purification and detailed characterisation of microdomains from Golgi membranes (GICs). Characterisation of its protein constituents show that these domains play a role in maintenance of Golgi structure and function. In addition, the data suggest that the Golgi complex plays a role in innate immunity. In line with these observations, it has been found by others that several intracellular pathogens target the Golgi complex for their intracellular survival and replication. With the development of lipidomics techniques, it now becomes evident that pathogens also take full advantage of the complexity of the host lipidome. Pathogens have devised ingenious ways to interfere with the host cell lipidome. Since early 2006 we have made a strong commitment to lipid research by implementation of a lipidomics "core" facility at our Department, fully dedicated to the analysis of lipids by mass spectrometry. Our research is supported by several grants from the Netherlands Research Organisation (NWO) and by support from Industry. The available technologies include MS based lipidomics techniques (three mass spectrometers, all equipped with ion sources (turbo-)ESI, nano-ESI, and APCI, autosamplers, micropumps, and UV detectors, HPLC, Evaporative Light Scattering Detectors wavelength UV detector, and variable wavelength Fluorescence detector), assays for lipid metabolism using heavy isotope labeld precursors, lipid isolation and separation techniques, isolation of primary liver cells, fractionation studies and isolation of subcellular organelles, and biochemical and biophysical analysis of protein-lipid interactions. The department also houses "The Center for Cell Imaging" that contains state of the art imaging equipment including a confocal and multi-photon microscope as well as a transmission electron microscope and carries shared responsibility for a FACS facility. The department is integrated into the Academic Biomedical centre of Utrecht University, allowing access to various facilities including 'the Netherlands Proteomics Centre' , state of the art electron

microscopy and tomography facilities, and microarray facilities.
ContributionsThe partner will be responsible for studying the mechanism and relevance of vitamin A deposition during hepatic stellate cell proliferation and differentiation for the known interaction with hepatocytes.
Member of TaskforcesTask Force I, Task Force V, and Task Force IX
Member of WorkpackagesWP2 and WP3

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