Participant 1A: Stichting VU-VUMC,
Department of Molecular and Cellular Neurobiology, The Netherlands
Prof. dr. Guus Smit
The group will focus on providing a quantitative description of the protein composition and interactome of the mammalian glutamatergic synapse. It will generate insight in the dynamics of protein complexes under different experimental conditions, including rest and activation, or up- or down regulation of synaptic genes in mouse mutants (100 lines) of disease. A map of the synaptic proteome and interactome of synaptic proteins is crucial for making realistic kinetic models for synapse function in health and disease. The group will provide a detailed characterisation of the synaptic phosphoproteome used to map dynamic responses of the proteome to learning/plasticity related events for a limited set of conditions in collaboration with partner Grant. The PI (A.B. Smit) will coordinate SynSys, assisted by an experienced EU manager from the SME (Sylics) for management, networking and training activities.
Participant 1B: Stichting VU-VUMC,
Center for Neurogenomics & Cognitive Research (CNCR), The Netherlands
Prof. dr. Huibert Mansvelder
The group will focus on providing a quantitative description of the role of individual protein members of the synaptic interactome in mammalian glutamatergic synapse function in neuronal networks. In the SynSyn program, the single cell and single synapse level will be integrated in large-scale neuronal networks by assessing short- and long-term synaptic plasticity in acute brain slices. The role of fifty to hundred candidate proteins in synapse function and plasticity will be assessed by manipulating expression levels of these proteins. Dynamical parameters of synapse strength during spike-timing-dependent plasticity will be related to pre- and postsynaptic calcium dynamics and synaptic protein mutations A quantitative functional description will provide the necessary rate constants for the kinetic models for synapse function in health and disease, and predictions made by the models about synapse function will be tested quantitatively.
Participant 1C: Stichting VU-VUMC
Department of Functional Genomics, The Netherlands
Prof. dr. Matthijs Verhage
The main task of this project partner is (A) the functional analysis of genes expressed in the presynaptic nerve terminal (B) generation of dynamic models for the presynaptic gene network and (C) the collective testing of genes in such networks for association of variation with human brain traits such as cognition and several brain disorders. The department has an extensive track record in the functional analysis of synaptic transmission, human genetics of cognition and secretory vesicle trafficking using a wide variety of high-end methods.
Participant 3: University of Edinburgh (UEDIN),
School of Informatics, Edinburgh, UK
Dr. J. Douglas Armstrong
The group will focus on providing on the building, validating and analysis of protein interaction networks. Our key role will be to assemble the proteomics, interaction, molecular and phenotype datasets into a general static interaction model. This model will form the basis for the consortium and will then be elaborated to include more detailed information for example pathway dynamics (e.g. partner Le Novere) and human genetic information (e.g. partner Synaptologics). At each cycle of addition and development we will produce an analysis of the network and discuss findings and predictions with the other partners in a concerted effort to close the loop between systems modelling and systematic neuroscience research.
Participant 3B: University of Edinburgh (UEDIN),
Genes to Cognition Program, Edinburgh, UK
Prof. dr. Seth Grant
The first major task (WP1 and 2) is to isolate and characterize the synapse proteome and its subcomplexes and phosphoproteome. The second major task is to provide bioinformatics with G2Cdb and warehouse and analyze the proteomic data. The group has an extensive track record in synapse proteomics and mouse genetic methods.
Participant 4A: Max Planck Institute of Experimental Medicine (MPG)
Department of Molecular Neurobiology, Göttingen, Germany
Prof. dr. Nils Brose
N. Brose’s main task will be to study the function of synaptic proteins. He will generate mouse mutants lacking individual synaptic proteins and study the phenotypic changes caused by these mutations at the single neuron level using a highly standardized culture system, i.e. autaptic hippocampal neurons. These studies will be complemented by analyses of neurons overexpressing the corresponding proteins.
Participant 4B: Max Planck Institute of Biophysical Chemistry (MPG)
Department of Neurobiology, Göttingen, Germany
Prof. dr. Reinhard Jahn
R. Jahns’ main task is to isolate and characterize subsynaptic protein complexes by immunoprecipitation, focussing on synaptic membrane proteins, and to participate in large-scale yeast two-hybrid screens to map underlying binary protein-protein interactions. Furthermore, the partner will be involved in the standardization of the HTS-procedure for screening compound libraries with respect to specific and selected protein-protein interactions.
Participant 5: Max-Delbrück-Centrum für Molekulare Medizin (MDC)
Prof. dr. Erich Wanker
An automated large-scale yeast three-hybrid (Y3H) system will be utilised for the identification of primary interactions between phosphoproteins using also predictive protein-protein-interaction (PPI) data delivered by the bioinformatics section. For interaction screenings, a prey-library arrayed in microtitre plates is available. It contains ~14,000 unique, full-length cDNAs and covers more than 75% of the human genome. The Y3H method recently developed in our laboratory can probably be adapted for the screening of Ca2+- dependency of PPIs. For the validation of Y3H interactions, a combination of experimental and computational procedures will be utilised. For the verification of the Y3H interactions, the cDNA fragments will be subcloned into vectors for the Lumier assay using the GATEWAY technology. The improved version of the Lumier assay recently established in the Wanker laboratory has the amenability to high-throghput screening approches as compared to conventional co-immunoprecipitation and Western blotting procedures.
Participant 6: EMBL-European Bioinformatics Institute (EMBL-EBI)
Wellcome-Trust Genome Campus, United-Kingdom
Dr. Nicolas Le Novère
The group will focus on providing models of the processes taking place at the pre- and post-synaptic levels. Qualitative networks of influence will be built in collaboration with the group of Armstrong. Quantitative kinetics models will be developed to understand the dynamics of pre-synaptic vesicles (together with Verhage), the modulation of synaptic weight (with Mansvelder), and the onset of plasticity (with Grant and Girault). Those models will feed back to the experimental workpackages. The group will also assist in encoding, annotating and sharing interactomes, pathways and models.
Participant 7: University of Copenhagen (UCPH)
Department of Neuroscience and Pharmacology, Faculty of Health Sciences, Denmark
Prof. dr. Jakob .B. Sørensen
The group will focus on providing detailed knowledge about the physiological function of specific presynaptic proteins. We will assess synaptic function using standardized preparations (autaptic cultures and chromaffin cells) following up-, down-regulation or mutation of synaptic proteins using available mouse mutants (100 lines) and viral knock-down/overexpression techniques. Detailed quantitative information on the pool size of synaptic vesicles and the rate and calcium-dependence of secretion is crucial for making realistic models of the presynapse. On the other hand, information from modelling will be helpful in designing experiments attacking proteins controlling key functions in the presynapse.
Participant 8: Karolinska Institutet (KAR)
Linné Centre for Developmental Biology and Regenerative Medicine (DBRM)
Department of Neuroscience, Stockholm, Sweden
Prof. dr. Oleg Shupliakov
To provide a dynamic 3-D map of protein localization in the mammalian glutamatergic synapse at rest and during synaptic activity. To analyse the consequences of up- and down regulation, genetic deletion, and mutations of proteins involved in neurological diseases on 3D-organization of the synapse and synaptic protein distribution.
Participant 9: Charite University Medicine Berlin (CHAR)
Institute of Physiology, Germany
Prof. dr. Robert Preissner
The main task of the group will be the investigation and analysis of the proteins of the synaptic proteome and the prediction of protein-protein interactions derived from conserved protein domain contacts. Putative binding sites will be further validated experimentally by the design of non-linear peptide libraries representing the interacting sites followed by the synthesis and screening of peptide microarrays. Furthermore, the experience in the design of peptidomimetics will be applied to interfere with specific protein-protein interaction or to disturb the complex formation of proteins.
Participant 11: Institut national de la santé et de la recherché médicale (Inserm)
Institut du Fer à Moulin, Paris, France
Prof. dr. Jean-Antoine Girault
The group will contribute to the consortium its expertise in study of intracellular signaling networks in vivo and in vitro. The work will include in vivo and in vitro studies of G proteins, protein phosphorylation pathways and other post-translational modifications in response to pharmacological and behavioural stimulation in wild type and mutant mice. They will study signaling at the synaptic and at the nuclear levels including its output on gene expression. They will closely interact with other partners and provide data for models and test hypothesis derived from these models.
Participant 12 : Katholieke Universiteit Leuven (VIB)
VIB at KUL, Belgium
Prof. dr. Claudia Bagni
The group will focus on providing the mRNP composition of the synaptosomes during development. The mRNA/RNA content will be analyzed on microarrays (in the dedicated VIB facility). In a parallel study we will isolate native mRNPs (translating and silent) through well-established sucrose gradients and the content of the two different components (RNA and protein) analyzed independently (microarray and mass spec). Finally these studies will be performed for a pathological condition such as mental retardation using three mouse models to study the Fragile X Syndrome and Autistic Spectrum Disorder.
Participant 13: The Institute for Molecular Medicine Finland (FIMM)
Prof. dr. Aarno Palotie
The main areas of activity will lie in: gathering human genetic variation, quality control and co-analysis of GWAS data, contribution of cohorts Finrisk, Health 2,000 and NFBC1966 for the common consortium database (in WP2) (total n= 73,204, GWA 8,129).
Participant 14: Synome Ltd (SME) (SYN)
Dr. Troels Jordansen
The main task will be to exploit Synome’s MEA methods to study the effects of gene disruption (WP 5) on synaptic physiology and network oscillations in brain slices on MEA. These in vitro neural network assays are complementary to physiological methods either in slices or patch clamping used in other WPs.
Participant 15: Brainwave-Discovery Ltd (SME) (BWD)
Prof. Wayne Davies
BWD will provide contract services whereby proteins identified by the SynSys partners as potential disease candidates will be engineered in normal and/or variant form into the fly brain. They will then be profiled using an array of physiological, anatomical and behavioural tests. These technologies will provide a system whereby new candidates can be assessed very rapidly and cost-effectively (approx 5x faster and 5x cheaper than rodent models) yet sill providing real living brain information. This will reduce the overall animal use by the consortium.
Participant 16: Beactica AB (SME) (Beactica)
Prof. dr. Helena Danielson
Beactica will develop assays for studying the interactions between synaptic proteins and perform detailed interaction studies of selected proteins. By competition experiments and ligand interference studies followed by computational structure modelling, the interactions will be structurally mapped. The kinetic details and importance of experimental conditions for the interactions will be explored in order to determine the characteristics of the interactions and their regulation. Models for protein interaction networks will be developed.
Participant 17: Sylics (SME) (SYL)
Amsterdam, The Netherlands
CEO: Prof. dr. Arjen Brussaard
The main task of Sylics (the tradename of Synaptologics BV) within SYNSYS is to provide a smooth operation process by supporting coordination and management activities of the coordinator. Whereas the coordinator (Smit) will be responsible for the overall program, and in particular for the financial mangement, Sylics will focus on project management and logisitcs, specifically implementing optimized and customized solutions for the partner groups, e.g., providing updated timetables and budgets, providing meeting schedules and organizing conferences, drafting reports and provide reporting to the EU, engaging in data-dissemination and webhosting as well as organizing webinars enhancing networking and training activities.