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See detailDe nouveaux enjeux sur l’espace : la délimitation des premières forêts communautaires au Gabon
Vermeulen, Cédric ULg; Schippers, C.; Ndouna, A. A. et al

in International Journal of Biological and Chemical Sciences (2009), 3(5), 1171-1181

Le Gabon s’est doté il y a quelques années d’une nouvelle loi forestière intégrant les populations locales dans la gestion durable des massifs forestiers à travers le concept de « forêts communautaires » ... [more ▼]

Le Gabon s’est doté il y a quelques années d’une nouvelle loi forestière intégrant les populations locales dans la gestion durable des massifs forestiers à travers le concept de « forêts communautaires ». L’une des premières étapes dans la mise en place de ces forêts communautaires est la délimitation de celles-ci. Cet article aborde le cas concret de la délimitation d’une première forêt communautaire dans ce pays, le cas du regroupement de villages de Ebe Messe Melane. La délimitation suit une approche intégrée afin de concilier d’une part les contraintes légales et d’autre part l’occupation de l’espace actuelle par les populations villageoises. Cet exemple permet d’illustrer les différents enjeux que soulève la délimitation des forêts communautaires. Des enjeux spatiaux, financiers ou identitaires qui impliquent les acteurs aux intérêts parfois divergents que sont les communautés villageoises, l’Etat et les opérateurs forestiers privés. [less ▲]

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See detailDe nouveaux entrelacs territoriaux, Globalisation et diversification des modes d'habiter.
Schmitz, Serge ULg

in Lask, Tomke (Ed.) Les constructions sociales de l'espace. Les territoires de l'anthropologie de la communicaiton. (2003)

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See detailDe nouveaux outils d’évaluation de l’arthrose
Henrotin, Yves ULg; Deberg, Michelle ULg

in Ortho-Rhumato (2010), 8

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See detailDe nouvelles problématiques pour la Géographie de l’agriculture
Merenne-Schoumaker, Bernadette ULg

in Acta Geographica Lovaniensia (2009), 38

Researches currently lead by experts of agriculture can be brought together in three fields: the globalization of agriculture and food and their impacts on food-processing systems, feeding the planet ... [more ▼]

Researches currently lead by experts of agriculture can be brought together in three fields: the globalization of agriculture and food and their impacts on food-processing systems, feeding the planet tomorrow and developing an agriculture which could face climatic, energetic and environmental stakes. Those three problematics cannot leave geographers cold, especially since those three fields show strong regional variations. So everything speaks in favour of geographers’ reinvestment in the field of agriculture’s geography, which has been widely neglected these last years. [less ▲]

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See detailDe novo backbone and sequence design of an idealized alpha/beta-barrel protein: Evidence of stable tertiary structure
Offredi, Fabrice; Dubail, Fabien; Kischel, Philippe ULg et al

in Journal of Molecular Biology (2003), 325(1), 163-174

We have designed, synthesized, and characterized a 216 amino acid residue sequence encoding a putative idealized alpha/beta-barrel protein. The design was elaborated in two steps. First, the idealized ... [more ▼]

We have designed, synthesized, and characterized a 216 amino acid residue sequence encoding a putative idealized alpha/beta-barrel protein. The design was elaborated in two steps. First, the idealized backbone was defined with geometric parameters representing our target fold: a central eight parallel-stranded beta-sheet surrounded by eight parallel alpha-helices, connected together with short structural turns on both sides of the barrel. An automated sequence selection algorithm, based on the dead-end elimination theorem, was used to find the optimal amino acid sequence fitting the target structure. A synthetic gene coding for the designed sequence was constructed and the recombinant artificial protein was expressed in bacteria, purified and characterized. Far-UV CD spectra with prominent bands at 222nm and 208nm revealed the presence of alpha-helix secondary structures (50%) in fairly good agreement with the model. A pronounced absorption band in the near-UV CD region, arising from immobilized aromatic side-chains, showed that the artificial protein is folded in solution. Chemical unfolding monitored by tryptophan fluorescence revealed a conformational stability (DeltaG(H2O)) of 35kJ/mol. Thermal unfolding monitored by near-UV CD revealed a cooperative transition with an apparent T(m) of 65 degrees C. Moreover, the artificial protein did not exhibit any affinity for the hydrophobic fluorescent probe 1-anilinonaphthalene-8-sulfonic acid (ANS), providing additional evidence that the artificial barrel is not in the molten globule state, contrary to previously designed artificial alpha/beta-barrels. Finally, 1H NMR spectra of the folded and unfolded proteins provided evidence for specific interactions in the folded protein. Taken together, the results indicate that the de novo designed alpha/beta-barrel protein adopts a stable three-dimensional structure in solution. These encouraging results show that de novo design of an idealized protein structure of more than 200 amino acid residues is now possible, from construction of a particular backbone conformation to determination of an amino acid sequence with an automated sequence selection algorithm. [less ▲]

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See detailDe novo C16- and C24-ceramide generation contributes to spontaneous neutrophil apoptosis.
Seumois, Gregory; Fillet, Marianne ULg; Gillet, Laurent ULg et al

in Journal of Leukocyte Biology (2007), 81(6), 1477-1486

Neutrophils rapidly undergo spontaneous apoptosis following their release from the bone marrow. Although central to leukocyte homeostasis, the mechanisms that regulate neutrophil apoptosis remain poorly ... [more ▼]

Neutrophils rapidly undergo spontaneous apoptosis following their release from the bone marrow. Although central to leukocyte homeostasis, the mechanisms that regulate neutrophil apoptosis remain poorly understood. We show here that apoptosis of cultured neutrophils is preceded by a substantial increase in the intracellular levels of 16 and 24 carbon atom (C(16)- and C(24))-ceramides, which are lipid second messengers of apoptosis and stress signaling. Treatment of neutrophils with fumonisin B(2), a selective inhibitor of the de novo pathway of ceramide synthesis, prevented accumulation of C(16)- and C(24)-ceramides. Moreover, fumonisin B(2) significantly reduced caspase-3, -8, and -9 activation and apoptosis in these cells. Conversely, 3-O-methylsphingomyelin and fantofarone, which are specific inhibitors of neutral and acid sphingomyelinases, respectively, neither inhibited C(16)- and C(24)-ceramide production nor decreased the apoptosis rate in neutrophils, indicating that in these cells, ceramides are not generated from membrane sphingomyelin. Further experiments showed that increasing endogenous C(16)- and C(24)-ceramide levels by using DL-threo-1-phenyl-2-palmitoylamino-3-morpholino-1-propanol and (1S,2R)-D-erythro-2-(N-myristoylamino)-1-phenyl-1-propanol, two inhibitors of ceramide metabolism, enhances caspase-3, -8, and -9 activity and increases neutrophil apoptosis. Similarly, apoptosis was induced rapidly when synthetic C(16)- and/or C(24)-ceramides were added to neutrophil cultures. Finally, GM-CSF, a cytokine that delays neutrophil apoptosis, abrogated C(16)- and C(24)-ceramide accumulation totally in cultured neutrophils, whereas Fas ligation accelerated apoptosis in these cells without affecting de novo ceramide production. We conclude that de novo generation of C(16)- and C(24)-ceramides contributes to spontaneous neutrophil apoptosis via caspase activation and that GM-CSF exerts its antiapoptotic effects on neutrophils, at least partly through inhibition of ceramide accumulation. [less ▲]

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See detailDe novo interstitial duplication 4q associated with sporadic young-onset dopa-responsive parkinsonism
Garraux, Gaëtan ULg; VANBELLINGHEN, Jean-François ULg; JAMAR, Mauricette ULg et al

in Movement Disorders : Official Journal of the Movement Disorder Society (2009), 24(Suppl. 1), 138-139

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See detailDe novo lipogenesis protects cancer cells from free radicals and chemotherapeutics by promoting membrane lipid saturation.
Rysman, Evelien; Brusselmans, Koen; Scheys, Katryn et al

in Cancer Research (2010), 70(20), 8117-26

Activation of de novo lipogenesis in cancer cells is increasingly recognized as a hallmark of aggressive cancers and has been implicated in the production of membranes for rapid cell proliferation. In the ... [more ▼]

Activation of de novo lipogenesis in cancer cells is increasingly recognized as a hallmark of aggressive cancers and has been implicated in the production of membranes for rapid cell proliferation. In the current report, we provide evidence that this activation has a more profound role. Using a mass spectrometry-based phospholipid analysis approach, we show that clinical tumor tissues that display the lipogenic phenotype show an increase in the degree of lipid saturation compared with nonlipogenic tumors. Reversal of the lipogenic switch in cancer cells by treatment with the lipogenesis inhibitor soraphen A or by targeting lipogenic enzymes with small interfering RNA leads to a marked decrease in saturated and mono-unsaturated phospholipid species and increases the relative degree of polyunsaturation. Because polyunsaturated acyl chains are more susceptible to peroxidation, inhibition of lipogenesis increases the levels of peroxidation end products and renders cells more susceptible to oxidative stress-induced cell death. As saturated lipids pack more densely, modulation of lipogenesis also alters lateral and transversal membrane dynamics as revealed by diffusion of membrane-targeted green fluorescent protein and by the uptake and response to doxorubicin. These data show that shifting lipid acquisition from lipid uptake toward de novo lipogenesis dramatically changes membrane properties and protects cells from both endogenous and exogenous insults. These findings provide important new insights into the role of de novo lipogenesis in cancer cells, and they provide a rationale for the use of lipogenesis inhibitors as antineoplastic agents and as chemotherapeutic sensitizers. [less ▲]

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See detailA De Novo Mutation in an Already Mutant Nucleotide of the Thyroïd Hormone Receptor beta Gene Perpetuates Resistance to Thyroid Hormone
Lado-Abeal, Joaquin; DUMITRESCU, Alexandra; LIAO, Xiao-Hui et al

in Journal of Clinical Endocrinology and Metabolism (2005), 90(3), 1760-1767

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See detailDe Novo Mutations in DENR Disrupt Neuronal Development and Link Congenital Neurological Disorders to Faulty mRNA Translation Re-initiation.
Haas, Matilda A.; Ngo, Linh; Li, Shan Shan et al

in Cell Reports (2016)

Disruptions to neuronal mRNA translation are hypothesized to underlie human neurodevelopmental syndromes. Notably, the mRNA translation re-initiation factor DENR is a regulator of eukaryotic translation ... [more ▼]

Disruptions to neuronal mRNA translation are hypothesized to underlie human neurodevelopmental syndromes. Notably, the mRNA translation re-initiation factor DENR is a regulator of eukaryotic translation and cell growth, but its mammalian functions are unknown. Here, we report that Denr influences the migration of murine cerebral cortical neurons in vivo with its binding partner Mcts1, whereas perturbations to Denr impair the long-term positioning, dendritic arborization, and dendritic spine characteristics of postnatal projection neurons. We characterized de novo missense mutations in DENR (p.C37Y and p.P121L) detected in two unrelated human subjects diagnosed with brain developmental disorder to find that each variant impairs the function of DENR in mRNA translation re-initiation and disrupts the migration and terminal branching of cortical neurons in different ways. Thus, our findings link human brain disorders to impaired mRNA translation re-initiation through perturbations in DENR (OMIM: 604550) function in neurons. [less ▲]

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See detailDe novo sequencing of unusual non tryptic peptides thanks to 4-sulfophenylisothiocyanate derivatization by post-source decay MALDI-MS.
Echterbille, Julien ULg; Quinton, Loïc ULg; Escoubas, Pierre et al

Poster (2013, June 11)

Introduction Due to the specificity of trypsin, tryptic peptides contain basic residues on the C-terminal side. This feature provides good ionization efficiency, and facilitates fragmentation processes ... [more ▼]

Introduction Due to the specificity of trypsin, tryptic peptides contain basic residues on the C-terminal side. This feature provides good ionization efficiency, and facilitates fragmentation processes. In the case of non tryptic peptides, the absence of basic residues at one extremity implicates lower fragmentation ratio and poor MS/MS spectra. Several methods have been developed to circumvent this drawback. Derivatization of peptides with compounds containing positive charge has been studied; Chen et al. (RCMS, 2004, 18, 191) demonstrated the simplification of CID spectra of tryptic peptides modified by 4-sulfophenylisothiocyanate. The result is a predominance of y-type ions. In this work, we evaluate the potential of SPITC for the de novo sequencing of unknown non-tryptic peptides containing disulfide bridges, i.e. peptide toxins from animal venoms. Methods 2µL of peptide solution (100 µM) were diluted in 6µL NH4HCO3 50mM (pH 8.7). As peptide toxins often contain disulfide bridges, reduction (2µL DTT 50mM, 1h at 56°C) and alkylation (2µL IAA 500mM, 1h in darkness at RT) of peptides were performed before the derivatization reaction. Peptides were then adsorbed on a C18 ZipTip micro-column followed by 10 µL of 4-sulfophenylisothiocyanate (SPITC) 50mM. The column was then incubated for 6h at 56°C. Peptides were washed by TFA 0.2% and eluted in 10µL 50/50 ACN/FA 0.1%, before being spotted in 2,5-DHB. MS experiments were performed using a Bruker Ultraflex II MALDI-TOF/TOF. FlexControl 3.0, FlexAnalysis 3.0, BioTools 3.2 and SequenceEditor 3.2 softwares (Bruker Daltonics, Bremen) were used for data acquisition and interpretation. Preliminary data According to our first results, SPITC derivatization allows in positive mode to direct the fragmentation thanks to the acidic character of the sulfonate moiety present on the modified molecule. Indeed, a large series of y-type ions is found in the CID spectra allowing determining easily large sequence tags. Moreover, the number of C-terminus ions (b- and a-type ions) decreases, which improve the simplification of MS/MS spectra. Due to this fragmentation pattern, SPITC derivatization is clearly valuable for the sequencing of peptides that are not described in databases (de novo sequencing). For example, animal venoms are composed of several hundreds of peptides that are poorly studied, up to now. These peptides display a high importance for pharmaceutical applications and their sequencing is, as a consequence, of prime interest. Peptide toxins, which are not resulting from an enzymatic digestion, are however difficult to sequence by classical MS/MS methods. In this work, we demonstrate that the modification of peptide toxins with SPITC reagent is suitable for “real” de novo sequencing. The method was applied to isolated peptides as well as chromatographic fractions that contain up to 30 toxins. The perspectives of this work rest on the study of the SPITC modified peptides in negative mode. We expect to obtain a better sensitivity due to the presence of the negative sulfonic acid group at the N-terminus extremity, and also interesting MS/MS spectra including mainly a- or b-type ions. The final challenge will be the application of the protocol to high throughput sequencing of peptide toxins from a large variety of animal venoms. Novel aspect De novo sequencing of unusual non-tryptic peptides thanks to 4-sulfophenylisothiocyanate derivatization by post-source decay MALDI-MS [less ▲]

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See detailDe novo sequencing using MELD proteolysis coupled to a "sequence assembly" algorithm
Mazzucchelli, Gabriel ULg; Zimmerman, Tyler A; Smargiasso, Nicolas ULg et al

Poster (2016, January 22)

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See detailDe novo sequencing using MELD proteolysis coupled to a "sequence assembly" algorithm
Mazzucchelli, Gabriel ULg; Zimmerman, Tyler; Smargiasso, Nicolas ULg et al

in 63rd ASMS Conference Proceedings, May 30 - June 4 2015, St. Louis, MO (2015, June)

Introduction Protein de novo sequencing requires a method that combines extensive MSMS fragmentation and an appropriate data processing. This can be applied either on intact protein or on its proteolytic ... [more ▼]

Introduction Protein de novo sequencing requires a method that combines extensive MSMS fragmentation and an appropriate data processing. This can be applied either on intact protein or on its proteolytic peptides. Peptide analysis has the advantage to be compatible with well-known workflows. Nevertheless the connectivity between peptides is lost. Taking these considerations into account, a specific digestion method and a sequence assembly software were developed. The MELD method relies on a combination of MultiEnzymatic AND Limited proteolytic Digestions. The MELD generates in a single experiment numerous different peptides with miss-cleavages that overlap when aligned on the matching protein sequence. The two major benefices are an increased probability to obtain the entire protein sequence and a redundancy in the protein sequence matches. Methods The MELD consists in two parallel 2h digestions both using an optimized protease mixture. The mixtures are composed of the same proteases but in different relative quantities. Analyses were performed by UPLC-Orbitrap (IClass, Waters, QExactive, Thermo). Data were processed with PEAKS (BSI) to generate de novo sequence candidates. After data importation into our software, a seed sequence is set or can be found automatically. The software extends the seed sequence in both directions with moving windows of three amino acids, plus a fourth one to be added. The added amino acid is validated in several ways, including by the total frequency of occurrence, by larger windows of aa, by the local spectrum-derived confidence, and by combinations of these factors. Preliminary Data The MELD protocol was first validated by applying a traditional database search workflow on several commercial proteins with an inter-day and inter-individual procedure. These experiments showed 100% sequence coverage for each protein analyzed, involving information on peptide identity and modifications localization. Strong confident identification was obtained due to multiple overlapping peptides matches with the given sequence and with a high number of overlapping peptides assignments. The analysis of the four proteins provided the following results: HSA, Myoglobin and Lysozyme were identified with 100% sequence coverage with respectively 890, 300 and 120 unique peptides (CV<10%, peptide FDR<0.1%). The variable region of each heavy and light chains of Adalimumab antibody were identified with 100% sequence coverage. With the MELD, an average of 10 different peptides covering each sequence stretch of the protein could be obtained. The combinatory effect of the multiple enzymes used and the limited digestions leads to an increased robustness, very high confidence identifications and allows clear localization of PTMs. The MELD protocol as presented here and tested on several pure proteins digested in solution, certainly improves the general "bottom-up" strategy applied for highly confident protein identification and would allow better protein characterization, even for those having PTMs. In addition, in our analysis, each fragment position of the entire protein sequence was evidenced either by a "y" or a "b" fragment ion. This high and confident amount of information enables extensive de novo sequencing using PEAKS software, followed by application of our “sequence assembly” algorithm. The first version of our assembling tool on MELD experimental data generated long sequence tags, up to 90 amino acids long. [less ▲]

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See detail"De novo" design of peptides with specific lipid-binding properties
Lins, Laurence ULg; Charloteaux, Benoît ULg; Heinen, C. et al

in Biophysical Journal (2006), 90(2), 470-479

In this study, we describe an in silico method to design peptides that can be made of non-natural amino acids and elicit specific membrane-interacting properties. The originality of the method holds in ... [more ▼]

In this study, we describe an in silico method to design peptides that can be made of non-natural amino acids and elicit specific membrane-interacting properties. The originality of the method holds in the capacities developed to design peptides from any non-natural amino acids as easily as from natural ones, and to test the structure stability by an angular dynamics rather than the currently-used molecular dynamics. The goal of this study was to design a non-natural tilted peptide. Tilted peptides are short protein fragments able to destabilize lipid membranes and characterized by an asymmetric distribution of hydrophobic residues along their helix structure axis. The method is based on the random generation of peptides and their election on three main criteria: mean hydrophobicity and the presence of at least one polar residue; tilted insertion at the level of the acyl chains of lipids of a membrane; and conformational stability in that hydrophobic phase. From 10,000,000 randomly-generated peptides, four met all the criteria. One was synthesized and tested for its lipid-destabilizing properties. Biophysical assays showed that the "de novo" peptide made of non-natural amino acids is helical either in solution or intolipids as tested by Fourier transform infrared spectroscopy and is able to induce liposome fusion. These results are in agreement with the calculations andvalidate the theoretical approach. [less ▲]

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See detailDe Orto/ Josquin (livret musical accompagnant un CD: traduction et restauration des textes des pièces en moyen français)
Henrard, Nadine ULg

in Rodin, Jesse (Ed.) De Orto/ Josquin, Musique à la Chapelle Sixtine autour de 1490 (2012)

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See detailDe Paepe-Willems Award 2010: Optimization and analysis of lock gates in the framework of the Seine-Escaut Est waterway upgrading
Gernay, Thomas ULg

Conference (2010, May 10)

This paper presents a research study performed lock gates. It concerns the downstream lock gates of the one of the four new locks planned within the framework of the “Seine-Escaut Est (SEE)” project in ... [more ▼]

This paper presents a research study performed lock gates. It concerns the downstream lock gates of the one of the four new locks planned within the framework of the “Seine-Escaut Est (SEE)” project in the Walloon Region of Belgium. At the stage of the basic preliminary design, it was decided to use four identical gates, all suspended and manoeuvred by lateral movement. On this basis, the present work tackles with different aspects of the lock gate study. The aim is double: on one hand, to advance in the study of the solution of the four downstream lock gates of the SEE project, and the other hand, to concentrate more particularly on the lock gate analysis, among which their design, optimization and structural behavior in the case of ship impact. We began with the design and optimization of the gate. This work was realized with the LBR5 lock gate optimization software, according to a method comparing a representative number of optimized solutions considering at the same time the cost and weight aspects of the structure. This method leaded to an optimized solution of the downstream gate on which further studies are concentrated. Indeed this optimized gate was modeled with the non linear finite elements software FINELG. This program was used to conduct a non linear numerical analysis of the effect of a boat impact on the downstream gate. Several analyses were performed that allowed us to discuss on the influence of the stiffener dimensions and the influence of the impact zone on the gate structural behavior submitted to the impact. Two different behaviors have been brought to light, a ductile one and a fragile one. The results of the numerical analysis with finite elements have underlined the importance of the development of a global plastic mechanism with the purpose of dissipating a large amount of energy. Finally, we have used an analytical model to calculate the gate theoretical strength in a case of a ship impact, and to compare this value with the FEM numerical analysis results. [less ▲]

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See detailDe pedagogische en politieke wortels van Belgisch Design
Prina, Daniela ULg

in Simon Thomas, Mienke; Huygens, Franck (Eds.) Design Derby - Nederlands - Belgie (1815-2015) (2015)

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See detailDe perceptie van het Poldernederlands in Vlaanderen
Perrez, Julien ULg

Master's dissertation (2002)

Detailed reference viewed: 91 (8 ULg)