References of "Depaulis, Antoine"
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See detailDYNAMIC PROTEOME ANALYSIS OF ANTERIOR MICE HIPPOCAMPUS
Jackers, Pascale ULg; Vafiadaki, Elizabeth; Arvanitis, D.A. et al

Poster (2010, September 07)

Neurodegeneration is a molecular process that occurs during several brain diseases (Parkinson, Alzheimer, Epilepsies). This process leads to the reorganization of synapses and neurons in the Central ... [more ▼]

Neurodegeneration is a molecular process that occurs during several brain diseases (Parkinson, Alzheimer, Epilepsies). This process leads to the reorganization of synapses and neurons in the Central Nervous System. The search for early medication to reduce neurodegeneration is a major challenge in Neuroscience. To this aim VALAPODYN, a European Commission-funded research network, develops functional genomics and proteomics related to the dynamics of molecular interaction networks (MIN). MIN modeling investigates protein-protein interactions and regulation networks. This study is established on scientific literature and on experimental data coming out of genomic and proteomic analyses. Experimental data are obtained thanks to a model of kainate inducing cell loss with focal epilepsy in mice hippocampi . This model permit the EU Consortium to get a transcriptome and proteome dynamic expression analysis conducted at 10 successive time-points during the first 24h after kainate induction. Proteome dynamic analysis is performed with total and fractionated proteins extracts. Obtained proteins are separated by two methods: (i) a classic method based on 2D-PAGE gel separation of these proteins; (ii) a method based on the 2D-HPLC liquid separation of digested peptides. When proteins are separated on 2D-PAGE, proteins spots are visualized thanks to 2 images analysis software’s using different mathematical algorithms. Proteins spots are picked and digested automatically using a spot picker and a recently acquired digester workstations. Mass spectrometry identification of digested peptides (2D PAGE MALDI-TOF/TOF and 2D-LC MS/MS) highlighted the modulation of the expression of 232 different proteins during the first 24h after kainate induction. The dynamic proteome analysis was performed thanks to complementary strategies to cover a large window of molecular events as a result of cellular loss induction. “User-friendly” documents were constructed to efficiently communicate proteome information. The obtained lists of proteins were extensively analysed with public databases (UniProtKB, NCBI, Pfam etc) to review interactions, biological functions, protein families with different isoforms and cellular-tissue localisation. We want also to emphasize that several proteins families showed multiple spots as a result of different isoforms. These isoforms are probably the consequence of natural chemical modifications. The study of these chemical modifications in the native conditions needs a dynamic analysis of the tri-dimensional structure and folding showed by these isoforms. This new study will permit to establish a link between proteomic, interactomic data and data issue from the structural biology. [less ▲]

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See detailIn Silico Dynamic Molecular Interaction Networks for the Discovery of New Therapeutic Targets
Vujasinovic, Todor; Zampera, André Sinisa; Jackers, Pascale ULg et al

in Current Pharmaceutical Design (2010), 16(20), 2241-2251

Systems biology has emerged as a major trend in biological research during the past decade. As living organisms are described in more and more detail, it aims at filling the gap between understanding ... [more ▼]

Systems biology has emerged as a major trend in biological research during the past decade. As living organisms are described in more and more detail, it aims at filling the gap between understanding basic molecular processes and complex biological systems in which new properties often emerge from the combination of these elementary processes. This approach culminates in the development of computer-based mathematical models of physiological and pathophysiological processes. We review the state of the art in dynamic modelling, with emphasis on two complementary approaches: the modelling of small systems that is mostly developed by academic teams and aims at understanding generic biological properties, and the modelling of large systems that is mostly implemented by industrial companies and aims at the generation of new therapeutic strategies. We also provide an example of such large-scale modelling applied to the identification of drug targets for neurodegeneration. [less ▲]

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See detailQuantitative dynamic proteome biology of anterior mice hippocampus
Jackers, Pascale ULg; Vafiadaki, Elizabeth; Arvanitis, D.A. et al

Poster (2009, September 27)

Neurodegeneration is a molecular process that occurs during several brain diseases (Parkinson, Alzheimer, Epilepsies). This process leads to the reorganization of synapses and neurons in the Central ... [more ▼]

Neurodegeneration is a molecular process that occurs during several brain diseases (Parkinson, Alzheimer, Epilepsies). This process leads to the reorganization of synapses and neurons in the Central Nervous System. The search for early medication to reduce neurodegeneration is a major challenge in Neuroscience. To this aim, VALAPODYN, a European Commission-funded research network, develops functional genomics and proteomics related to the dynamics of molecular interaction networks (MIN). MIN modeling investigates protein-protein interactions and regulation networks. Using a mouse model of induced hippocampal cell loss associated with focal epilepsy, dynamic protein expression analyses were conducted at 10 successive time-points during the first 24h. Protein expression was analysed by mass spectrometry, using a “classical” gel-based method as a means of covering all modulated proteins at each considered time-points. Proteins were extracted from minutes amount of frozen hippocampal samples and subjected on two-dimensional difference in-gel electrophoresis (2D-DIGE). This analysis allows quantification of cyanine-labelled proteins. A total of 252 differentially regulated proteins spots were picked digested and identified using MALDI/TOF-TOF mass spectrometry. Overall the expressions of 127 different proteins were identified as reproducibly modulated over the time-range studied. Several proteins have multiple protein spots resulting from different isoforms. The functional annotation of these proteins shows that, among other mechanisms, most of them are involved in the response to stress, synapse remodelling, neuron development, and intracellular signal transduction. [less ▲]

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See detailFinalized experimental procedures for proteins analysis - WP N°: 2 Deliverable N°: D2.5
Jackers, Pascale ULg; Sanoudou, Despina; Depaulis, Antoine

Report (2009)

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See detailMembrane and cytoplasmic proteome biology of anterior mice hippocampus
Jackers, Pascale ULg; Massart, Anne-Cécile; Depaulis, Antoine et al

Poster (2008, October 10)

The prevalence of neurodegenerative diseases increases steadily and proteomics on disease-related brain areas become more and more complex, whereas suitable samples are scarce. Due to this difficulty ... [more ▼]

The prevalence of neurodegenerative diseases increases steadily and proteomics on disease-related brain areas become more and more complex, whereas suitable samples are scarce. Due to this difficulty, animal models are indispensable in understanding human biology and disease, and the most commonly used model is the mouse (Mus musculus). Mice share many genetic and physiological characteristics with humans, breed rapidly, and can be genetically modified leading to the functional characterisation of many proteins. As for human, the mouse hippocampus is one of the most important areas of the brain and has therefore been an object of intensive investigation for many years. Mouse hippocampus has served as models for degenerating brain diseases associated with Alzheimer's disease, Parkinson's disease, ischemia, epilepsy, synaptic plasticity and underlying mechanisms of learning and memory. Using 2 anterior parts of normal mouse hippocampi, we intend to characterize membrane and cytoplasmic proteome using a modified procedure previously established (WISNIEWSKI et al., 2008). This method permit the preparation and analysis of 2 individual fractions enriched in membrane and cytoplasmic proteins. The method for separation of membrane and cytoplasm fractions comprises a stepwise depletion of non-integral membrane proteins from entire tissue homogenate by high-salt, carbonate, and urea washes. The cytoplasmic proteins obtained from high-salt depletion are considered as the soluble fraction. The membrane proteins obtained from the stepwise depletion are considered as the insoluble fraction. Enzymatic digestion of both membrane and cytoplasmic fractions are carried out without use of detergents by double digestion with endoproteinase Lys-C and trypsin. Digested peptide fractions are loaded on StageTips for rapid desalting and are separated by online reversed-phase (RP) nanoscale capillary liquid chromatography (nanoLC). Separated peptides are analyzed by electrospray tandem mass spectrometry (HPLC-ESI-MS/MS). The entire procedure allows rapid processing and preparation of samples from minute amounts as 30-40 mg frozen tissue leading to about 70 g of membrane proteins and 500 g of cytoplasmic proteins. This can be extremely helpful for proteomic profiling of small pieces of tissue and clinical material. Analyses of membrane fraction identified about 45% total membrane proteins. This fraction includes glutamate receptor 1 and 2, proteins involved into the trafficking of synaptic vesicles, lipid-anchor proteins, G proteins involved in various transmembrane signalling systems, NMDAR signalling complex proteins, voltage channel proteins… Analyses of the cytoplasmic fraction identify various proteins belonging to different compartments and/or pathways. A large amount of these proteins are specifically expressed into the hippocampus and/or into the nervous system. [less ▲]

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See detailVALAPODYN: A new systems biology approach to develop predictive dynamic models of complex intracellular networks for neurological disease
Sanoudou, Despina; Depaulis, Antoine; Vafiadaki, Elizabeth et al

Poster (2008, August 22)

Objective: VALAPODYN, a European Commission funded research network, is using an original systems biology approach for the development of an innovative dynamic model of molecular interaction networks (MIN ... [more ▼]

Objective: VALAPODYN, a European Commission funded research network, is using an original systems biology approach for the development of an innovative dynamic model of molecular interaction networks (MIN) in relation to cell death and survival for the detection of new therapeutic targets for human neurological diseases. To this end, a comprehensive multidisciplinary strategy has been established combining functional genomics, proteomics and bioinformatics. Results: Using a mouse model of induced hippocampal sclerosis associated with focal epilepsy, dynamic expression analyses are conducted at different time points. Proteomic databases are being used along with advanced microarray and proteomics platform systems to investigate protein-protein interactions and regulation networks, identify and validate biological targets in complex intracellular pathways. The first phase involves whole genome and proteome analysis, integrating biological and statistical data in order to functionally annotate genes and proteins. Using Affymetrix microarrays, 2D-DIGE and MALDI/TOF-TOF, we are evaluating whole genome and proteome expression profiles bringing to light critical new pathways and molecular targets implicated in neurodegeneration. Conclusion: VALAPODYN develops a dynamic and quantitative analysis method for new therapeutic targets through MIN dynamic models and specifically addresses the systems biology of complex cellular pathways and transcriptional networks. Novel predictive dynamic models will be validated by testing the selected drug targets on innovative in vivo and in vitro models of CNS pathologies. VALAPODYN will provide a cutting-edge highly accurate in silico tool for identifying novel and effective therapeutic targets in a faster, more efficient and more economical way than it is possible today. [less ▲]

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See detailDeveloping predictive dynamic models of complex intracellular networks for neurological disease
Vafiadaki, Elizabeth; Depaulis, Antoine; Jackers, Pascale ULg et al

in FEBS Journal (2008, June 28), 275(Issue s1), 206

Introduction: VALAPODYN, a European Commission funded research network, is an original systems biology approach for the development of an innovative model on the dynamics of molecular interaction networks ... [more ▼]

Introduction: VALAPODYN, a European Commission funded research network, is an original systems biology approach for the development of an innovative model on the dynamics of molecular interaction networks (MIN) in relation to cell death and survival for the detection of new therapeutic targets for human neurological diseases. To this end, a comprehensive multidisciplinary strategy has been established combining functional genomics, proteomics and bioinformatics. Methods and Results: Using a mouse model of induced hippocampal sclerosis associated with focal epilepsy, dynamic expression analyses are conducted at different time points. Proteomic databases are being used along with advanced microarray and proteomics platform systems to investigate protein-protein interactions and regulation networks, identify and validate biological targets in complex intracellular pathways. The first phase involves whole genome and proteome analysis, integrating biological and statistical data in order to functionally annotate genes and proteins. Using Affymetrix microarrays, 2D-DIGE and MALDI/TOF-TOF, we are evaluating whole genome and proteome expression profiles bringing to light critical new pathways and molecular targets implicated in neurodegeneration. Discussion: VALAPODYN develops a dynamic and quantitative analysis method for new therapeutic targets through MIN dynamic models and specifically addresses the systems biology of complex cellular pathways and transcriptional networks. Novel predictive dynamic models will be validated by testing the selected drug targets on innovative in vivo and in vitro models of CNS pathologies. VALAPODYN will provide a cutting-edge highly accurate in silico tool for identifying novel and effective therapeutic targets in a faster, more efficient and more economical way than it is possible today. [less ▲]

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See detailDynamic proteomics of mice hippocampus to study apoptosis
Jackers, Pascale ULg; Bertrand, Virginie ULg; Vafiadaki, Elizabeth et al

Poster (2008, May 30)

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See detailQuality control procedures from task 2.4 - WP N°: 2 Deliverable N°: D2.4
Jackers, Pascale ULg; Despina, Sanoudou; Depaulis, Antoine

Report (2008)

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See detailDynamic proteomics of mice hippocampus to study apoptosis
Jackers, Pascale ULg; Bertrand, Virginie ULg; Vafiadaki, Elizabeth et al

Poster (2008, February 15)

Apoptosis or physiological programmed cell death is a molecular process observed during neurodegenerative diseases (Epilepsies, Alzheimer…). The neurodegeneration leads to the reorganization of synapses ... [more ▼]

Apoptosis or physiological programmed cell death is a molecular process observed during neurodegenerative diseases (Epilepsies, Alzheimer…). The neurodegeneration leads to the reorganization of synapses and neurons in the CNS. Consequently, searches for early medication are a major challenge in Neuroscience. To this aim, VALAPODYN, a European Commission funded research network, develops functional genomics and proteomics related to the dynamics of molecular interaction networks (MIN). MIN modeling investigates protein-protein interactions and regulation networks. Using a model of induced hippocampal sclerosis associated with focal epilepsy in the mouse, dynamic expression analyses are conducted at different time points. Hippocampal samples were subjected on 2D-DIGE analysis which allows quantification of cyanine labelled proteins. Biological variation analysis yields about 1500 protein spots. These spots include 34 protein spots to be differentially regulated. The distribution is consistent with the literature showing that CNS proteins are mainly composed of acidic and neutral proteins. Several proteins have multiple protein spots likely resulting from different isoforms. Spots of interest will be digested with proteases and analysed using MALDI/TOF-TOF. Total proteins mixture will also be submitted to ESI-MS after HPLC separation as a means of improving both protein and proteome coverage by using complementary instruments. [less ▲]

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See detailA SYSTEMS BIOLOGY APPROACH TARGETING NEUROLOGICAL DISEASE- FROM GENOMICS TO IN SILICO PREDICTIVE MODELS
Vafiadaki, Elizabeth; Depaulis, Antoine; Jackers, Pascale ULg et al

Poster (2007, December 07)

VALAPODYN, a European Commission funded research network, is constructing an original system biology approach for the development of multidisciplinary functional genomics related to complex biological ... [more ▼]

VALAPODYN, a European Commission funded research network, is constructing an original system biology approach for the development of multidisciplinary functional genomics related to complex biological processes and cellular networks. The aim is to generate an innovative model on the dynamics of molecular interaction networks (MIN) in relation to cell death and survival for the detection of new therapeutic targets to treat human brain diseases. Proteomic databases are being used along with leading microarray and proteomics platform systems to investigate protein-protein interactions and regulation networks. This will help to identify and validate biological targets in complex intracellular pathways to cure multifactorial diseases. Dynamic modeling specifically addresses the systems biology of complex cellular pathways and transcriptional networks. Novel dynamic models will be validated by testing the selected drug targets on innovative in vivo and in vitro models of CNS pathologies. The first phase involves fundamental genomics research, integrating statistical data analysis with real biological data in order to functionally annotate genes and proteins. Using Affymetrix microarrays, we are evaluating whole genome expression profiles generated from dissected mouse brains following different treatments at various time points. Through the simultaneous analysis of ~40,000 genes, critical pathways and molecular targets implicated in neurodegeneration are being revealed. VALAPODYN develops a dynamic and quantitative analysis method for new therapeutic targets through MIN dynamic models. It will provide a cutting-edge highly accurate in silico tool for identifying novel and effective therapeutic targets in a faster, more efficient and more economical way than it is possible today. (www.valapodyn.eu). dsanoudou@bioacademy.gr [less ▲]

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See detailDynamic proteomics of mice hippocampus to study apoptosis
Jackers, Pascale ULg; Bertrand, Virginie ULg; Vafiadaki, Elizabeth et al

Poster (2007, September 04)

Apoptosis or physiological programmed cell death is a molecular process observed during neurodegenerative diseases (Epilepsies, Alzheimer…). The neurodegeneration leads to the reorganization of synapses ... [more ▼]

Apoptosis or physiological programmed cell death is a molecular process observed during neurodegenerative diseases (Epilepsies, Alzheimer…). The neurodegeneration leads to the reorganization of synapses and neurons in the CNS. Consequently, searches for early medication are a major challenge in Neuroscience. To this aim, VALAPODYN, a European Commission funded research network, develops functional genomics and proteomics related to the dynamics of molecular interaction networks (MIN). MIN modeling investigates protein-protein interactions and regulation networks. Using a model of induced hippocampal sclerosis associated with focal epilepsy in the mouse, dynamic expression analyses are conducted at different time points. Hippocampal samples were subjected on 2D-DIGE analysis which allows quantification of cyanine labelled proteins. Biological variation analysis yields about 1500 protein spots. These spots include 34 protein spots to be differentially regulated. The distribution is consistent with the literature showing that CNS proteins are mainly composed of acidic and neutral proteins. Several proteins have multiple protein spots likely resulting from different isoforms. Spots of interest will be digested with proteases and analysed using MALDI/TOF-TOF. Total proteins mixture will also be submitted to ESI-MS after HPLC separation as a means of improving both protein and proteome coverage by using complementary instruments. [less ▲]

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See detailVALAPODYN: Validated Predictive Dynamic Model of Complex Intracellular Pathways Related to Cell Death and Survival
Depaulis, Antoine; Vafiadaki, Elizabeth; Jackers, Pascale ULg et al

in European Journal of Human Genetics (2007, June 16), 15(Supp 1), 307

VALAPODYN is a research network funded by the European Commission (6th Framework Program) which is developing an original systems biology approach focused on the development of multidisciplinary ... [more ▼]

VALAPODYN is a research network funded by the European Commission (6th Framework Program) which is developing an original systems biology approach focused on the development of multidisciplinary functional genomics related to complex biological processes and cellular networks. The aim is to generate an innovative approach to model the dynamics of molecular interaction networks (MIN) in relation to cell death and survival to detect new therapeutic targets to treat human brain diseases. The project consists of fundamental genomics research which is integrating statistical data analysis with real biological data in order to functionally annotate genes and proteins. Specialized genomics and proteomics databases for MIN modeling are being used along with leading microarray and proteomics platform systems to investigate protein-protein interactions and regulation networks. This will help to identify and validate biological targets in complex intracellular pathways to cure multifactorial diseases. Dynamic modeling specifically addresses the systems biology of complex cellular pathways and transcriptional networks. The novel dynamic models will be validated by testing the selected drug targets on innovative in vivo and in vitro models of CNS pathologies. As opposed to most current biological data analysis methods, VALAPODYN develops a dynamic and quantitative analysis method for new therapeutic targets through MIN dynamic models. It will provide a cutting-edge highly accurate in silico tool for identifying novel and effective therapeutic targets in a much faster, more efficient and more economical way than it is possible today. (www.valapodyn.eu). [less ▲]

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See detailVALAPODYN: VALIDATED PREDICTIVE DYNAMIC MODEL OF COMPLEX INTRACELLULAR PATHWAYS RELATED TO CELL DEATH AND SURVIVAL
Depaulis, Antoine; Vafiadaki, Elizabeth; Jackers, Pascale ULg et al

Poster (2007, May 17)

VALAPODYN is a research network funded by the European Commission (6th Framework Program) which is developing an original systems biology approach focused on the development of multidisciplinary ... [more ▼]

VALAPODYN is a research network funded by the European Commission (6th Framework Program) which is developing an original systems biology approach focused on the development of multidisciplinary functional genomics related to complex biological processes and cellular networks. The aim is to generate an innovative approach to model the dynamics of molecular interaction networks (MIN) in relation to cell death and survival to detect new therapeutic targets to treat human brain diseases. The project consists of fundamental genomics research which is integrating statistical data analysis with real biological data in order to functionally annotate genes and proteins. Specialized genomics and proteomics databases for MIN modeling are being used along with leading microarray and proteomics platform systems to investigate protein-protein interactions and regulation networks. This will help to identify and validate biological targets in complex intracellular pathways to cure multifactorial diseases. Dynamic modeling specifically addresses the systems biology of complex cellular pathways and transcriptional networks. The novel dynamic models will be validated by testing the selected drug targets on innovative in vivo and in vitro models of CNS pathologies. As opposed to most current biological data analysis methods, VALAPODYN develops a dynamic and quantitative analysis method for new therapeutic targets through MIN dynamic models. It will provide a cutting-edge highly accurate in silico tool for identifying novel and effective therapeutic targets in a much faster, more efficient and more economical way than it is possible today. (www.valapodyn.eu). [less ▲]

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