References of "Trefois, Christophe 50003220"
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See detailLight microscopy applications in systems biology: opportunities and challenges.
Antony, Paul UL; Trefois, Christophe UL; Stojanovic, Aleksandar UL et al

in Cell Communication and Signaling (2013), 11(1), 1-19

Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various ... [more ▼]

Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various biological scales in living cells. The combination of molecular biology and imaging provides a bottom-up tool for direct insight into how molecular processes work on a cellular scale. However, imaging can also be used as a top-down approach to study the behavior of a system without detailed prior knowledge about its underlying molecular mechanisms. In this review, we highlight the recent developments on microscopy-based systems analyses and discuss the complementary opportunities and different challenges with high-content screening and high-throughput imaging. Furthermore, we provide a comprehensive overview of the available platforms that can be used for image analysis, which enable community-driven efforts in the development of image-based systems biology. [less ▲]

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See detailThe Parkinson's Disease Map: A Framework for Integration, Curation and Exploration of Disease-related Pathways
Ostaszewski, Marek UL; Fujita, Kazuhiro; Matsuoka, Yukiko et al

Poster (2013, March 09)

Objectives: The pathogenesis of Parkinson's Disease (PD) is multi-factorial and age-related, implicating various genetic and environmental factors. It becomes increasingly important to develop new ... [more ▼]

Objectives: The pathogenesis of Parkinson's Disease (PD) is multi-factorial and age-related, implicating various genetic and environmental factors. It becomes increasingly important to develop new approaches to organize and explore the exploding knowledge of this field. Methods: The published knowledge on pathways implicated in PD, such as synaptic and mitochondrial dysfunction, alpha-synuclein pathobiology, failure of protein degradation systems and neuroinflammation has been organized and represented using CellDesigner. This repository has been linked to a framework of bioinformatics tools including text mining, database annotation, large-scale data integration and network analysis. The interface for online curation of the repository has been established using Payao tool. Results: We present the PD map, a computer-based knowledge repository, which includes molecular mechanisms of PD in a visually structured and standardized way. A bioinformatics framework that facilitates in-depth knowledge exploration, extraction and curation supports the map. We discuss the insights gained from PD map-driven text mining of a corpus of over 50 thousands full text PD-related papers, integration and visualization of gene expression in post mortem brain tissue of PD patients with the map, as well as results of network analysis. Conclusions: The knowledge repository of disease-related mechanisms provides a global insight into relationships between different pathways and allows considering a given pathology in a broad context. Enrichment with available text and bioinformatics databases as well as integration of experimental data supports better understanding of complex mechanisms of PD and formulation of novel research hypotheses. [less ▲]

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See detailDifferentiated SH-SY5Y Cells as PD Model for Mitochondrial Dysfunction: From Whole Genome Sequencing to an Educated Design of High-Throughput Experiments
Antony, Paul UL; Krishna, Abhimanyu UL; May, Patrick UL et al

Poster (2013)

Objectives: Mitochondrial dysfunction is a cellular hallmark of Parkinson's disease (PD) and energetic stress of dopaminergic neurons appears to be a physiological risk factor for mitochondrial ... [more ▼]

Objectives: Mitochondrial dysfunction is a cellular hallmark of Parkinson's disease (PD) and energetic stress of dopaminergic neurons appears to be a physiological risk factor for mitochondrial dysfunction. It is however challenging to assess the high variety of factors regulating mitochondrial physiology in living neurons in a high throughput manner. To overcome this bottleneck, we established an analysis platform, using the neuroblastoma cell line SH-SY5Y. For the first time ever we have characterized the SH-SY5Y cell line in an integrated whole genome, transcriptome, and proteome approach. In addition, we show that neuronal differentiation improves the physiological properties of this experimental model for studying mitochondrial dysfunction in PD. Methods: Whole genome sequencing, RNA-Seq, qRT-PCR, MS, FRET using Voltage sensing proteins, Immunofluorescence, cytometry, and live cell imaging. Results: The integrated molecular characterization of SH-SY5Y uncovers the level of molecular network integrity and hence the relevance of this cell line for targeted studies in selected molecular processes. Furthermore, we dissect changes in mitochondrial and energetic stress factors during the process of neuronal differentiation. Conclusions: In terms of both morphology and energetic stress response, differentiated SH-SY5Y cells are more similar to dopaminergic neurons than their undifferentiated precursors. Thanks to dividing progenitors and the short duration of differentiation, combined with the use of specific endpoints analysed with high-content microscopy, our platform paves the route for high throughput experiments on a neuronal cell culture model for PD. Our genomic characterization and expression profiling of SH-SY5Y cells furthermore helps guiding the experimental design and interpretation of such studies. [less ▲]

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See detailAnalysis of critical transitions in Parkinson's disease
Trefois, Christophe UL; Antony, Paul UL; Baumuratov, Aidos UL et al

Poster (2011, December 12)

Background Parkinson’s disease is the most common neurodegenerative movement disorder and is clinically characterized by resting tremor, bradykinesia and cogwheel rigidity. The disease affects 1-2% of the ... [more ▼]

Background Parkinson’s disease is the most common neurodegenerative movement disorder and is clinically characterized by resting tremor, bradykinesia and cogwheel rigidity. The disease affects 1-2% of the global population with prevalence in the people above 65 years of age. The main pathological hallmark of Parkinson’s disease is a progressive loss of dopaminergic neurons in the substantia nigra. Therefore, one important challenge is to improve the understanding of regime shifts between health and disease states. Improving predictions of critical transitions triggering the onset of parkinsonian phenotypes could contribute to the improvement of preventive treatments. Methods Based on cellular models, we will use the mathematical concept of critical transitions to create a toolbox for potentially predicting tipping points towards cellular Parkinson’s disease phenotypes, e.g. mitochondrial dysfunction. Experimentally, we will induce and analyze potential critical transitions in the SH-SY5Y cell line. To do this, we will apply Parkinson’s disease relevant chemical and genetic perturbations and analyze multiple scales of the resulting temporal system behavior. We will combine high content imaging with genetic and biochemical data. A significant informatics challenge arises from the aim to perform the analysis of high time-resolved 3D imaging data. We are therefore developing an automated image analysis pipeline that relies on latest technologies and techniques, such as 3D deconvolution and 3D particle tracking. This pipeline will be applied to study parameters, such as mitochondrial dynamics, which include for instance velocity, morphology, and spatial organization. [less ▲]

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See detailEfficient Access Control for Wireless Sensor Data
Sorniotti, Alessandro; Molva, Refik; Gomez, Laurent et al

in International Journal of Wireless Information Networks (2009), 6(3), 165--174

Abstract Although very developed in many sectors (databases, filesystems), access control schemes are still somewhat elusive when it comes to wireless sensor net- works. However, it is clear that many WSN ... [more ▼]

Abstract Although very developed in many sectors (databases, filesystems), access control schemes are still somewhat elusive when it comes to wireless sensor net- works. However, it is clear that many WSN systems—such as healthcare and automotive ones—need a controlled access to data that sensor nodes produce, given its high sensitivity. Enforcing access control in wireless sensor networks is a particularly difficult task due to the limited computational capacity of wireless sensor nodes. In this paper we present a full-fledged access control scheme for wireless sensor data. We enforce access control through data encryption, thus embedding access control in sensor data units. We also propose a lightweight key generation mechanism, based on cryptographic hash functions, that allows for hierarchical key derivation. The suggested pro- tocol only relies on simple operations, does not require interactions between nodes and data consumers and has minimal storage requirements. [less ▲]

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