P02 UU

From LipidomicsWiki

(Difference between revisions)
Jump to: navigation, search
Current revision (13:15, 8 August 2011) (view source)
 
(20 intermediate revisions not shown.)
Line 1: Line 1:
{{Infobox_Institution
{{Infobox_Institution
-
|myInstitutionname=Protagen AG - Stefan Müllner, Protagen AG, Dortmund
+
|myInstitutionname=[http://www.uu.nl/uupublish/homeuu/1main.html Utrecht University - Bernd Helms, Department of Biochemistry and Cell Biology]
-
|myLogo=
+
|myLogo=[[Image:UniUtrechtlogo.gif]]
-
|myCountry=Germany
+
|myPrincipal_investigator=[[User:Bernd_Helms|Prof. Dr. Bernd Helms]]
-
|myBenefitnr=P20
+
EMail: [mailto:j.b.helms@vet.uu.nl Bernd Helms]
-
|myAbout=
+
Telephone: +31 30 2535375
-
|myContribution=
+
|myCountry=Netherland
-
Protagen AG provides a unique technology platform addressing all aspects in modern protein
+
|myBenefitnr=P02
-
science including:
+
|myAbout=Our research is focused on understanding the molecular principles of membrane dynamics in
-
* '''2-dimensional electrophoresis of lipid binding proteins'''
+
animal cells. In the cell, membranes are continuously transported between organelles. This
-
A highly reproducible method for the differential display of membrane and plasma membrane proteins, i.e. lipid associated proteins, based on the Large Gel 2-dimensional gel electrophoresis method (2DE) developed by Joachim Klose a method for highly reproducible
+
process includes protein and lipid sorting during transport to maintain the unique membrane
-
differential display of membrane proteins was developed.
+
composition of each organelle. Within membranes, a select group of lipids and proteins can
-
* '''Identification of high affinity protein binders and binding proteins'''
+
dynamically segregate into microdomains or so-called lipid rafts to regulate cellular
-
In order to identify high affinity protein ligands and other high-affinity binding molecules, e.g. lipids, aptamers, small molecules and nucleic acids Protagen employs a high content protein macroarray. The macroarrays contain His-tagged > 37.000 DNA sequenced human protein
+
processes. The dynamic properties of biological membranes appear to play a crucial role in
-
expression products produced in E.coli.
+
many normal cellular functions and many diseases result from dysfunction of membrane
-
* '''Protein Microarrays and Fast Selection of the best Antibody'''
+
dynamics. We study (dys)functions of membrane dynamics in tissue repair in the liver, hostpathogen
-
The set of binders used in the project for pull downs and other methods will be tested for specificity on protein Microarrays - UNIchip® - in order to significantly reduce the false positive rate. This technology allows the quantitative analysis of the off-target binding partners and ensitivity/affinity testing.Specialised Microarrays for quantitative and statistical significant studies of protein lipid interaction will be produced employing the high-throughput capabilities at Protagen.
+
interactions, and in reproduction.
-
* '''Posttranslational Modifications of Target Proteins'''
+
The role of lipids in the pathogenesis of these disorders is a main focus of our Department.
-
Modiro® - a new software tool developed by Protagen allows the precise identification of all known and even hitherto unknown posttranslational protein modifications (PTM) in proteins and peptides. MS/MS spectra generated by machines from all manufactures can be analysed.
+
We previously described the purification and detailed characterisation of microdomains from
-
* '''Automated Protein Identification Platform'''
+
Golgi membranes (GICs). Characterisation of its protein constituents show that these
-
The latest generation of mass spectrometers by Bruker Daltonics were acquired in December 2006 – Ultraflex III, HCT Ultra and MicroTOF-Q - by Protagen. In addition, a highthroughput and robotised workflow for proteome analysis is established and functional at Protagen. This platform is accessible for all project partners.
+
domains play a role in maintenance of Golgi structure and function. In addition, the data
-
|myTaskforces=
+
suggest that the Golgi complex plays a role in innate immunity. In line with these
-
|myWorkpackages=
+
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.
 +
|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.
 +
|myTaskforces=[[Task_Force_I|Task Force I]], [[Task_Force_V|Task Force V]], and [[Task_Force_IX|Task Force IX]]
 +
|myWorkpackages=[[WP2|WP2]] and [[WP3|WP3]]
 +
}}<br> <br>
 +
 +
 
 +
[[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

Back to List of Beneficiaries




Personal tools
Create a book