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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 genome mining, a new approach to detect novel lipopeptides potentially involved in biological control
Leclere, V.; Krier, F.; Deravel, J. et al

Poster (2012)

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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 model of an antenna of a phycobilisome and energy transfer rates determination by theoretical Forster approach.
Figueroa, Maximiliano ULg; Martinez-Oyanedel, Jose; Matamala, Adelio R. et al

in Protein Science : A Publication of the Protein Society (2012)

Energy transfer (ET) in phycobilisomes, a macrocomplex of phycobiliproteins and linker proteins, is a process that is difficult to understand completely. A model for a rod composed of two hexamers of ... [more ▼]

Energy transfer (ET) in phycobilisomes, a macrocomplex of phycobiliproteins and linker proteins, is a process that is difficult to understand completely. A model for a rod composed of two hexamers of Phycocyanin and two hexamers of Phycoerythrin was built using an in silico approach and the three-dimensional structures of both phycobiliproteins from Gracilaria chilensis. The model was characterized and showed 125 A wide and 230 A high, which agree with the dimensions of a piling of four hexamers as observed in the images of subcomplexes of phycobilisomes obtained by transmission electron microscopy. ET rates between every pair of chromophores in the model were calculated using the Forster approach, and the fastest rates were selected to draw preferential ET pathways along the rod. Every path indicates that the ET is funneled toward the chromophores located at Cysteines 82 in Phycoerythrin and 84 in Phycocyanin. The chromophores that face the exterior of the rod are phycoerythrobilins, and they also show a preferential ET toward the chromophores located at the center of the rod. The values calculated, in general, agree with the experimental data reported previously, which validates the use of this experimental approach. [less ▲]

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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 regenerative medicine: how computational tools allow regulatory and financial challenges to be addressed in a volatile market.
Geris, Liesbet ULg; Guyot, Y.; Schrooten, J. et al

in Interface focus (2016), 6(2), 20150105

The cell therapy market is a highly volatile one, due to the use of disruptive technologies, the current economic situation and the small size of the market. In such a market, companies as well as ... [more ▼]

The cell therapy market is a highly volatile one, due to the use of disruptive technologies, the current economic situation and the small size of the market. In such a market, companies as well as academic research institutes are in need of tools to advance their understanding and, at the same time, reduce their R&D costs, increase product quality and productivity, and reduce the time to market. An additional difficulty is the regulatory path that needs to be followed, which is challenging in the case of cell-based therapeutic products and should rely on the implementation of quality by design (QbD) principles. In silico modelling is a tool that allows the above-mentioned challenges to be addressed in the field of regenerative medicine. This review discusses such in silico models and focuses more specifically on the bioprocess. Three (clusters of) examples related to this subject are discussed. The first example comes from the pharmaceutical engineering field where QbD principles and their implementation through the use of in silico models are both a regulatory and economic necessity. The second example is related to the production of red blood cells. The described in silico model is mainly used to investigate the manufacturing process of the cell-therapeutic product, and pays special attention to the economic viability of the process. Finally, we describe the set-up of a model capturing essential events in the development of a tissue-engineered combination product in the context of bone tissue engineering. For each of the examples, a short introduction to some economic aspects is given, followed by a description of the in silico tool or tools that have been developed to allow the implementation of QbD principles and optimal design. [less ▲]

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See detailIn silico screening to predict chondrocyte hypertrophy using a semiquantitative gene network model
Kerkhofs, Johan ULg; Leijten, Jeroen; Luyten, Frank et al

Poster (2015, April 30)

PURPOSE: In development, chondrocyte hypertrophy is a crucial and well-studied step in endochondral ossification. Hypertrophy may also play a role in pathophysiological processes, including osteoarthritis ... [more ▼]

PURPOSE: In development, chondrocyte hypertrophy is a crucial and well-studied step in endochondral ossification. Hypertrophy may also play a role in pathophysiological processes, including osteoarthritis. We employ a computational approach to estimate the effect of individual factors in this complex process. METHODS: We have combined information gleaned from a high number of publications on chondrocyte differentiation into a gene regulatory network of 46 factors and over 150 interactions. This network can estimate the stability of proliferative chondrocytes/permanent cartilage (stable state with SOX9 activity) and hypertrophic chondrocytes (stable state with RUNX2 activity) by employing 2 measures. A first measure is a Monte Carlo analysis that assesses stability in the face of random initial conditions, the second modifies stable states to estimate the sensitivity to perturbation. RESULTS: For each factor, these qualitative measures are calculated in silico under knockout and overexpression conditions and compared to the wild type situation. This enables screening of the effects of all incorporated factors on cartilage homeostasis, differentiation and pathogenesis via the initiation of hypertrophy. Indeed, our gene network analysis indicated multiple candidate genes for the development of osteoarthritis. Factors that amplify the SOX9 attractor basin include TGFβ, PPR, IGF-I, and PKA. The presence of RAS, IHH, GLI2 and FGF is required for the Runx2 stable state. Using a literature study, we corroborated several of the proposed factors. CONCLUSIONS: In silico screening of overexpression and knockout presents a novel strategy to improve bone and cartilage tissue engineering approaches, and can be used to propose a list of putative therapeutic targets for e.g. osteoarthritis. [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 87Sr/86Sr LA-MC-ICPMS on biogenic apatites: a matrix matched standard correction approach
Lugli, Federico; Cipriani, Anna; Mazzucchelli, Maurizio et al

Conference (2016)

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See detailIn Situ Analysis of Bacterial Lipopeptide Antibiotics by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging
Debois, Delphine ULg; Ongena, Marc ULg; Cawoy, H. et al

in Nonribosomal Peptide and Polyketide Biosynthesis : Methods and Protocols (2016)

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See detailIn situ analysis of lipid oxidation in oilseedbased food products using near-infrared spectroscopy and chemometrics: The sunflower kernel paste (tahini) example
Mureșan; Danthine, Sabine ULg; Mureșan, Andruța Elena et al

in Talanta (2016), 155

A new near-infrared (NIR) spectroscopic method was developed for the analytical measurement of lipid oxidation in sunflower kernel paste (tahini), which was chosen as an example of a complex oilseed-based ... [more ▼]

A new near-infrared (NIR) spectroscopic method was developed for the analytical measurement of lipid oxidation in sunflower kernel paste (tahini), which was chosen as an example of a complex oilseed-based food product. The NIR spectra of sunflower tahini were acquired for the extracted fat phase (EFP) and for the intact sunflower tahini (IST) samples during controlled storage. The best peroxide value (PV) calibration models were considered suitable for quality control (ratio of performance of deviation [RPD] >5). The best PV partial least squares (PLS) model result for EFP (RPD 6.36) was obtained when using standard normal variate (SNV) and the Savitzky-Golay first derivative in the 1140-1184 nm, 1388-1440 nm and 2026-2194 nm regions. In the case of IST spectra, the best PV models (RPD 5.23) were obtained when either multiple scattering correction (MSC) or SNV were followed by the Savitzky-Golay second derivative for the 1148-1180 nm and 2064-2132 nm regions. There were poor correlations between the NIR-predicted values and the reference data of the panisidine value (pAV) for both EFP and IST. Overall, the results obtained showed that NIR spectroscopy is an appropriate analytical tool for monitoring sunflower paste PV in situ. Due to the nonexistence of the extraction step, it demonstrates a unique and substantial advantage over presently known methods. Based on these results it is strongly recommended that, when using NIR PLS models to assess lipid oxidation in situ in similar oilseedbased food products (e.g., sesame tahini, hazelnut and cocoa liquor used for chocolate production, peanut butter, hazelnut, almond, pistachio spreads), suitable calibration sets containing samples of different particle sizes and stored at different temperatures be selected. [less ▲]

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See detailIn situ and laboratory mechanical characterization of a loess sequence from Middle Belgium
Delvoie, Simon ULg; Charlier, Robert ULg; Collin, Frédéric ULg

Conference (2016, May 25)

A 10 m thick loess (aeolian silt) layer located beside the Romont quarry (Eben-Emael, Middle Belgium) has been investigated in order to characterize the mechanical behaviour of the silty material. Cone ... [more ▼]

A 10 m thick loess (aeolian silt) layer located beside the Romont quarry (Eben-Emael, Middle Belgium) has been investigated in order to characterize the mechanical behaviour of the silty material. Cone penetration tests (CPT) have been performed with different cones (M1-type, M2-type and electric) in order to evaluate the influence of the cone on the mechanical behaviour interpretation. Concurrently, laboratory tests have been performed on undisturbed samples from core drillings. Laboratory tests consist of a physical characterization (grain size distribution, Atterberg limits) and a mechanical characterization (oedometer tests). This comprehensive investigation study focuses on the comparison of the loess characterization between in situ and laboratory approaches. CPT-based soil behaviour type charts are analyzed and compared with the Unified Soil Classification System. Many relations also exist in the literature between parameters obtained from CPT results and from laboratory tests. The study explores the existing relations between the cone resistance and the oedometer constrained modulus in order to verify the related coefficients proposed in the literature for silty material. [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 (2015), 62

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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