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Peer Reviewed
See detailIn search of the Latin American Faulkner
Vanden Berghe, Kristine ULg

in Target : International Journal of Translation Studies (1997), 9(2), 399-400

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See detailIn Search of the Lost Serial
Capart, Philippe; Dejasse, Erwin ULg

in Beaty, Bart; Miller, Ann (Eds.) The French Comics Theory Reader (2014)

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See detailIn silico and in vivo combinatorial design of Octarellin VI, an artificial protein modeled on the (B/A)8 fold
Figueroa Yévenes, Maximiliano ULg; Taralla, Sébastien; Buscetta, Marco et al

Poster (2012, November 16)

One way to gain insight into the sequence-structure-function relationship in proteins is to perform de novo design of artificial proteins. The applications of such a study are varied. For example, in ... [more ▼]

One way to gain insight into the sequence-structure-function relationship in proteins is to perform de novo design of artificial proteins. The applications of such a study are varied. For example, in medicine and industry, it would give us the ability to precisely engineer proteins to perform a specific function under a wider range of conditions. Despite impressive successes in the de novo protein design, designing a folded protein of more than 100 amino acids remains a challenge. In our lab, four generations of Octarellins, de novo polypeptides of more than two hundred amino acids modelled on the (beta/alpha)8 barrel fold, have been built and structurally characterized using biophysical and spectroscopic methods. The last generation of Octarellins was designed following a hierarchical method combining the specificity of rational design and the power of computational design. The resulting artificial protein, named Octarellin VI, was expressed in E. coli and purified from inclusion bodies. The biophysical characterization showed a monomeric protein, with a secondary structure level similar to the computationally designed model and thermostability. However, the poor solubility in bacteria and low stability of the protein at long term make impossible determine its structure to criticize the model. To improve these negative features, we performed a directed evolution process over the Octarellin, following the improvement at solubility level in the bacteria, thanks to the fusion of Octarellin to the fluorescent folding reporter GFP. After 8 cycles of directed evolution by Error Prone PCR technique, we obtained a most soluble protein, with a 92% of sequence identity with the original protein. This soluble variant is under study to characterize its structural features. The combination between in silico design and directed evolution process emerges as a powerful tool for protein engineering, showing be complementaries techniques and the information obtained by the whole process of design and posterior comparison between 3D structure of Octarellin with the computational model will allow to improve the algorithms for protein design. [less ▲]

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See detailIn silico biology of bone modelling and remodelling: regeneration.
Geris, Liesbet ULg; Vander Sloten, J.; Van Oosterwyck, H.

in Philosophical Transactions : Mathematical, Physical & Engineering Sciences (2009), 367(1895), 2031-53

Bone regeneration is the process whereby bone is able to (scarlessly) repair itself from trauma, such as fractures or implant placement. Despite extensive experimental research, many of the mechanisms ... [more ▼]

Bone regeneration is the process whereby bone is able to (scarlessly) repair itself from trauma, such as fractures or implant placement. Despite extensive experimental research, many of the mechanisms involved still remain to be elucidated. Over the last decade, many mathematical models have been established to investigate the regeneration process in silico. The first models considered only the influence of the mechanical environment as a regulator of the healing process. These models were followed by the development of bioregulatory models where mechanics was neglected and regeneration was regulated only by biological stimuli such as growth factors. The most recent mathematical models couple the influences of both biological and mechanical stimuli. Examples are given to illustrate the added value of mathematical regeneration research, specifically in the in silico design of treatment strategies for non-unions. Drawbacks of the current continuum-type models, together with possible solutions in extending the models towards other time and length scales are discussed. Finally, the demands for dedicated and more quantitative experimental research are presented. [less ▲]

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See detailIn silico biology of bone regeneration inside calcium phosphate scaffolds
Carlier, Aurélie ULg; Van Oosterwyck, Hans; Geris, Liesbet ULg

in Tissue Engineering: Computer Modeling, Biofabrication and Cell Behavior (2014)

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See detailIn silico design of treatment strategies in wound healing and bone fracture healing
Geris, Liesbet ULg; Schugart, R.; Van Oosterwyck, H.

in Philosophical Transactions : Mathematical, Physical & Engineering Sciences (2010), 368(1920), 2683-2706

Wound and bone fracture healing are natural repair processes initiated by trauma. Over the last decade, many mathematical models have been established to investigate the healing processes in silico, in ... [more ▼]

Wound and bone fracture healing are natural repair processes initiated by trauma. Over the last decade, many mathematical models have been established to investigate the healing processes in silico, in addition to ongoing experimental work. In recent days, the focus of the mathematical models has shifted from simulation of the healing process towards simulation of the impaired healing process and the in silico design of treatment strategies. This review describes the most important causes of failure of the wound and bone fracture healing processes and the experimental models and methods used to investigate and treat these impaired healing cases. Furthermore, the mathematical models that are described address these impaired healing cases and investigate various therapeutic scenarios in silico. Examples are provided to illustrate the potential of these in silico experiments. Finally, limitations of the models and the need for and ability of these models to capture patient specificity and variability are discussed. [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 detailIN SILICO GENOTYPING OF THOUSANDS OF SNP IN DAIRY CATTLE FOR THE EUROGENOMICS PROJECT
Druet, Tom ULg; Schrooten, C.; de Roos, A. P. W.

in Proceedings of the 9th World Congress oN Genetics Applied to Livestock Production (2010)

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See detailIn silico identification and characterization of putative differentially expressed genes involved in common bean (Phaseolus vulgaris L.) seed development
Abid, Ghassen ULg; Muhovski, Y.; Jacquemin, J.-M. et al

in Plant Cell, Tissue & Organ Culture (2011)

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See detailIn silico predictions of 3D structures of linear and cyclic peptides with natural and non-proteinogenic residues.
Beaufays, Jérôme ULg; Lins, Laurence ULg; Thomas, Annick ULg et al

in Journal of Peptide Science : An Official Publication of the European Peptide Society (2012), 18(1), 17-24

We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio ... [more ▼]

We extended the use of Peplook, an in silico procedure for the prediction of three-dimensional (3D) models of linear peptides to the prediction of 3D models of cyclic peptides and thanks to the ab initio calculation procedure, to the calculation of peptides with non-proteinogenic amino acids. Indeed, such peptides cannot be predicted by homology or threading. We compare the calculated models with NMR and X-ray models and for the cyclic peptides, with models predicted by other in silico procedures (Pep-Fold and I-Tasser). For cyclic peptides, on a set of 38 peptides, average root mean square deviation of backbone atoms (BB-RMSD) was 3.8 and 4.1 A for Peplook and Pep-Fold, respectively. The best results are obtained with I-Tasser (2.5 A) although evaluations were biased by the fact that the resolved Protein Data Bank models could be used as template by the server. Peplook and Pep-Fold give similar results, better for short (up to 20 residues) than for longer peptides. For peptides with non-proteinogenic residues, performances of Peplook are sound with an average BB-RMSD of 3.6 A for 'non-natural peptides' and 3.4 A for peptides combining non-proteinogenic residues and cyclic structure. These results open interesting possibilities for the design of peptidic drugs. Copyright (c) 2011 European Peptide Society and John Wiley & Sons, Ltd. [less ▲]

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See detailIn silico simulations of bone remodeling with improved parameter estimation from local strains and dynamic morphometry in vivo
Levchuk, Alina; Sommer, Remo; Badilatti, Sandro D. et al

in JOURNAL OF BONE AND MINERAL RESEARCH (2013), 28(1),

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See detailIn silico study of antimicrobial cyclic peptides Sequence analysis, molecular modelling and multi-scale molecular dynamics
Crowet, Jean-Marc ULg; Soumillion, Patrice; Brasseur, Robert ULg et al

Poster (2013, February 26)

The selection and use of antimicrobial cyclic peptides is an active way of research. These peptides are naturally produced by several microorganisms et libraries of biosynthetic peptides are actually ... [more ▼]

The selection and use of antimicrobial cyclic peptides is an active way of research. These peptides are naturally produced by several microorganisms et libraries of biosynthetic peptides are actually build to find new antibiotics candidats. However, the mecanism of action of these peptides is not well known and it exists several hypothesis for their interactions with membrane. These peptides are causing broad perturbations to lipidic membranes and it has been shown that they can form disordered toroidal pores or self assemble as amphipathic nanotubes leading to lipid extrusion. Through the analysis of several peptides from the libraries of Pr Soumillion with increasing activity it will be possible to study the relation between the sequence/structure and the membrane activity of these peptides. This will help to decipher between preferential modes of action and the parameters important for the activity. [less ▲]

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See detailIn silico study of the interaction of the Myelin Basic Protein C-terminal a-helical peptide with DMPC and mixed DMPC/DMPE lipid bilayers
Bessonov, Kyrylo ULg

Conference (2010, May)

Biological membranes continue to be extensively investigated in different ways. This paper presents the benefits of Molecular Dynamics (MD) approaches to study the properties of biological membranes and ... [more ▼]

Biological membranes continue to be extensively investigated in different ways. This paper presents the benefits of Molecular Dynamics (MD) approaches to study the properties of biological membranes and proteins using the freely available GROMACS package, in the context of the Myelin Basic Protein (MBP) C-terminal a-helical peptide. A mixed membrane consisting of 2-Dimyristoyl-sn-Glycero-3-phosphocholine/1,2-Dimyristoyl-sn-Glycero-3- phosphoethanolamine (DMPC/DMPE), and pure DMPC membranes, composed of 188 and 248 lipids, respectively, were simulated for 200 ns at 309 K. The DMPC membrane was approximately three times more fluid compared to the DMPC/DMPE system, with the diffusion coefficients (D) being 0.0207x10-5 cm2/s and 0.0068x10-5 cm2/s, respectively. In addition, the 14-residue peptide representing the C-terminal a-helical region of murine Myelin Basic Protein (MBP), with amino acid sequence NH2-A141YDAQGTLSKIFKL154-COOH , was simulated in both membrane systems for 200 ns. The peptide penetrated further into the DMPC bilayer compared to the mixed DMPC/DMPE bilayer, potentially because of the reduced accessibility of the charged peptide amino acid side chains to the formal positive charge of the amine N atom surrounded by methyl and methylene groups in DMPC, that might have resulted in greater overall peptide mobility [3]. These findings are significant in their implication that membrane composition affects the behavior of MBP, providing further insights into myelin structure. Our preliminary results suggest that local changes in membrane composition (e.g. enrichment in DMPE molecules), as well as, electrostatic nature of primary amino acid sequence could cause localized denaturation / instability of external MBP a-helices possibly augmenting the degradation of myelin in multiple sclerosis (MS), resulting in a subsequent decrease of nerve impulse propagation efficiency. [less ▲]

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See detailIn Silico tilted properties of the 67-78 fragment of alpha-synuclein are responsible for membrane destabilization and neurotoxicity
Crowet, Jean-Marc ULg; Lins, Laurence ULg; Dupiereux-Fettweis, Ingrid ULg et al

in Proteins-Structure Function and Bioinformatics (2007), 68(4), 936-947

Alpha-synuclein is a 140 residue protein associated with Parkinson's disease. Intraneural inclusions called Lewy bodies and Lewy neurites are mainly composed of alpha-synuclein aggregated into amyloid ... [more ▼]

Alpha-synuclein is a 140 residue protein associated with Parkinson's disease. Intraneural inclusions called Lewy bodies and Lewy neurites are mainly composed of alpha-synuclein aggregated into amyloid fibrils. Other amyloidogenic proteins, such as the beta amyloid peptide involved in Alzheimer's disease and the prion protein (PrP) associated with Creuztfeldt-Jakob's disease, are known to possess "tilted peptides". These peptides are short protein fragments that adopt an oblique orientation at a hydrophobic/hydrophilic interface, which enables destabilization of the membranes. In this paper, sequence analysis and molecular modelling predict that the 67-78 fragment of alpha-synuclein is a tilted peptide. Its destabilizing properties were tested experimentally. The alpha-synuclein 67-78 peptide is able to induce lipid mixing and leakage of unilamellar liposomes. The neuronal toxicity, studied using human neuroblastoma cells, demonstrated that the alpha-synuclein 67-78 peptide induces neurotoxicity. A mutant designed by molecular modelling to be amphipathic was shown to be significantly less fusogenic and toxic than the wild type. In conclusion, we have identified a tilted peptide in alpha-synuclein, which could be involved in the toxicity induced during amyloidogenesis of alpha-synuclein. [less ▲]

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See detailIn situ aortic allograft insertion to repair a primary aortoesophageal fistula due to thoracic aortic aneurysm
Pirard, Laurence ULg; Creemers, Etienne ULg; Van Damme, Hendrik ULg et al

in Vascular Surgery (2005), 42

Aortoesophageal fistula due to thoracic aortic aneurysm is an uncommon cause of gastrointestinal bleeding and has an extremely poor prognosis. In the English literature, we found only 27 successfully ... [more ▼]

Aortoesophageal fistula due to thoracic aortic aneurysm is an uncommon cause of gastrointestinal bleeding and has an extremely poor prognosis. In the English literature, we found only 27 successfully managed cases of primary aortoesophageal fistula due to thoracic aortic aneurysm. We present a case of 74-year-old man who experienced the erosion of a thoracoabdominal aortic aneurysm into the esophagus. We successfully performed resection and replacement of the thoracoabdominal aorta with a cryopreserved allograft and total thoracic esophagectomy. A few months later, the esophagus was reconstructed with orthotopic colonic interposition. The patient recovered well and resumed a normal life (12 months’ follow-up). [less ▲]

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See detailIn situ bidentate to tetradentate ligand exchange reaction in cobalt-mediated radical polymerization
Kermagoret, Anthony ULg; Jérôme, Christine ULg; Detrembleur, Christophe ULg et al

in European Polymer Journal (in press)

Organometallic-mediated radical polymerization (OMRP) has seen a significant growth in the last years notably due to the development of new metal complexes, especially cobalt derivatives. Despite of this ... [more ▼]

Organometallic-mediated radical polymerization (OMRP) has seen a significant growth in the last years notably due to the development of new metal complexes, especially cobalt derivatives. Despite of this, none of the reported complexes offers optimal control for monomers with very different reactivity, which somewhat limits the synthesis of copolymers. In order to expand the scope of cobalt-mediated radical polymerization (CMRP), we investigated an in situ ligand exchange reaction for modulating the properties of the cobalt complex at the polymer chain-end and adjusting the C-Co bond strength involved in the control process. With the aim of improving the synthesis of poly(vinyl acetate)-b-poly(n-butyl acrylate) copolymers, bidentate acetylacetonate ligands, which impart high level of control to the polymerization of vinyl acetate (VAc), were replaced in situ at the PVAc-cobalt chain-end by tetradentate Salen type ligands that are more suited to acrylates. [less ▲]

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See detailIn situ characterization in freeze-fractured mouse thymuses of lymphoepithelial complexes ultrastructurally similar to isolated thymic nurse cells.
Defresne, Marie-Paule ULg; Goffinet, Gerhard ULg; Boniver, Jacques ULg

in Tissue & Cell (1986), 18(3), 321-30

Scanning and transmission electron microscopy of the cracked surfaces of cryofractured pre-fixed C57BL/Ka mouse thymus reveals the existence of cell complexes, distinct from the surrounding cell ... [more ▼]

Scanning and transmission electron microscopy of the cracked surfaces of cryofractured pre-fixed C57BL/Ka mouse thymus reveals the existence of cell complexes, distinct from the surrounding cell organization, in which groups of lymphocytes are delimited by large cytoplasmic sheets or envelopes. These complexes, located in the subcapsular and cortical regions, display morphological features similar to that of the thymic nurse cells (TNCs), which can be isolated from the mouse or human thymus enzymatically dissociated. They can be considered as dynamic systems able to modify their three-dimensional organization, namely with regard to intrathymic cellular traffic involved in T-lymphocyte maturation. [less ▲]

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