References of "Joris, Bernard"
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See detailBiosensor based on optical fibers
Lismont, Marjorie ULg; Vandewalle, Nicolas ULg; Joris, Bernard ULg et al

Poster (2015, May)

Medical diagnosis and biotechnology progresses are strongly dependent on the development of sensing devices, which, ideally, would allow the reliable detection of very low amounts of biological species in ... [more ▼]

Medical diagnosis and biotechnology progresses are strongly dependent on the development of sensing devices, which, ideally, would allow the reliable detection of very low amounts of biological species in various environments. In addition to these requirements, the detection tools would also be easy to use and would rapidly response. Fluorescent based biosensors fulfil most of these characteristics. In our work, the intersection between two crossed optical fibers is used as the basic unit of an original optical biosensor. As illustrated by figure 1, one optical fiber is used to carry probe molecules and excite fluorescence while the second one is devoted to carry the target species and collect the optical signal arising from the species interacting at the node. The advantages of our set-up over traditional optical sensors are no surface functionalization, use of low amounts of biological species, limitation of the denaturation risk, ease to use and low detection threshold. The developed biosensor is validated on two systems. The first one is a fluorescent calcium indicator, Oregon green 488 BAPTA-2, whose optical emission signal is affected by Ca2+ ions concentration. The second one is based on Rh-Con A and FITC-Dextran complex for which the FRET phenomenon is affected by glucose concentration. In both cases, the results are in agreement with the ones obtained in cuvettes attesting the efficiency of the sensing device. We also show a prototype of a multichannel device composed of multiple crossed optical fibers which are used as species and light carriers. [less ▲]

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See detailGenome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009
Calusinska, Magda; Hamilton, Christopher; Monsieurs, Pieter et al

in Biotechnology for Biofuels (2015), 8(27), 1-16

Background: Molecular hydrogen, given its pollution-free combustion, has great potential to replace fossil fuels in future transportation and energy production. However, current industrial hydrogen ... [more ▼]

Background: Molecular hydrogen, given its pollution-free combustion, has great potential to replace fossil fuels in future transportation and energy production. However, current industrial hydrogen production processes, such as steam reforming of methane, contribute significantly to the greenhouse effect. Therefore alternative methods, in particular the use of fermentative microorganisms, have attracted scientific interest in recent years. However the low overall yield obtained is a major challenge in biological H2 production. Thus, a thorough and detailed understanding of the relationships between genome content, gene expression patterns, pathway utilisation and metabolite synthesis is required to optimise the yield of biohydrogen production pathways. Results: In this study transcriptomic and proteomic analyses of the hydrogen-producing bacterium Clostridium butyricum CWBI 1009 were carried out to provide a biomolecular overview of the changes that occur when the metabolism shifts to H2 production. The growth, H2-production, and glucose-fermentation profiles were monitored in 20 L batch bioreactors under unregulated-pH and fixed-pH conditions (pH 7.3 and 5.2). Conspicuous differences were observed in the bioreactor performances and cellular metabolisms for all the tested metabolites, and they were pH dependent. During unregulated-pH glucose fermentation increased H2 production was associated with concurrent strong up-regulation of the nitrogenase coding genes. However, no such concurrent up-regulation of the [FeFe] hydrogenase genes was observed. During the fixed pH 5.2 fermentation, by contrast, the expression levels for the [FeFe] hydrogenase coding genes were higher than during the unregulated-pH fermentation, while the nitrogenase transcripts were less abundant. The overall results suggest, for the first time, that environmental factors may determine whether H2 production in C. butyricum CWBI 1009 is mediated by the hydrogenases and/or the nitrogenase. Conclusions: This work, contributing to the field of dark fermentative hydrogen production, provides a multidisciplinary approach for the investigation of the processes involved in the molecular H2 metabolism of clostridia. In addition, it lays the groundwork for further optimisation of biohydrogen production pathways based on genetic engineering techniques. [less ▲]

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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 detailEnantioselective synthesis of [small alpha]-benzylated lanthionines and related tripeptides for biological incorporation into E. coli peptidoglycan
Denoel, Thibaut; Zervosen, Astrid ULg; Lemaire, Christian ULg et al

in Organic & Biomolecular Chemistry (2014)

The synthesis of modified tripeptides (S)-Ala-[gamma]-(R)-Glu-X, where X = (R,S) or (R,R) diastereomers of [small alpha]-benzyl or [small alpha]-(4-azidobenzyl)lanthionine, was carried out. The chemical ... [more ▼]

The synthesis of modified tripeptides (S)-Ala-[gamma]-(R)-Glu-X, where X = (R,S) or (R,R) diastereomers of [small alpha]-benzyl or [small alpha]-(4-azidobenzyl)lanthionine, was carried out. The chemical strategy involved the enantioselective alkylation of a 4-MeO-phenyloxazoline. The reductive opening of the alkylated oxazolines, followed by cyclization and oxidation, led to four PMB-protected sulfamidates. Subsequent PMB removal, Boc protection and regioselective opening with cysteine methyl ester led to protected lanthionines. These compounds were further converted in a one pot process to the corresponding protected tripeptides. After ester and Boc deprotection, the four tripeptides were evaluated as potential analogues of the natural tripeptide (S)-Ala-[gamma]-(R)-Glu-meso-A2pm. These compounds were evaluated for introduction, by means of the biosynthetic recycling pathway, into the peptidoglycan of Escherichia coli. A successful in vitro biosynthesis of UDP-MurNAc-tripeptides from the tripeptides containing [small alpha]-benzyl lanthionine was achieved using purified murein peptide ligase (Mpl). Bioincorporation into E. coli W7 did not occur under different tested conditions probably due to the bulky benzyl group at the C[small alpha] carbon of the C-terminal amino acid. [less ▲]

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See detailFiber based optofluidic biosensors
Lismont, Marjorie ULg; Vandewalle, Nicolas ULg; Joris, Bernard ULg et al

in Applied Physics Letters (2014)

Medicinal diagnosis requires the development of innovative devices allowing the detection of small amounts of biological species. Among the large variety of available biosensors, the ones based on ... [more ▼]

Medicinal diagnosis requires the development of innovative devices allowing the detection of small amounts of biological species. Among the large variety of available biosensors, the ones based on fluorescence phenomenon are really promising. Here, we show a prototype of the basic unit of a multi-sensing biosensor combining optics and microfluidics benefits. This unit makes use of two crossed optical fibers: the first fiber is used to carry small probe molecules droplets and excite fluorescence, while the second one is devoted to target molecules droplets transport and fluorescence detection. Within this scheme, the interaction takes place in each fiber node. The main benefits of this detection setup are the absence of fibers functionalization, the use of microliter volumes of target and probe species, their separation before interaction, and a better detection limit compared to cuvettes setups. [less ▲]

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See detailStereoselective synthesis of lanthionine derivatives in aqueous solution and their incorporation into the peptidoglycan of Escherichia coli.
Denoel, Thibaut; Zervosen, Astrid ULg; Gerards, Thomas ULg et al

in Bioorganic & medicinal chemistry (2014), 22(17), 4621-8

The three diastereoisomers-(R,R), (S,S) and meso-of lanthionine were synthesized in aqueous solution with high diastereoselectivity (>99%). The (S) and (R) enantiomers of two differently protected ... [more ▼]

The three diastereoisomers-(R,R), (S,S) and meso-of lanthionine were synthesized in aqueous solution with high diastereoselectivity (>99%). The (S) and (R) enantiomers of two differently protected sulfamidates were opened by nucleophilic attack of (R) or (S)-cysteine. Acidification and controlled heating liberated the free lanthionines. Using the same chemistry, an alpha-benzyl lanthionine was also prepared. The proposed method, which avoids the need of enrichment by recrystallization, opens the way to the labelling of these compounds with (35)S. Furthermore, in vivo bioincorporation into Escherichia coli W7 was studied. No incorporation of alpha-benzyl lanthionine was observed. In contrast, meso-lanthionine can effectively replace meso-diaminopimelic acid in vivo, while in the presence of (R,R)-lanthionine the initial increase of bacterial growth was followed by cell lysis. In the future, meso-[(35)S]lanthionine could be used to study the biosynthesis of peptidoglycan and its turnover in relation to cell growth and division. [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 detailSynthesis and biological evaluation of potential threonine synthase inhibitors: Rhizocticin A and Plumbemycin A
Gahungu; Arguelles Arias, Anthony ULg; Fickers, Patrick ULg et al

in Bioorganic & Medicinal Chemistry (2013), 21

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See detailISOLATION OF THE ANTIMICROBIAL CYCLIC PEPTIDE SUBTILOSIN A FROM A GUT-ASSOCIATED BACILLUS SUBTILIS STRAIN
Schyns, Ghislain; Serra, Claudia; Henriques, Adriano et al

in American Journal of Biochemistry & Biotechnology (2013), 9(3),

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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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