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Distantly related lipocalins share two conserved clusters of hydrophobic residues: use in homology modeling
Benoit Adam, Benoit Charloteaux, Jerome Beaufays, Luc Vanhamme, Edmond Godfroid, Robert Brasseur, Laurence Lins
BMC Structural Biology , 2008, DOI: 10.1186/1472-6807-8-1
Abstract: The pairwise sequence identity is low among this family, often below 30%, despite a well conserved tertiary structure. Under the 30% identity threshold, alignment methods do not correctly assign and align proteins. The only safe way to assign a sequence to that family is by experimental determination. However, these procedures are long and costly and cannot always be applied. A way to circumvent the experimental approach is sequence and structure analyze. To further help in that task, the residues implicated in the stabilisation of the lipocalin fold were determined. This was done by analyzing the conserved interactions for ten lipocalins having a maximum pairwise identity of 28% and various functions.It was determined that two hydrophobic clusters of residues are conserved by analysing the ten lipocalin structures and sequences. One cluster is internal to the barrel, involving all strands and the 310 helix. The other is external, involving four strands and the helix lying parallel to the barrel surface. These clusters are also present in RaHBP2, a unusual "outlier" lipocalin from tick Rhipicephalus appendiculatus. This information was used to assess assignment of LIR2 a protein from Ixodes ricinus and to build a 3D model that helps to predict function. FTIR data support the lipocalin fold for this protein.By sequence and structural analyzes, two conserved clusters of hydrophobic residues in interactions have been identified in lipocalins. Since the residues implicated are not conserved for function, they should provide the minimal subset necessary to confer the lipocalin fold. This information has been used to assign LIR2 to lipocalins and to investigate its structure/function relationship. This study could be applied to other protein families with low pairwise similarity, such as the structurally related fatty acid binding proteins or avidins.Lipocalins are small secreted proteins (160–200 residues), typically structured in a 8 strands up and down β-barrel. A 310
OspA heterogeneity of Borrelia valaisiana confirmed by phenotypic and genotypic analyses
Karine Ryffel, Olivier Péter, Eric Dayer, Anne-Gabrielle Bretz, Edmond Godfroid
BMC Infectious Diseases , 2003, DOI: 10.1186/1471-2334-3-14
Abstract: This study describes a mAb that targets OspA of B. valaisiana and primers targeting the OspA gene of this species. As the monoclonal antibody A116k did not react with strains NE231, M7, M53 and Frank and no amplification was observed with strains NE231, M7 and M53, the existence of two subgroups among European B. valaisiana species was confirmed.The association of both monoclonal antibody A116k and primers Bval 1F and Bval 1R allows to specific identification of the B. valaisiana isolates belonging to subgroup 1.Lyme borreliosis (LB) caused by a spirochetal species Borrelia burgdorferi sensu lato (sl.) is a multisystemic illness distributed worldwide [1]. In North America and Eurasia, LB is the most common tick-borne disease [2]. On the basis of protein profiles, DNA-DNA relatedness and rRNA gene restriction pattern, B. burgdorferi sl. strains have been previously divided into three species: B. burgdorferi sensu stricto (ss.), B. garinii and B. afzelii [3,4]. B. burgdorferi ss. was found in ticks and patients infected in Europe as well as in North America, whereas B. garinii and B. afzelii were only found in ticks and patients infected in Eurasia [4,5]. B. andersonii and B. bissettii were described in North America [6,7], while B. japonica has been defined in Japan [8] and B. lusitaniae in Portugal [9].First isolated in Valais-CH, from an I. ricinus tick, VS116 was characterized as B. valaisiana novel species [10]. As other species, it appeared that its geographical distribution was not uniform. In Switzerland, Scandinavia and the Netherlands, B. valaisiana was less frequently isolated than B. garinii and B. afzelii. In Ireland however, B. valaisiana was described as the most prevalent genospecies [11]. More recently, B. valaisiana has been isolated in Japan and East Asia from I. nipponensis, I. columnae and I. granulatus [12,13].An association between clinical outcome and infection by strains of different genospecies has been suggested and suspicion of a pathogenic
Ixodes ricinus Tick Lipocalins: Identification, Cloning, Phylogenetic Analysis and Biochemical Characterization
Jér?me Beaufays, Beno?t Adam, Yves Decrem, Pierre-Paul Prév?t, Sébastien Santini, Robert Brasseur, Michel Brossard, Laurence Lins, Luc Vanhamme, Edmond Godfroid
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003941
Abstract: Background During their blood meal, ticks secrete a wide variety of proteins that interfere with their host's defense mechanisms. Among these proteins, lipocalins play a major role in the modulation of the inflammatory response. Methodology/Principal Findings Screening a cDNA library in association with RT-PCR and RACE methodologies allowed us to identify 14 new lipocalin genes in the salivary glands of the Ixodes ricinus hard tick. A computational in-depth structural analysis confirmed that LIRs belong to the lipocalin family. These proteins were called LIR for “Lipocalin from I. ricinus” and numbered from 1 to 14 (LIR1 to LIR14). According to their percentage identity/similarity, LIR proteins may be assigned to 6 distinct phylogenetic groups. The mature proteins have calculated pM and pI varying from 21.8 kDa to 37.2 kDa and from 4.45 to 9.57 respectively. In a western blot analysis, all recombinant LIRs appeared as a series of thin bands at 50–70 kDa, suggesting extensive glycosylation, which was experimentally confirmed by treatment with N-glycosidase F. In addition, the in vivo expression analysis of LIRs in I. ricinus, examined by RT-PCR, showed homogeneous expression profiles for certain phylogenetic groups and relatively heterogeneous profiles for other groups. Finally, we demonstrated that LIR6 codes for a protein that specifically binds leukotriene B4. Conclusions/Significance This work confirms that, regarding their biochemical properties, expression profile, and sequence signature, lipocalins in Ixodes hard tick genus, and more specifically in the Ixodes ricinus species, are segregated into distinct phylogenetic groups suggesting potential distinct function. This was particularly demonstrated by the ability of LIR6 to scavenge leukotriene B4. The other LIRs did not bind any of the ligands tested, such as 5-hydroxytryptamine, ADP, norepinephrine, platelet activating factor, prostaglandins D2 and E2, and finally leukotrienes B4 and C4.
Variability and Action Mechanism of a Family of Anticomplement Proteins in Ixodes ricinus
Bernard Couvreur, Jér?me Beaufays, Cédric Charon, Kathia Lahaye, Fran?ois Gensale, Valérie Denis, Beno?t Charloteaux, Yves Decrem, Pierre-Paul Prév?t, Michel Brossard, Luc Vanhamme, Edmond Godfroid
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0001400
Abstract: Background Ticks are blood feeding arachnids that characteristically take a long blood meal. They must therefore counteract host defence mechanisms such as hemostasis, inflammation and the immune response. This is achieved by expressing batteries of salivary proteins coded by multigene families. Methodology/Principal Findings We report the in-depth analysis of a tick multigene family and describe five new anticomplement proteins in Ixodes ricinus. Compared to previously described Ixodes anticomplement proteins, these segregated into a new phylogenetic group or subfamily. These proteins have a novel action mechanism as they specifically bind to properdin, leading to the inhibition of C3 convertase and the alternative complement pathway. An excess of non-synonymous over synonymous changes indicated that coding sequences had undergone diversifying selection. Diversification was not associated with structural, biochemical or functional diversity, adaptation to host species or stage specificity but rather to differences in antigenicity. Conclusions/Significance Anticomplement proteins from I. ricinus are the first inhibitors that specifically target a positive regulator of complement, properdin. They may provide new tools for the investigation of role of properdin in physiological and pathophysiological mechanisms. They may also be useful in disorders affecting the alternative complement pathway. Looking for and detecting the different selection pressures involved will help in understanding the evolution of multigene families and hematophagy in arthropods.
Teachers’ Attitudes and Perceptions: Association of Teachers’ Attitudes toward Traditional and Modern Teaching Methodology According to RWCT as Well as Teachers’ Perceptions for Teaching as a Profession  [PDF]
Xhevahire Karanezi, Edmond Rapti
Creative Education (CE) , 2015, DOI: 10.4236/ce.2015.66061
Abstract: Teaching methodologies that are chosen to be used by teachers in their daily work are highly impacted by their attitudes and perceptions. According to Schoenfeld (1992) attitudes and perceptions influence teachers not only how, but what, he or she teaches. The data collection for this study was conducted using quantitative and qualitative method. There were 473 school teachers throughout Kosovo that participated in this study. Questionnaires were used to collect all quantitative data, which were compiled and adjusted in accordance with the study objectives. Focus groups discussions were conducted for the purpose of collecting the qualitative data. The data showed significant negative association between teachers’ attitudes toward traditional teaching methodologies and modern teaching methodologies according to RWCT (r = 0.446, sig = 0.000). The data also showed that there was a significant negative association between attitudes toward traditional teaching methodology and teachers’ perceptions for teaching as a profession (r = 0.092, sig = 0.046). The quantitative results were in the same line with the qualitative findings of the study.
Ir-LBP, an Ixodes ricinus Tick Salivary LTB4-Binding Lipocalin, Interferes with Host Neutrophil Function
Jér?me Beaufays, Beno?t Adam, Catherine Menten-Dedoyart, Laurence Fievez, Amélie Grosjean, Yves Decrem, Pierre-Paul Prév?t, Sébastien Santini, Robert Brasseur, Michel Brossard, Michel Vanhaeverbeek, Fabrice Bureau, Ernst Heinen, Laurence Lins, Luc Vanhamme, Edmond Godfroid
PLOS ONE , 2008, DOI: 10.1371/journal.pone.0003987
Abstract: Background During their blood meal, ticks secrete a wide variety of proteins that can interfere with their host's defense mechanisms. Among these proteins, lipocalins play a major role in the modulation of the inflammatory response. Methodology/Principal Findings We previously identified 14 new lipocalin genes in the tick Ixodes ricinus. One of them codes for a protein that specifically binds leukotriene B4 with a very high affinity (Kd: ±1 nM), similar to that of the neutrophil transmembrane receptor BLT1. By in silico approaches, we modeled the 3D structure of the protein and the binding of LTB4 into the ligand pocket. This protein, called Ir-LBP, inhibits neutrophil chemotaxis in vitro and delays LTB4-induced apoptosis. Ir-LBP also inhibits the host inflammatory response in vivo by decreasing the number and activation of neutrophils located at the tick bite site. Thus, Ir-LBP participates in the tick's ability to interfere with proper neutrophil function in inflammation. Conclusions/Significance These elements suggest that Ir-LBP is a “scavenger” of LTB4, which, in combination with other factors, such as histamine-binding proteins or proteins inhibiting the classical or alternative complement pathways, permits the tick to properly manage its blood meal. Moreover, with regard to its properties, Ir-LBP could possibly be used as a therapeutic tool for illnesses associated with an increased LTB4 production.
Ex-Ante Asymmetric Regulation and Retail Mmarket Competition: Evidence from Europe’s Mobile Industry  [PDF]
Edmond Baranes, Cuong Hung Vuong
Technology and Investment (TI) , 2011, DOI: 10.4236/ti.2011.24031
Abstract: The aim of this paper is to assess the impacts of ex-ante asymmetric mobile termination rate regulation on ex-post market competition in the Europe’s mobile industry. Two regulatory instruments associated with the asymmetry between operators are implemented, namely glide path regulation and asymmetric regulation. The first regulatory device is to gradually decrease asymmetric treatment between mobile and fixed network operators while the second one is associated with asymmetric flexibility in setting MTRs between European mobile operators. With different model specifications, our study demonstrates that when the MTRs are regulated to lower levels, later entrants are likely to cut retail prices to gain more subscribers, and resulting in lower average national service prices. Furthermore, we find that asymmetric regulation plays a positive role on entrant penetration as well as the competitiveness of Europe’s mobile markets.
Partons and jets in a strongly-coupled plasma from AdS/CFT
Iancu, Edmond
High Energy Physics - Phenomenology , 2008,
Abstract: We give a pedagogical review of recent progress towards understanding the response of a strongly coupled plasma at finite temperature to a hard probe. The plasma is that of the N=4 supersymmetric Yang-Mills theory and the hard probe is a virtual photon, or, more precisely, an R-current. Via the gauge/gravity duality, the problem of the current interacting with the plasma is mapped onto the gravitational interaction between a Maxwell field and a black hole embedded in the AdS_5 x S^5 geometry. The physical interpretation of the AdS/CFT results can be then reconstructed with the help of the ultraviolet/infrared correspondence. We thus deduce that, for sufficiently high energy, the photon (or any other hard probe: a quark, a gluon, or a meson) disappears into the plasma via a universal mechanism, which is quasi-democratic parton branching: the current develops a parton cascade such that, at any step in the branching process, the energy is almost equally divided among the daughter partons. The branching rate is controlled by the plasma which acts on the colored partons with a constant force ~ T^2. When reinterpreted in the plasma infinite momentum frame, the same AdS/CFT results suggest a parton picture for the plasma structure functions, in which all the partons have fallen at very small values of Bjorken's x. For a time-like current in the vacuum, quasi-democratic branching implies that there should be no jets in electron-positron annihilation at strong coupling, but only a spatially isotropic distribution of hadronic matter.
Partons and jets at strong coupling from AdS/CFT
Iancu, Edmond
High Energy Physics - Phenomenology , 2008, DOI: 10.1143/PTPS.174.306
Abstract: Calculations using the AdS/CFT correspondence can be used to unveil the short-distance structure of a strongly coupled plasma, as it would be seen by a `hard probe'. The results of these calculations admit a natural physical interpretation in terms of parton evolution in the plasma: via successive branchings, essentially all partons cascade down to very small values of the longitudinal momentum fraction x and to transverse momenta smaller than the saturation momentum Q_s\sim T/x. This scale Q_s controls the energy loss and the transverse momentum broadening of an energetic jet propagating through the plasma. This picture has some striking consequences, like the absence of jets in electron-proton annihilation at strong coupling, of the absence of particle production at forward and backward rapidities in hadron-hadron collisions, which look very different from the corresponding predictions of perturbative QCD and also from the known experimental situation.
Appropriation, déconstruction du fran ais et insécurité linguistique dans la littérature africaine d’expression fran aise
Edmond Biloa
Synergies Afrique Centrale et de l'Ouest , 2007,
Abstract:
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