References of "Joris, Bernard"
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See detailStereoselective synthesis of peptidoglycan fragments on solid support
Simon, Justine ULg; Lamborelle, Nicolas ULg; Joris, Bernard ULg et al

Poster (2014, June)

The mammalian proteins, Nod1 and Nod2, are able to recognize peptidoglycan motifs during bacterial infection. Interestingly, Nod1 is a detector of peptides and muropeptides containing the meso-2,6 ... [more ▼]

The mammalian proteins, Nod1 and Nod2, are able to recognize peptidoglycan motifs during bacterial infection. Interestingly, Nod1 is a detector of peptides and muropeptides containing the meso-2,6-diaminopimelic acid (m-A2pm), a non-proteinogenic amino acid found in Gram- bacteria. In this work, we describe a synthesis of peptidoglycan motifs entirely on solid support. Solid-Phase Peptide Synthesis (SPPS), Cross Metathesis (CM) and sugar chemistry are three methods to anchor respectively amino acids, m-A2pm and sugars derivatives on a resin as solid support. [less ▲]

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See detailStudies of the Domains II and III of Bacillus subtilis PBP4a in relation with the protein localization
Vanden Broeck, Arnaud ULg; Van Der Heiden, Edwige ULg; Sauvage, Eric ULg et al

Poster (2014, April 23)

Bacillus subtilis PBP4a belongs to the class-C1 PBPs characterized by two internal additional domains of unknown function. Seven lysine residues (K) are protruding from domain II. Four of them have been ... [more ▼]

Bacillus subtilis PBP4a belongs to the class-C1 PBPs characterized by two internal additional domains of unknown function. Seven lysine residues (K) are protruding from domain II. Four of them have been mutated in glutamine residues (Q). Both proteins (WT and Mut4KQ PBP4a) have been produced without signal peptide in E. coli and their sub-cellular localizations determined by measuring the DD-carboxypeptidase activities in the different compartments (cytoplasmic vs membrane attached proteins). In order to detect a possible influence of the PBP4a domain III in the localization of the protein, its encoding sequence has been cloned into pET-28b-BlaP, a vector allowing the production of WT BlaP β-lactamase or BlaP/DIII chimeric protein (with domain III inserted in a permissive loop of BlaP). The nitrocefin hydrolysis activities of BlaP or BlaP/DIII have been measured in the different cellular compartments. [less ▲]

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See detailMicrofluidic on optical fibers: Towards a new kind of fluorescent biosensor
Lismont, Marjorie ULg; Vandewalle, Nicolas ULg; Weyer, Floriane ULg et al

Poster (2014, February)

In recent works, the behavior of droplets moving along vertical treads due to gravity was studied. It appeared that the droplet can be stopped by encountering a horizontal fiber depending on droplet ... [more ▼]

In recent works, the behavior of droplets moving along vertical treads due to gravity was studied. It appeared that the droplet can be stopped by encountering a horizontal fiber depending on droplet volumes and fiber characteristics. On the basis of this behavior and by replacing treads by two crossed optical fibers, it is possible to combine fluidics and optics to develop a new kind of fluorescent sensor. In our work, the intersection between two crossed optical fibers is used as the basic unit of an original optofluidic biosensor. These two optical fibers are used as droplets carriers: one for probe molecules and the other one for target species. The fiber's junction catches the droplets and act as a reaction center. The main advantage of using optical fibers resides in their ability to propagate and collect light to and from the droplet localized at the fiber's crossing. This optical fiber configuration can therefore allow the study of biological interactions using fluorescent labels. This new and versatile detection scheme was validated on a calcium indicator where ions detection is accomplished by using a dye, Oregon green Bapta-2, that has a Ca 2+ recognition group as well as an entity exhibiting fluorescence. A FRET recognition event, between Rh-Con A and FITC-Dextran, was also investigated to detect glucose. Finally, a prototype of a multiplexing device, composed of several juxtaposed fibers' junctions, was developed. [less ▲]

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See detailStudy of the Bacillus subtilis ATCC21332 pbpE-racX operon in relation with the formation or disassembly of biofilms
Vanden Broeck, Arnaud ULg; Van Der Heiden, Edwige ULg; Joris, Bernard ULg et al

Poster (2013, December 20)

Bacillus subtilis is a PGPR (Plant Growth Promoting Rhizobacterium) Gram positive bacterium and a model for studying the in vitro formation or disruption of biofilms. At the liquid/air interface of ... [more ▼]

Bacillus subtilis is a PGPR (Plant Growth Promoting Rhizobacterium) Gram positive bacterium and a model for studying the in vitro formation or disruption of biofilms. At the liquid/air interface of standing cultures, B. subtilis forms thick pellicles of limited lifetimes. Some D-amino acids have been reported among the factors playing a role in the disassembly of B. subtilis biofilms and ylmE or racX mutants (in which the racemases YlmE or RacX are absent) show a delay in pellicle disruption [I. Kolodkin et al. Science (2010) 328:627-629]. The racX encoding gene is part of a bicistronic operon in which the first gene (pbpE) codes for a Penicillin-Binding Protein, the PBP4* whose function is not characterized. Our studies aim to delete the complete pbpE-racX operon and compare the phenotypes of mutants and parental strains ATCC21332 or ATCC6051 in standing cultures. The substrate specificity of the purified RacX racemase is currently under investigation as well as the functional characterization of PBP4*, a protein possessing a lipocalin-like domain. [less ▲]

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See detailSAHBNET, An Accessible Surface-Based Elastic Network to Insert a Protein in a Complex Lipid Membrane
Dony, Nicolas ULg; Crowet, Jean-Marc ULg; Joris, Bernard ULg et al

Conference (2013, November 11)

Study of membrane proteins have become one of the most challenging fields in biology. Solving their structure is one important step toward the understanding of their physiological activity but despite the ... [more ▼]

Study of membrane proteins have become one of the most challenging fields in biology. Solving their structure is one important step toward the understanding of their physiological activity but despite the recent advances in membrane protein crystallization, it represents less than 1 % of the entries in the Protein Data Bank. Therefore, calculation methods to study membrane proteins are helpful to complement experimental studies and fill the gap between the information obtained from the sequence and/or structure, the experimental results and the biological activity. Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. However, these approaches have two main drawbacks, the preparation of complex systems and the preservation of the 3D protein structure, which is not trivial in coarse grained approach. To circumvent these problems, we propose to use a modified version of the Gromacs tool genbox to easily insert lipids and a network based on hydrogen bonds and accessible surface to maintain the protein 3D structure. This protocol is available through a website (gcgs.gembloux.ulg.ac.be). [less ▲]

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See detailInsertion of domain III of Bacillus subtilis and Bacillus amyloliquefaciens PBP4a in the Bacillus licheniformis BlaP β-lactamase to study the binding to peptidoglycan and whole bacteria
Van Der Heiden, Edwige ULg; Hoebreck, Charline ULg; Freichels, Régine ULg et al

Poster (2013, October 03)

Domain III of Bacillus subtilis and B. amyloliquefaciens DD-endopeptidase PBP4a was introduced in the BlaP beta-lactamse of Bacillus licheniformis. Domain III of Bacillus licheniformis binds to ... [more ▼]

Domain III of Bacillus subtilis and B. amyloliquefaciens DD-endopeptidase PBP4a was introduced in the BlaP beta-lactamse of Bacillus licheniformis. Domain III of Bacillus licheniformis binds to peptidoglycan of Bacillus subtilis 168 and to itself whole cells. [less ▲]

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See detailA Pathway closely related to the D-tagatose pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis
Van Der Heiden, Edwige ULg; Delmarcelle, Michaël ULg; Lebrun, Sarah ULg et al

Poster (2013, June)

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium ... [more ▼]

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. [less ▲]

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See detailA Pathway closely related to the D-tagatose pathway of Gram-Negative Enterobacteria Identified in the Gram-Positive Bacterium Bacillus licheniformis
Van Der Heiden, Edwige ULg; Delmarcelle, Michaël ULg; Lebrun, Sarah ULg et al

in Applied and Environmental microbiology (2013), 79(11), 3511-3515

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium ... [more ▼]

We report the first identification of a gene cluster involved in d-tagatose catabolism in Bacillus licheniformis. The pathway is closely related to the d-tagatose pathway of the Gram-negative bacterium Klebsiella oxytoca, in contrast to the d-tagatose 6-phosphate pathway described in the Gram-positive bacterium Staphylococcus aureus. [less ▲]

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See detailSAHBNET, an Accessible Surface-Based Elastic Network: An Application to Membrane Protein
Dony, Nicolas ULg; Crowet, Jean-Marc ULg; Joris, Bernard ULg et al

in International Journal of Molecular Sciences (2013), 14(6), 11510-26

Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an ... [more ▼]

Molecular Dynamics is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. Here, we present an elastic network, SAHBNET (Surface Accessibility Hydrogen-Bonds elastic NETwork), that will maintain the structure of soluble or membrane proteins based on the hydrogen bonds present in the atomistic structure and the proximity between buried residues. This network is applied on the coarse-grained beads defined by the MARTINI model, and was designed to be more physics-based than a simple elastic network. The SAHBNET model is evaluated against atomistic simulations, and compared with ELNEDYN models. The SAHBNET is then used to simulate two membrane proteins inserted in complex lipid bilayers. These bilayers are formed by self-assembly and the use of a modified version of the GROMACS tool genbox (which is accessible through the gcgs.gembloux.ulg.ac.be website). The results show that SAHBNET keeps the structure close to the atomistic one and is successfully used for the simulation of membrane proteins. [less ▲]

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See detailPrediction of membrane protein structures and TM interactions Rosetta and molecular dynamic studies
Crowet, Jean-Marc ULg; Dony, Nicolas ULg; Joris, Bernard ULg et al

Poster (2013, February 26)

The structures of membrane domains of the Divisome proteins and BlaR are not known and there is no homolog proteins of known structure to build homolgy models. Although the structure prediction of ... [more ▼]

The structures of membrane domains of the Divisome proteins and BlaR are not known and there is no homolog proteins of known structure to build homolgy models. Although the structure prediction of membrane proteins seems easier than for globular proteins, their ab initio prediction remains a difficult task. Only few methods have been used and validated on experimental pdb structures. By using the MARTINI or Bond coarse grain representation, the multimerization of transmembrane helices has been carried out by molecular dynamics, and the structure of several membrane proteins has been predicted by a tool of the Rosetta package. These methods are used here to predict the structure of the membrane embedded part of the politopic proteins from the divisome (FtsW, FtsK, FtsX and MraY) and BlaR. In a following part the MARTINI force field can be used to predict the TM helices interactions between the Divisome protein members. [less ▲]

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See detailSAHBEN, an accessible surface-based elastic network to insert a protein in a complex lipid membrane
Dony, Nicolas ULg; Crowet, Jean-Marc ULg; Joris, Bernard ULg et al

Poster (2013, February 26)

Study of membrane proteins have become one of the most challenging fields in biology. Solving their structure is one important step toward the understanding of their physiological activity but despite the ... [more ▼]

Study of membrane proteins have become one of the most challenging fields in biology. Solving their structure is one important step toward the understanding of their physiological activity but despite the recent advances in membrane protein crystallization, it represents less than 1 % of the entries in the Protein Data Bank. Therefore, calculation methods to study membrane proteins are helpful to complement experimental studies and fill the gap between the information obtained from the sequence and/or structure, the experimental results and the biological activity. Molecular Dynamics (MD) is a method of choice for membrane simulations and the rising of coarse-grained forcefields has opened the way to longer simulations with reduced calculations times. However, these approaches have two main drawbacks, the preparation of the membrane system and the preservation of the 3D protein structure, which is not trivial in CG approach. To circumvent these problems, we propose to use a modified version of the Gromacs tool genbox to easily insert lipids and a network based on hydrogen bonds and accessible surface to maintain the protein 3D structure. This protocol is available through a website (gcgs.gembloux.ulg.ac.be). [less ▲]

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See detailSevoflurane inhibits equine myeloperoxidase release and activity in vitro.
MINGUET, Grégory ULg; de la Rebière de Pouyade, Geoffroy ULg; Franck, Thierry ULg et al

in Veterinary Anaesthesia & Analgesia (2013), 40

Objective To investigate the effects of the volatile anaesthetic sevoflurane on the release of total and active myeloperoxidase (MPO) by non-stimulated and stimulated polymorphonuclear neutrophils (PMNs ... [more ▼]

Objective To investigate the effects of the volatile anaesthetic sevoflurane on the release of total and active myeloperoxidase (MPO) by non-stimulated and stimulated polymorphonuclear neutrophils (PMNs) in whole blood from healthy horses. Study design In vitro experimental study. Animals Adult healthy horses. Methods Samples of whole venous blood were collected and incubated in air or in air plus 2.3% or 4.6% sevoflurane for 1 hour. PMNs were stimulated with N-formyl-methionyl-leucyl-phenylalanine (fMLP), with a combination of cytochalasin B (CB) and fMLP or with phorbol myristate acetate (PMA). Total and active MPO contents released by PMNs in blood were measured by enzyme-linked immunosorbent assay (ELISA) and specific immunological extraction followed by enzymatic detection (SIEFED) respectively. Additional experiments were performed to assess the effect of sevoflurane on the peroxidase and chlorination cycles of purified equine MPO using Amplex Red and 3'-(p-aminophenyl) fluorescein as fluorogenic substrates respectively. Results As compared with air alone, 1 hour exposure of whole blood to 4.6% sevoflurane in air significantly inhibited the release of total and active MPO by unstimulated and both fMLP- and CB + fMLP-stimulated PMNs but not by PMA-stimulated PMNs. Although 2.3% sevoflurane had no effect on total MPO release by unstimulated and stimulated PMNs, it significantly reduced the release of active MPO by unstimulated and fMLP-stimulated PMNs. Additionally, sevoflurane reversibly inhibited the activity of MPO, especially the peroxidase cycle of the enzyme. Conclusions and clinical relevance Although our experimental study was not designed to assess the effects of sevoflurane in vivo, this inhibition of MPO release and activity may have relevance for anaesthetized horses and deserves further studies to examine the clinical importance of these findings. [less ▲]

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See detailCharacterization of amylolysin, a novel lantibiotic from Bacillus amyloliquefaciens GA1
Arias, A. A.; Ongena, Marc ULg; Devreese, B. et al

in PLoS ONE (2013), 8(12),

Background: Lantibiotics are heat-stable peptides characterized by the presence of thioether amino acid lanthionine and methyllanthionine. They are capable to inhibit the growth of Gram-positive bacteria ... [more ▼]

Background: Lantibiotics are heat-stable peptides characterized by the presence of thioether amino acid lanthionine and methyllanthionine. They are capable to inhibit the growth of Gram-positive bacteria, including Listeria monocytogenes, Staphylococcus aureus or Bacillus cereus, the causative agents of food-borne diseases or nosocomial infections. Lantibiotic biosynthetic machinery is encoded by gene cluster composed by a structural gene that codes for a pre-lantibiotic peptide and other genes involved in pre-lantibiotic modifications, regulation, export and immunity. Methodology/Findings: Bacillus amyloliquefaciens GA1 was found to produce an antimicrobial peptide, named amylolysin, active on an array of Gram-positive bacteria, including methicillin resistant S. aureus. Genome characterization led to the identification of a putative lantibiotic gene cluster that comprises a structural gene (amlA) and genes involved in modification (amlM), transport (amlT), regulation (amlKR) and immunity (amlFE). Disruption of amlA led to loss of biological activity, confirming thus that the identified gene cluster is related to amylolysin synthesis. MALDI-TOF and LC-MS analysis on purified amylolysin demonstrated that this latter corresponds to a novel lantibiotic not described to date. The ability of amylolysin to interact in vitro with the lipid II, the carrier of peptidoglycan monomers across the cytoplasmic membrane and the presence of a unique modification gene suggest that the identified peptide belongs to the group B lantibiotic. Amylolysin immunity seems to be driven by only two AmlF and AmlE proteins, which is uncommon within the Bacillus genus. Conclusion/Significance: Apart from mersacidin produced by Bacillus amyloliquefaciens strains Y2 and HIL Y-85,544728, reports on the synthesis of type B-lantibiotic in this species are scarce. This study reports on a genetic and structural characterization of another representative of the type B lantibiotic in B. amyloliquefaciens. Copyright: © 2013 Arguelles Arias et al. [less ▲]

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See detailSynthesis and biological evaluation of potential threonine synthase inhibitors: Rhizocticin A and Plumbemycin A.
Gahungu, Mathias; Arguelles-Arias, Anthony; Fickers, Patrick et al

in Bioorganic & Medicinal Chemistry (2013), 21(17), 4958-67

Rhizocticins and Plumbemycins are natural phosphonate antibiotics produced by the bacterial strains Bacillus subtilis ATCC 6633 and Streptomyces plumbeus, respectively. Up to now, these potential ... [more ▼]

Rhizocticins and Plumbemycins are natural phosphonate antibiotics produced by the bacterial strains Bacillus subtilis ATCC 6633 and Streptomyces plumbeus, respectively. Up to now, these potential threonine synthase inhibitors have only been synthesized under enzymatic catalysis. Here we report the chemical stereoselective synthesis of the non-proteinogenic (S,Z)-2-amino-5-phosphonopent-3-enoic acid [(S,Z)-APPA] and its use for the synthesis of Rhizocticin A and Plumbemycin A. In this work, (S,Z)-APPA was synthesized via the Still-Gennari olefination starting from Garner's aldehyde. The Michaelis-Arbuzov reaction was used to form the phosphorus-carbon bond. Oligopeptides were prepared using liquid phase peptide synthesis (LPPS) and were tested against selected bacteria and fungi. [less ▲]

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See detail2-nitrobenzyl esters of penam and cephem derivatives as inhibitors of penicillin-binding proteins
Brulé, Cédric; Grugier, Jérôme; Brans, Alain ULg et al

in Asian Journal of Organic Chemistry (2013), 2

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See detailThe MicroH2 project:an association of four laboratories to improve theknowledge on biohydrogen production precesses
Beckers, Laurent ULg; Calusinska, Magdalena ULg; Hamilton, Christopher ULg et al

Poster (2012, June 04)

This poster presents a collaborative research project (MicroH2) held at the University of Liège (Belgium) since 2007 (www.microh2.ulg.ac.be) and involving four different research groups. The project aims ... [more ▼]

This poster presents a collaborative research project (MicroH2) held at the University of Liège (Belgium) since 2007 (www.microh2.ulg.ac.be) and involving four different research groups. The project aims to develop a center of excellence in the fields of photo- and dark- biohydrogen production. Our studies contribute to improve the knowledge of the processes involved in the microbiological production of hydrogen, from a fundamental and practical point of view. Some results are highlighted here. The research concerning photofermentation focuses on the interactions between respiration, photosynthesis and H2-producing pathways in algal microorganisms, by using mitochondrial mutants and genetically modified strains with modified ability for hydrogen production [1-2]. To study the metabolism of the hydrogen production by anaerobic bacteria, pure cultures and defined consortia are used and their production of biogas and soluble metabolites is measured. Moreover, we have developed and optimized molecular tools, like quantitative RT-PCR and FISH, to monitor the variations of bacterial populations in novel bioreactors for hydrogen production [3-4]. We have also mined the complete genomes of Clostridium spp. for putative hydrogenase genes and found a large diversity of them [5]. [less ▲]

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See detailSynthesis and evaluation of boronic acids as inhibitors of Penicillin Binding Proteins of classes A, B and C
Zervosen, Astrid ULg; Sauvage, Eric ULg; Bouillez, André ULg et al

Poster (2012, April 18)

The widespread use of beta-lactam antibiotics has lead to the worldwide appearance of drug-resistant strains. Bacteria have developed resistance to beta-lactams by three main mechanisms: the production of ... [more ▼]

The widespread use of beta-lactam antibiotics has lead to the worldwide appearance of drug-resistant strains. Bacteria have developed resistance to beta-lactams by three main mechanisms: the production of beta-lactamases that catalyze hydrolysis of beta-lactams, the production of low-affinity, drug resistant Penicillin Binding Proteins (PBPs) and the over expression of resistant PBPs. PBPs are interesting targets because they catalyse the last steps of the biosynthesis of peptidoglycan, which is unique in bacteria and has no mammalian analogs, outside the cytoplasmic membrane. Various non-ß-lactam inhibitors of PBPs have been developed with the objective of attempting to stall the development of ß-lactam resistance. Boronic acids are potent beta-lactamase inhibitors and have been shown to display some specificity for soluble transpeptidases and PBPs, but their potential as inhibitors of the latter enzymes is yet to be widely explored. Recently, a (2, 6-dimethoxybenzamido)methylboronic acid was identified as being a potent inhibitor of Actinomadura sp. R39 transpeptidase (IC50: 1.3 µM). Here, we will discuss the synthesis of a number of acylaminomethylboronic acids, analogs of (2, 6-dimethoxybenzamido)methylboronic acid, and their potential as inhibitors of PBPs. Several boronic acids of this library were able to inhibit PBPs of classes A, B and C from penicillin sensitive strains. Thus (2-nitrobenzamido)methylboronic acid was identified as a good inhibitor of class A PBP (PBP1b from S. pneumoniae, IC50 = 26 µM), class B PBP (PBP2xR6 from S. pneumoniae, IC50 = 138 µM) and class C PBP (R39 from Actinomadura sp., IC50 = 0.6 µM). Crystal structures of complexes of R39 and PBP1b with boronic acid analogs of our library have already been solved and allowed an interpretation of results. We believe that this work opens new avenues towards the development of molecules that will inhibit PBPs, and eventually display bactericidal effect, on distinct bacterial species. [less ▲]

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