Heidelberg - Mannheim

Klingmüller - Dooley

• Subject: SOPs
  Details: Generation of SOPs for hepatocyte isolation, culture and transport, which had to be specifically modified in dependence of the investigation (e.g. signal transduction, imaging, adenovirus infection).

• Subject: TGF-ß signaling pathway
  Details: Intrinsic overlap with activities regarding the chronic damage and the regeneration of the liver; both groups had and will have frequent meetings to discuss strategies, share data and reagents and adapt SOPs for various investigations, e.g., adenoviral infection, phosphoprotein analysis, reportergene analysis, mRNA expression analysis of TGF-ß target genes in hepatocytes and so on; in future on jointly goal is the generation of TGF-ß dependent target gene expression profiles in hepatocytes; some of the array data will be used by the group of Klingmüller for quantitative evaluation.

Heidelberg - Leipzig

Klingmüller - Hengstler

• Subject: Analysis of signaling pathways
  Details: Special SOPs for the preparation, cultivation and starvation of primary murine hepatocytes have been developed.

Freiburg - Leipzig

von Weizsäcker - Hengstler

• Subject: SOPs
  Details: Refining and optimizing the existing SOPs, transfer of the isolation procedure.

Walz/Merfort - Hengstler

• Subject: SOPs
  Details: Refining and optimizing the existing SOPs, quality control of cultured hepatocytes.

von Weizsäcker - Gebhardt

• Subject: Investigating of the phenotype of periportal hepatocytes.

Walz/Merfort - Gebhardt

• Subject: Transfection of primary hepatocytes.

Timmer - Heinrich/Bader

• Subject: Epo-receptor
  Details: Working in common on the analysis.

Timmer - Hengstler

• Subject: SOPs
  Details: Development of the experimental design for fixing the standard operating procedures for primary mouse hepatocytes.

Hecht - Gebhardt

• Subject: Modeling of Wnt/ß-catenin pathway in hepatocytes
  Details: The group of Hecht identified Wnt-factors, which activate the pathway, relevant cell cultures were established in Leipzig and the Wnt-factors were identified in Freiburg (Gebhardt et al. 2005), work will be extended to other LEF/Tcf target genes (e.g. axin), therefor the inter-network collaboration works now with respect to the characterization of a set of novel GSK3ß inhibitors (L4, L7, and L10), Prof. Gebhardt provided Dr. Hecht with samples of these chemicals which are applied to the cell culture systems, the group of Dr. Hecht analyzed whether these substances were capable of inducing a cytoplasmic pool of hypophosphorylated ß-catenin and of activating target gene expression. All three agents induced partial activation of Wnt/ß-catenin signaling, but compared to LiCl, SB216763 or Wnt3a proved to be less effective, the results of the experiments were returned to Prof. Gebhardt, the results are also important for the model calculations of the groups of Heinrich and Holzhütter (Platform Modeling), the calculations will therefore be performed in Berlin and Freiburg.

Timmer - Gebhardt

• Subject: Modeling of induction of the glutamine synthetase after stimulation with LiCl
  Details: The wet lab experiments (induction of the glutamine synthetase after stimulation with LiCl) have been transferred to the group of Timmer for further modeling, this approach will allow to compare different strategies of modeling.

Freiburg - Magdeburg

Merfort - Gilles

• Subject: Modelling of NF-kappa/B
  Details: Mutual visits and talks.

Mohr - Gilles

• Subject: Modelling of EGF-signaling pathways
  Details: Mutual visits and talks.

Borner - Gilles

• Subject: Modelling apoptosis
  Details: Mutual visits and talks.

Timmer - Gilles

• Subject: Mathematical analysis of generated data for the modeling tool ProMoT/DIVA
  Details: Transfer of the advanced parameter estimation methods based on the multiple-shooting approach developed in the Timmer group for implementation in the modeling tool.

• Subject: Visualization of cooperation within HepathoSys for the web page
  Details: Data survey for and development and implementation of an illustration of cooperation.

Timmer - Gilles

• Subject: Data management
  Details: Contribution to the requirement specification for data management system for the competence network.

Mannheim - Stuttgart

Dooley - Lange/Dippon

• Subject: TGF-ß Pathway
  Details: For generating TGF-ß dependent target gene expression profiles in hepatocytes, we attended a meeting of the gene expression profiling consortium in Stuttgart and now have contact to the groups of Lange and Dippon (Stuttgart) for seeking a collaboration.

Heidelberg - Magdeburg

Kummer - Gilles

• Subject: Complexity reduction methods
  Details: J. Saez-Rodriguez was invited to give a talk, further collaboration is planned.

Berlin - Mannheim

Nüssler - Dooley

• Subject: Investigation of TGF-ß signaling in human hepatocytes and Neo-Hep cells
  Details: Establishing a collaboration, where we isolate monocytes from alcoholic patients and establish Neo-Hep cells from these in our lab for further investigations.

Berlin - Jena

Zeilinger - Pfaff/Guthke

• Subject: Data-exchange
  Details: Mathematical data analysis and construction of dynamic models to describe and to predict the functional performance of human liver cell bioreactors.

Berlin - Stuttgart

Holzhütter - Mauch

• Subject: Flux balance approach
  Details: Comparison of the experimentally obtained flux distributions with flux balance analysis results.

Jena - Leipzig

Pfaff/Guthke - Zellmer/Gebhardt

• Subject: Data-exchange
  Details: Several hepatocyte transcriptome data sets were obtained from Leipzig and results of the respective data analysis as well as reconstructions of regulatory networks were returned to these groups.

• Subject: Modeling liver heterogenity
  Details: Analyzing of metabolic liver heterogeneity of periportal and pericentral hepatocytes using Affimetrix chip data in cooperation with the group of Dr. Guthke. The wet lab data were generated in Leipzig and the dry lab data were calculated in Jena. Modeling will be performed in Berlin. The data will be essential for modeling of liver heterogeneity.

• Subject: Modeling for the induction of the glutamine synthetase after stimulation with LiCl
  Details: Mathematical models for the induction of the glutamine synthetase after stimulation with LiCl were developed. The wet lab experiments were performed in Leipzig and the data analysis was done in Jena.

Guthke - Hengstler

• Subject: SOPs
  Details: Characterisation of hepatocyte preparations with respect to heterogeneity, influence of relative representation of subpopulations on performance in bioreactors.

• Subject: Regulatory networks
  Details: Reconstruction of regulatory networks responsible for hepatocyte differentiation.

• Subject: Modeling of the Wnt/ß-Catenin pathway.

Dresden - Heidelberg

Habermann/Deutsch - Wade/Kummer

• Subject: Protein structural models
  Details: Estimating parameters for mathematical models being developed at TU Dresden to interpret experimental data from MPI Dresden on the Rab5 machinery.

Freiburg - Mannheim

Timmer - Dooley

• Subject: Modeling of TGF-ß internalization trafficking and signaling in primary hepatocytes
  Details: Establishing of equations for a mathematical model of endocytosis in TGF-beta signalling, defining the steps of the TGF-ß signaling pathway, that need to be quantitatively determined. Jointly analyzing of the data.

Hamburg - Leipzig

Herrenknecht - Hengstler

• Subject: Supply with cultured mouse hepatocytes
  Details: Provision of primary hepatocytes is concerned, particularly with regards to establish conditions for preparation and shipment of frozen hepatocytes for this group.

Bochum - Leipzig

Emans - Gebhardt

• Subject: Wnt/ß-catenin pathway in hepatocytes
  Details: The expression of glutamine synthetase in hepatocytes transfected with ß-catenin was studied; cells were isolated, cultured, transfected and stained in Leipzig; Co-expression of glutamine synthetase and the GFP-ß-catenin construct was determined with high throughput analysis in the group of Emans; techniques for transfection of primary hepatocytes and isolation of cells were transferred to this group.

Leipzig - Stuttgart

Hengstler - Zanger

• Subject: SOPs
  Details: Mutual exchange of protocols and know-how in hepatocyte culture; measurement of drug metabolism in various cell lines.

Leipzig - Mannheim

Hengstler - Dooley

• Subject: SOPs
  Details: Generation of SOPs for hepatocyte isolation, culture and transport, which had to be specifically modified in dependence of the investigation (e.g. signal transduction, imaging, adenovirus infection), generation of an animal model to monitor EMT of hepatocytes during fibrogenesis.

Zellmer - Fischer/Dooley

• Subject: SOPs
  Details: Establishing transfection protocols of primary cultured hepatocytes, the exchange of transgenic animals and reagents (e.g. Smad7 antibody for immunostainings) was organized.

• Subject: Expression of glutamine synthetase in hepatocytes transfected with ß-catenin
  Details: Cells were isolated, cultured, transfected and stained in Leipzig. Co-expression of glutamine synthetase and the GFP-ß-catenin construct was determined with high throughput analysis in the group of Emans. Techniques for transfection of primary hepatocytes and isolation of cells were transferred to this group.

Freiburg - Heidelberg

Timmer - Keppler

• Subject: Modeling of vectorial transport of two different substrates by recombinant uptake (OATP1B3) and efflux (MRP2) transporters of human hepatocytes
  Details: Stably transfected in MDCKII cells, the model can simultaneously describe the different substrates for untransfected, single and double transfected cells, it shows that endogenous transporters, intracellular buffers, and paracellular transport play an additional, although minor role in this process, the kinetics of transport by uptake and efflux transporters have been successfully described by mathematical modeling.

Timmer - Klingmüller

• Subject: Modeling
  Details: Providing models for testing model reduction methods.

• Subject: Epo-receptor
  Details: Working in common on an analysis.

• Subject: Modeling of TGF-ß internalization trafficking and signaling in primary hepatocytes.

• Subject: Several hepatocyte signaling pathways (STAT, MAPK, Wnt/ß-catenin)
  Details: Experimental planning, model building and evaluation in close collaboration.

• Subject: Modeling of TGF-ß internalization trafficking and signaling in primary hepatocytes.

Magdeburg - Stuttgart

Gilles - Reuss

• Subject: FluxAnalyzer
  Details: The FluxAnalyzer package has been provided for structural network studies (minimal cut sets).

• Subject: Modeling of detoxification metabolism.

Leipzig - Magdeburg

Heinrich/Bader - Gilles

• Subject: Modeling of oxygen stress and TNF-induction in bioreactors
  Details: Providing of experimental data to verify the mathematical models; modeling for automated readings.

Berlin - Freiburg

Höfer - Timmer

• Subject: Modeling of growth factor signaling through Jak/Stat pathways relevant in liver development and regeneration
  Details: Based on recent experimental data, it is planned to adapt the model of the interferon/Stat1 network to the IL 6/Stat3 pathway both of which exhibit similarly complex molecular mechanisms of nuclear transport of the Stat transcription factors.

Herzel - Timmer

• Subject: Modeling of the G1/S transition of the cell cycle.

Berlin - Dresden

Höfer - Brusch/Deutsch

• Subject: Data-exchange
  Details: Investigations on interrelation of endocytosis and signaling pathways.

Heidelberg - Stuttgart

Kummer - Reuss

• Subject: Evaluation of modeling simulation tools
  Details: Providing models for testing model reduction methods.

Kummer - Schmid/Pleiss

• Subject: Detoxification and dedifferentiation in hepatocytes
  Details: Modeling and simulation of cytochrome P450s.

Kummer - Mauch

• Subject: Modeling of the central carbon metabolism of primary human hepatocytes
  Details: Model is made available to the group of Kummer, model will be used for validation of simulation tools developed at EML Research gGmbH.

Berlin - Erlangen

Holzhütter - Gasteiger

• Subject: Flux-balance approach
  Details: The specific features of the BIOPATH (biochemical pathways) data base developed in the group of Gasteiger and the experimental flux analysis (Group of Reuss) was edited together. Two Meetings (Stuttgart, Erlangen 2005) was devoted to the problem of efficiently merging the BIOPATH pathway data base with the stochiometric hepatocyte model built up by the Holzhütter group, local installation of the BIOPATH data base.

Berlin - Heidelberg

Höfer - Kummer

• Subject: Development of the calcium signal transduction model.

Höfer - Klingmüller

• Subject: Modeling of the Jak/Stat pathway
  Details: Plan to incorporate a detailed model together.

Berlin - Magdeburg

Holzhütter - Gilles

• Subject: FluxAnalyzer package
  Details: The package has been provided together for structural network studies.

Heinrich - Gilles

• Subject: Data-exchange
  Details: Exchange of experimental data necessary for the parameter estimation and realistic simulations.

Berlin - Leipzig

Heinrich - Bader

• Subject: Wnt/ß-Catenin pathway
  Details: Proposals for new experiments and for an extension of the existing model, preliminary theoretical results exchanged concerning the kinetic properties of a mutant form of ß-catenin.

Heinrich - Hengstler

• Subject: HGF signaling pathway via ERK1/2 and Akt/PKB
  Details: Monitoring the temporal dynamics of ERK and Akt during continuous stimulation and after a short transient stimulation of the pathway, modeling of the HGF/c-met signaling pathway in hepatocytes of B6 mice.

Heinrich - Gebhardt

• Subject: Wnt/ß-Catenin pathway
  Details: Jointly modeling of the Wnt/ß-Catenin pathway (Mus musculus), a kinetically oriented approach for modeling was used, it shall lead to some interesting predictions about ß-catenin function in situations (often met in liver tumours) where there is also a truncated form of ß-catenin. Wet lab experiments are under way in Leipzig, in order to validate these predictions and to supply additional data for further modeling in Berlin.

Berlin - Bochum

Marcus - Nüssler

• Subject: Supply of primary hepatocytes
  Details: Primary hepatocytes for subsequent proteome analysis are provided by the group of Prof. Nüssler.

Jena - Magdeburg

Pfaff/Guthke - Gilles

• Subject: Data-exchange
  Details: Selected data and analysis results were passed to the group of Gilles for further mechanistic modeling.

Freiburg - Jena

Timmer - Pfaff/Guthke

• Subject: Modeling
  Details: Selected pre-processed data were provided for jointly further analysis and mechanistic modeling. Development of mathematical models for the induction of the glutamine synthetase after stimulation with LiCl together with Prof. Gebhardt, Leipzig. The wet lab experiments were performed in Leipzig and the data analysis was done in Jena. The group of Timmer got these data for further modeling. This approach will allow to compare different strategies of modeling.

Berlin - Berlin

Holzhütter - Zeilinger

• Subject: Flux-analysis in the amino acid metabolism of hepatocytes
  Details: Data on the time-dependent kinetics of 18 amino acids, ammonia and urea from several runs of the 3D liver cell bioreactor were delivered to Dr. Guthke (Platform Cell Biology, Jena) and Prof. Holzhütter. In a first step, these data were analysed in the group of Dr. Guthke by means of a phenomenological two-compartment model consisting of a system of 42 differential equations. It is now planned to analyse the data on the basis of the flux-balance model of the complete hepatocyte metabolism developed in the group of Prof. Holzhütter.

Dresden

Conference

• European Conference on Mathematical and Theoretical Biology (ECMTB) July 18.-22. 2005: organised by the Deutsch group; 800 participants; during the meeting all modeling groups of HepatoSys were present and interacted closely; Prof. Höfer and Dr. Brusch (Platform Modeling) presented their results in a Mini-Symposium that had been organised by Dr. Peletier and Prof. Westerhoff; Prof. Timmer (Network Regeneration) together with Prof. Deutsch (Platform Cell Biology), Dr. Kummer and Prof. Gilles (Platform Modeling) organised a Mini-Symposia on 'Parameter identification and model discrimination for cellular systems: methods, tools and applications'.

Magdeburg

Server

• The central data management for all working groups of HepatoSys is located at the MPI Magdeburg. It is performed by Dr. Bannasch (Platform Modeling). The software products Expressionist and Phylosopher of the company Genedata AG have been installed on the central database server for HepatoSys at the MPI Magdeburg. An integrated database for HepatoSys that currently is being developed by Genedata will be available in 05/2007.

Freiburg

Server

• Development and Implementation of the Data-exchange-server for all members of HepatoSys through Dr. Heisner (Project Management) in August 2005.

Hepatocytes Supply

• Group of Prof. Timmer (Network Regeneration): Supply of the Network Regeneration with mouse hepatocytes.

Heidelberg

Conferences

• International Conference on Systems Biology (ICSB): October 9.-13. 2004 the 5th International Conference on Systems Biology was hosted in Heidelberg/Germany with participation of all working groups of HepatoSys; about 800 international experts from 37 countries presented and discussed their work in numerous poster sessions, workshops, and oral presentations, reaching from microbial systems biology to methods and software, and systems biology for medicine.

• 4th Workshop on Computation of Biochemical Pathways and Genetic Networks organized by Dr. Kummer (September, 12.-13. 2005).

• Conference on Systems Biology of Mammalian Cells (SBMC) 2006: July, 12.-14. 2006 at the Convention Center; promoted by the competence network HepatoSys.

Leipzig

Hepatocytes Supply

• Group of Prof. Hengstler (Platform Cell Biology): Establishing network-wide procedures for cultivation of hepatocytes (SOP); establishing conditions for preparation and shipment of frozen hepatocytes, supply of most of the working groups of HepatoSys with cultured mouse-, rat and human hepatocytes.

Berlin

Hepatocytes Supply

• Group of Prof. Nüssler (Platform Cell Biology): Supply of the Network Detoxification and Dedifferentiation with rat hepatocytes.

Freiburg - Heidelberg

Timmer - Kummer

• Subject: Providing models for testing model reduction methods.

Berlin - Freiburg

Zeilinger - Timmer

• Subject: Public relation
  Details: Providing a functioning bioreactor together with an display dummy to show how an external bioreactor with human hepatocytes is working; collection of these presentation material for the purpose of public relations.

Berlin - Leipzig

Affeld - Gebhardt

• Subject: Development of a novel bioreactor
  Details: Prototypes of the novel bioreactor have been exchanged and pressure sensors for constant flow rates have been adopted; hepatocytes will be seeded in these novel bioreactors within the next months; the influence of oxygen tension on hepatocyte differentiation in a 3D bioreactor will be tested.

• Subject: Technical support for Bioreactors
  Details: The newly developed bioreactors were used by the groups of Hengstler and Gebhardt; sterilization of the bioreactors with ethylene oxide had to be solved and pressure valves and electrical connections had to be adapted.

Zeilinger - Hengstler

• Subject: Validation of the metabolic activity of cultured mice and human hepatocytes
  Details: Characterisation of hepatocyte preparations with respect to heterogeneity. Influence of relative representation of subpopulations on performance in bioreactors.

Zeilinger - Gebhardt

• Subject: Investigation of zonation processes in 3D bioreactor co-cultures of human hepatocytes and non-parenchymal cells
  Details: Characterization of enzymatic parameters of hepatocytes in the liver reactors of the group of Zeilinger; parts of the reactors were sent from Berlin to Leipzig where the analysis was performed; these data will help to determine the ratio of periportal and pericentral hepatocytes within the liver bioreactor, which determines its metabolic capacity.

Berlin - Magdeburg

Zeilinger - Gilles

• Subject: Cell culture bioreactor
  Details: Providing experimental data that are used to verify the mathematical models.

Dresden - Heidelberg

Deutsch - Klingmüller

• Subject: Modeling of TGF-ß
  Details: Modeling of TGF-ß internalization trafficking and signaling in primary hepatocytes.

Zerial - Klingmüller

• Subject: Contruct of endosome biogenesis and transport
  Details: Intensify interaction with other network modeling groups to facilitate and construct the reconstitution of a protein and lipid network of components acting in endosome biogenesis and transport.

Erlangen - Stuttgart

Gasteiger - Schmid/Pleiss

• Subject: Dynamic Flux Analysis
  Details: Prediction of the regioselectivity of the phase I metabolism by cytochrome P450.

Gasteiger - Mauch

• Subject: Phase I Drug Metabolism
  Details: The databases on the endogenous and xenobiotic metabolism (BIOPATH resp. XENIA) developed in the group of Prof. Gasteiger have been linked to the INSILICO Biotechnology modeling software in order to automatically generate transition matrices.

Gasteiger - Zanger

• Subject: Model Validation
  Details: Experimental data from IKP is used to validate the selectivity models developed in the CCC.

Bochum - Stuttgart

Marcus - Schmid/Lange

• Subject: Comparative transcriptome and proteome analysis
  Details: Experimental data from the transcriptome and proteome analyses are compared and combined. Transcriptome data are used for targeted proteome analysis.

Marcus - Zanger/Eichelbaum

• Subject: CYP450 induction/dedifferentiation; AQUA
  Details: a) Results from the IKP concerning CYP450 induction and dedifferentiation processes in primary hepatocytes provide the basis for the differential proteome study (selection of time points etc.)
  b) The MPC provides new established methods for an absolute quantification of relevant proteins involved in phase I and phase II metabolism.

Marcus - Reuss

• Subject: a) Model validation; b) sample supply
  Details: a) Modeling data from the IBTV is confirmed by experimental proteome data at the MPC to validate the models. Additionally absolute quantification (AQUA) of relevant (membrane) proteins involved in phase I and phase II metabolism is used for model validation.
  b) Primary hepatocytes are centrally prepared at the IBTV for subsequent proteome analysis.

Marcus - Pleiss

• Subject: Development of AQUA technique
  Details: The cytochrome P450 database established by the group of Pleiss provides the basis fort he selection of suitable AQUA peptides.

Bochum - Magdeburg

Marcus - Bannasch

• Subject: Central data management
  Details: Development of a central data management for the whole project; integration of proteomics data.

Aachen - Leipzig

Fischer - Hengstler

• Subject: SOPs
  Details: Testing other source of primary hepatocytes to make it available for the group of Fischer, especially hepatocytes isolated from rats and in particular cryopreserved hepatocytes.

Fischer - Zellmer

• Subject: Wnt/ß-catenin pathway in hepatocytes
  Details: Imaging ß-catenin GFP fusion proteins to trace translocation phenomena coupled to ß-catenin and Wnt signaling in primary hepatocytes using the Opera platform.

Dresden - Freiburg

Zerial - Timmer

• Subject: Contruct of endosome biogenesis and transport
  Details: Intensify interaction with other network modeling groups to facilitate and construct the reconstitution of a protein and lipid network of components acting in endosome biogenesis and transport.

Berlin - Bochum

Heinrich - Füchslin/McCaskill

• Subject: Data exchange
  Details: Applying the specific theoretical concepts commonly used by the participating groups (mathematical modeling in the frame work of chemical reaction kinetics on one hand and reactive dissipative particle dynamics on the other) to the computational investigation of spatial phenomena involved in the formation of vesicles and in endocytosis.

• Subject: Compartment differentiation by vesicular traffic
  Details: Shall link up our theoretical tools (reactive DPD) on the elaborated models of endocytotic compartment differentiation via vesicular traffic with the chemical kinetic analysis of the groups in Berlin, a detailed workplan is assembled in October 2005.

The infrastructure of HepatoSys

How to use:

• All Network and Platform members of HepatoSys are represented by a colored spot at their place of work. The color of the spot indicates which Platform or Network the working group is belonging to (see legend).

• Collaborations are represented by links (dark gray lines). While navigating with the mouse over the illustration (especially over spots), all established collaborations of the working group within HepatoSys can be studied.

• When clicking on a certain spot, the activities of this HepatoSys member are displayed. When clicking on a certain link, a detailed description of the collaborations are given.

• When navigating over the label 'Germany', all collaborations within HepatoSys are shown.