http://hdl.handle.net/2268/149 Search this channel search http://orbi.ulg.ac.be/simple-search http://hdl.handle.net/2268/148459 Title: Replacing explicit water and membrane molecules in molecular dynamics simulation to boost simulation speed <br/> <br/>Author, co-author: Steinhauer, Sven; Crowet, Jean-Marc; Lins, Laurence; Brasseur, Robert <br/> <br/>Abstract: Molecular dynamics (MD) is an appropriate method for investigation of biomolecular systems and helps in explaining results from wet lab experiments or in getting further insight into details, which are not accessible by experimental methods(Lindahl, 2008). By now, many biologically relevant processes for drug design, toxicological studies and other fields of application, can not be performed by atomistic MD simulations (Lindahl, 2008). In MD, the necessary time effort for carrying out a simulation is considerable and depends mainly on (1) the complexity of the simulated system (2) the simulated time scale (3) the simulation method (4) the efficiency of used hardware and software algorithms. Carried out MD simulations nowadays may still take weeks of calculation on high end computers. In practice, biologically relevant processes, as e.g. protein folding, take usually place above the time scale of milli seconds. They can take up to the order of some thousands of seconds (in case of the folding of membrane proteins). Molecular dynamics computer simulations have reached the scale of micro seconds for simulations of systems where each atom was described and simulated over time.(Lindahl, 2008) Nevertheless, MD has risen to an important promoter methodology for many different fields of application. By replacing bunches of atoms by artificial particles, complexity of the systems can be reduced. This method is called the coarse grain method (CG). Biggin and Bond (2008) found an acceleration of their simulation processes for self assembling membrane / protein systems in water by factor 100. They estimated one to two days of calculation for a simulated time scale of 0.1 to 0.2 micro seconds for their systems. Implicit force fields like "IMPALA", aim to describe water and/or membrane molecules in simulations by a couple of simple and partially precalculable equations. “IMPALA” is a force field initially developed by our laboratory. Using this method, thousands of water and lipid molecules can be replaced, leading to a reduced complexity of the system to be simulated. "IMPALA"(Ducarme et al., 1998) based on the assumption of rigid peptides and aimed to find the insertion characteristics of such in membranes. Elimination of the necessity for simulating the aqueous and lipid phase atom by atom in the software package "Gromacs"(Berendsen et al., 1995) will permit both: a gain of speed, as it was already the case for the introduction of the coarse grain method, and a gain of precision by turning rigid molecules flexible through "Gromacs". Our current work is the integration of the "IMPALA" implicit force field into "Gromacs". Biggin, P.C. & Bond, P.J. Molecular dynamics simulations of membrane proteins. Methods Mol. Biol. 443, 147-60(2008). Berendsen, et al. (1995) Comp. Phys. Comm. 91: 43-56. Ducarme, P., Rahman, M. & Brasseur, R. IMPALA: a simple restraint field to simulate the biological membrane in molecular structure studies. Proteins 30, 357-71(1998). Lindahl, E.R. (2008). Molecular dynamics simulations. Methods Mol. Biol. 443, 3-23. Tue, 14 May 2013 12:12:29 GMT http://hdl.handle.net/2268/148375 Title: Les dommages causés par les tempêtes en forêt wallonne : comment se préparer et gérer la crise ? <br/> <br/>Author, co-author: Riguelle, Simon Mon, 13 May 2013 12:52:04 GMT http://hdl.handle.net/2268/148373 Title: Les dommages causés par les tempêtes en forêt wallonne : comment se préparer et gérer la crise ? <br/> <br/>Author, co-author: Riguelle, Simon Mon, 13 May 2013 12:48:48 GMT http://hdl.handle.net/2268/148371 Title: Les dommages causés par les tempêtes en forêt wallonne : comment gérer la crise ? <br/> <br/>Author, co-author: Riguelle, Simon Mon, 13 May 2013 12:45:04 GMT http://hdl.handle.net/2268/148368 Title: Evaluation et mesures d'atténuation des impacts économiques des tempêtes en forêt <br/> <br/>Author, co-author: Riguelle, Simon <br/> <br/>Abstract: Le passage d'une violente tempête (ouragan) sur un territoire donné provoque des dommages autant pour la population que pour le milieu forestier. Évaluer ces dommages en termes monétaires est assez simple tant pour les catégories de biens immobiliers et mobiliers que pour les dommages corporels, car il existe des échelles claires établies par les compagnies d'assurance. Celles-ci interviennent d'ailleurs la plupart du temps lors de tels phénomènes, et en outre si la catastrophe naturelle est reconnue comme calamité publique, une indemnité (non cumulable avec une prime d'assurance) du sinistré est possible. L'impact d'une tempête sur le milieu forestier est beaucoup plus difficile à cerner. Au choc émotionnel important s'ajoute en effet une multitude de coûts directs et indirects, certains ne se faisant sentir que des années après le cataclysme. Pourtant, des grilles d'évaluation des pertes de valeur marchande et potentielle des arbres et des peuplements existent et sont utilisées en cas de chablis pour estimer le préjudice du propriétaire, et les industriels sont à même d'estimer grossièrement leurs pertes potentielles (baisse de qualité des produits et de productivité). Cependant, l'ampleur du désastre économique sera directement fonction de la manière dont la crise est gérée ultérieurement par les pouvoirs publics et les intervenants de la filière. Une gestion de crise efficace, reposant sur l'établissement d'un plan de prévention et d'urgence, est donc nécessaire autant pour soutenir les sinistrés que pour rassurer le marché. Le plan chablis de la Région wallonne a ainsi pour objectif de prendre la crise forestière à bras le corps afin de ne laisser place ni à l'improvisation ni à l'individualisme. L'ambition du Service public de Wallonie est aussi de pouvoir collaborer efficacement avec les autres disciplines impliquées dans la gestion d'une crise consécutive au passage d'une tempête, comme avec les autorités provinciales et communales. Mon, 13 May 2013 12:35:05 GMT http://hdl.handle.net/2268/147340 Title: Livret - Guide. Voyage d'étude dans l'Oriental marocain <br/> <br/>Author, co-author: Denis, Antoine <br/> <br/>Abstract: Ce document est utilisé comme livret-guide d'un voyage d’étude d'une semaine dans l'Oriental marocain et a pour thème la gestion de l'environnement. Ce voyage est organisé dans le cadre du Master Complémentaire en Sciences et Gestion de l’Environnement dans les Pays en Développement de l'Université de Liège. Ce livre guide contient essentiellement un résumé de toutes les problématiques environnementales abordées au cours du voyage (station d'épuration de l'eau, décharges, dégradation des sols et désertification, reboisement, parc naturel, gestion d'une oasis, aménagement du litoral, etc. Thu, 25 Apr 2013 12:56:59 GMT http://hdl.handle.net/2268/147206 Title: La sécurité alimentaire et nutritionnelle au Niger : cas de Tchirozérine <br/> <br/>Author, co-author: Andres, Ludovic Mon, 22 Apr 2013 12:02:41 GMT http://hdl.handle.net/2268/147205 Title: La sécurité alimentaire et nutritionnelle au Niger : l'identification des populations vulnérables <br/> <br/>Author, co-author: Andres, Ludovic Mon, 22 Apr 2013 11:54:45 GMT http://hdl.handle.net/2268/147180 Title: Current Pericopsis elata (Fabaceae) patches in southeastern Cameroon: remnants of a long and rich Human-rainforest relationship? <br/> <br/>Author, co-author: Bourland, Nils; Cerisier, François; Livingstone Smith, Alexandre; Hubau, Wannes; Beeckman, Hans; Brostaux, Yves; Fétéké, Fousséni; Lejeune, Philippe; Ntoude Tiba, Eric; Doucet, Jean-Louis <br/> <br/>Abstract: Pericopsis elata is one of the most valuable African timber species. This IUCN Red Listed tree suffers from a lack of regeneration, thus its current presence provokes questioning. Our work aimed at understanding its origins so as to help securing its future. This study, lead away from engineering works, was conducted in four different sites located within the natural distribution area of the species and taking into account the different growing conditions were the species occurs. Our observations are based on an analysis of charcoal elements and pottery fragments discovered in subsurface layers of soils as well as current botanical and pedological surveys. Evidence of past human activities we found led to the assumption that this part of the Congo Basin was much more inhabited than previously thought. Some of the results obtained for P. elata could apply for other long lived light demanding species growing in the same environment Mon, 22 Apr 2013 07:37:03 GMT http://hdl.handle.net/2268/147123 Title: Boundary lines in symbiosis forms <br/> <br/>Author, co-author: Parmentier, Eric; Michel, Loïc <br/> <br/>Abstract: Symbiosis can take different forms (parasitism, mutualism, commensalism, etc.) but boundaries between different types of symbiotic interactions are not well defined. The kinds of symbiotic associations between organisms cannot however be restricted to isolated and distinct categories. These associations are part of a broad continuum in which it is difficult to know where one type of association ends and another begins. Moreover, different scientists use the same term to mean different things or different terms tomean the same thing. This can obscure what is biologically important and what is not. This communication proposes a new classification scheme, which simply and comprehensively illustrates relationships between the various kinds of associations. The scheme illustrates relationships clearly and highlights the continuum between types of associations. It further indicates where modifications to the scheme are possible over time. The classification of the association between two organisms can be reduced to two factors: 1) the impact incurred by the host (benefit or damage) and 2) the relative duration of the association (RDA), i.e. the ratio of the duration of the association to the life expectancy of the symbiont. The conceptual figure provides concrete examples and illustrates some relationships that can change during different life stages. This figure should help teachers and students in the understanding of symbiosis, and could be a starting point for future discussions in the continuously developing research fields studying ecological and evolutionary implications of symbiotic relationships. <br/> <br/>Commentary: There is a mistake in the MS: loxosoma does not belong to Bryozoa but to Entoprocta Fri, 19 Apr 2013 05:38:16 GMT http://hdl.handle.net/2268/146624 Title: Dissecting the mechanisms underlying old male mating advantage in a butterfly <br/> <br/>Author, co-author: Karl, Isabell; Heuskin, Stéphanie; Fischer, Klaus <br/> <br/>Abstract: Selection is expected to maximize an individual’s own genetic reward regardless of the potential fitness consequences for its sexual partners, which may cause sexual conflict. Although performance in holometabolous insects typically diminishes with age, old male mating advantage has been documented in a few species. Whether this pattern arises from female preference for older males based on, e.g., pheromone blends (intersexual selection), or from increased eagerness to mate in older compared to younger males is currently debated. We explore the mechanistic basis of old male mating advantage, using a series of experiments including behavioral as well as manipulative approaches, in the tropical butterfly Bicyclus anynana. Consistent with the residual reproductive value hypothesis, old male mating advantage was associated with a greater eagerness to mate, evidenced by a two times higher flying and courting activity in older than in younger males. In contrast, we found only limited support for a contribution of female preference for older males based on pheromone composition, although male sex pheromones clearly do play a role in mating success. Our results suggest that male behavior may play a primary role in old male mating advantage, and that pheromones are likely of secondary importance only. Male mating success was related to higher overall pheromone titers rather than variation in a single component. A dominant importance of male behavior in determining mating success may result in sexual conflict. Thu, 11 Apr 2013 06:53:59 GMT http://hdl.handle.net/2268/146347 Title: Western lowland gorilla populations and logging concessions: is the coexistence possible? <br/> <br/>Author, co-author: Haurez, Barbara; Petre, Charles-Albert; Doucet, Jean-Louis <br/> <br/>Abstract: Timber exploitation is rapidly expanding throughout the Congo Basin. Around 26 % of the moist forests are devoted to logging activities. Logging concessions largely overlap with the range of western lowland gorilla (WLG) considered as critically endangered by IUCN. However, this species could play an essential role in maintaining vegetal diversity notably through seed dispersal services. Particularly some tree species harvested for their timber may be dispersed by WLG. In this communication interactions between WLG and a timber exploitation are studied in Central Gabon. WLG density is estimated in an Annual Allowable Cut (AAC), and nesting behavior is described. Seeds dispersed by WLG are identified through fecal analysis and germination trials are conducted to assess seed viability after gut passage. Four treatments are realized for the most abundant species: passed seeds, passed seeds in fecal matrix, seeds surrounded by fresh pulp and seeds extracted from fresh fruits. A relatively high WLG density is observed in the AAC (2.0 weaned gorillas/km²). WLG nest preferentially in open terra firme forest and frequently use old logging road covered with herbaceous vegetation for nesting and feeding. They avoid nesting in closed terra firme forest. Seed dispersal and impacts of the passage in gorilla’s gut on seed germination are currently described. Germination success after gut passage depends on the seed species and varies from 0.0 to 100% in the course of monitoring time. The first results of this study suggest that timber exploitation and WLG conservation are not mutually exclusive. WLG are important agents of forest regeneration by dispersing seeds in logged areas. Nest sites in logging gaps could be particularly favorable for seedlings development. This consideration must encourage forest managers to strengthen WLG-conservative practices in their concessions. Sun, 07 Apr 2013 17:55:11 GMT http://hdl.handle.net/2268/145841 Title: Livre Blanc Céréales <br/> <br/>Author, co-author: Bodson, Bernard; Destain, Jean-Pierre Sun, 31 Mar 2013 03:00:32 GMT http://hdl.handle.net/2268/145787 Title: L’analyse du cycle de vie ou de l’intérêt d’une réflexion plus holistique pour soutenir le développement de systèmes de production plus durables <br/> <br/>Author, co-author: Debouche, Charles <br/> <br/>Abstract: Description de l'analyse du cycle de vie et de son apport dans le développement de systèmes de production plus durables Fri, 29 Mar 2013 10:41:52 GMT http://hdl.handle.net/2268/145186 Title: Deuxième campagne de mesure des odeurs sur le site de traitement des déchets de Tenneville Estimation des nuisances olfactives <br/> <br/>Author, co-author: Nicolas, Jacques; Thomas, Jean-François; Delva, Julien; Romain, Anne-Claude; Waczek, Cédric <br/> <br/>Abstract: The study is conducted in the frame of a programme of monitoring of all landfill sites in Wallonia. The "odour" part is assigned to ULg. The present report concerns more particularly a second campaign on the site of Tenneville, which is more than a simple landfill area, as it includes also other waste treatment faciliities : composting, biogas production and drying of wastewater sludges. Besides the usual field inspection technique, the research group has applied a 3D analysis to study the shape and the size of the odour plume in this uneven region. Wed, 20 Mar 2013 22:10:30 GMT http://hdl.handle.net/2268/145185 Title: Deuxième campagne de mesure des odeurs sur le site de traitement des déchets de Habay Estimation des nuisances olfactives <br/> <br/>Author, co-author: Nicolas, Jacques; Waczek, Cédric; Delva, Julien; Thomas, Jean-François; Cerisier, Christophe; Romain, Anne-Claude <br/> <br/>Abstract: The study is conducted in the frame of a programme of monitoring of all landfill sites in Wallonia. The "odour" part is assigned to ULg. The present report concerns more particularly a second campaign on the site of Habay, which is more than a simple landfill area, as it includes also other waste treatment facilities, such as composting and biodrying. Besides the usual field inspection technique, the research group has applied the electronic nose methodology to monitor the odour in the vicinity of the sources and a survey in the surroundings to try to validate the different results. Wed, 20 Mar 2013 21:47:34 GMT http://hdl.handle.net/2268/145172 Title: Impacts environnementaux des unités de biométhanisation <br/> <br/>Author, co-author: Nicolas, Jacques; Neyrinck, Roland; Cerisier, Christophe; Waczek, Cédric; Molitor, Noémie; Romain, Anne-Claude <br/> <br/>Abstract: The report presents a study conducted in the frame of a European Interreg project. The role of the research group was to investigate the possible environmental impacts of on-farm biogas production from anaerobic reactors. The odour impact was chiefly analysed with the aim of assessing the odour generated by farms equipped for biogas production compared to classical farms. Also, the odour levels in the head space of various materials, either prior or after methanation were compared, using different methods. Wed, 20 Mar 2013 16:06:23 GMT http://hdl.handle.net/2268/145166 Title: Quatrième campagne de mesure des odeurs sur le CET "Champ de Beaumont" à Monceau-sur-Sambre Estimation et monitoring des nuisances olfactives <br/> <br/>Author, co-author: Nicolas, Jacques; Thomas, Jean-François; Delva, Julien; Waczek, Cédric; Romain, Anne-Claude <br/> <br/>Abstract: The study is conducted in the frame of a programme of monitoring of all landfill sites in Wallonia. The "odour" part is assigned to ULg. The present report concerns more particularly a fourth campaign on the site of "Champ de Beaumont at Monceau-sur-Sambre. Besides the usual field inspection technique, the research group has used electronic noses to monitor the emissions of odours near the source so as the analysis of complaints in the surroundings. Wed, 20 Mar 2013 14:44:25 GMT http://hdl.handle.net/2268/145163 Title: Finalisation de la formule, applicable en Région wallonne, de la distance minimale d'implantation des porcheries et des poulaillers par rapport aux habitations. <br/> <br/>Author, co-author: Cobut, Pierre; Nicolas, Jacques; Lalande, Dominique; Delva, Julien; Waczek, Cédric <br/> <br/>Abstract: A formulae to calculate the minimum distance between livestock buildings and residential areas was designed by the research group in 2006. This report concerns a study aiming at finalizing the approach towards a guideline applicable in Wallonia. Different enhancements to the former formulae are proposed, taking into account recent technical improvements, and a comparison with the odour percentile concept is presented. Wed, 20 Mar 2013 14:35:27 GMT http://hdl.handle.net/2268/145160 Title: Convention de sous-traitance "FIDOR-Action" Etude de faisabilité du FIDOR dans le milieu récepteur de différents sites industriels et de sa capacité à agir sur la réduction de l'odeur. <br/> <br/>Author, co-author: Cerisier, Christophe; Collard, Laurent; Romain, Anne-Claude; Delva, Julien; Nicolas, Jacques <br/> <br/>Abstract: The report presents the results of a study conducted in the waste treatment facility of Habay and is the continuation of a former study which was aiming at designing the e-nose network named FIDOR. The present study concerns the ability of the FIDOR concept to forecast the odour annoyance in the surroundings and to control an odour abatement technique. An important part of the report concerns the validation of the predicted odour plume with resident observations. The report is the property of the company Odometric which commissioned the study. <br/> <br/>Commentary: Rapport confidentiel réservé à l'entreprise Odometric Wed, 20 Mar 2013 14:17:31 GMT