References of "De Pauw, Edwin"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailProbing the conformational changes during desolvation of ions using orthogonal mobility methods (CE-IM MS)
Far, Johann ULg; Kune, Christopher ULg; Delvaux, Cédric ULg et al

Poster (2014, June 24)

Routine analyses using Mass Spectrometry (MS) detection became a very popular due to the low limit of detection, great sensitivity, selectivity and specificity. Moreover MS enables structural elucidation ... [more ▼]

Routine analyses using Mass Spectrometry (MS) detection became a very popular due to the low limit of detection, great sensitivity, selectivity and specificity. Moreover MS enables structural elucidation and physical (or physicochemical) properties determination using low amount of not especially pure samples. One of these properties is substantially the stoichiometry determination of non-covalent complexes such as Ligand receptor systems (e.g. DNA-drugs, Hormones/drugs-receptor, quaternary structure arrangement of polypeptides, …). MS determination in native condition (Native MS) of this stoichiometry allows large scale screening of potential drugs candidates in pharmaceutical context. The addition of Ion-Mobility (IM) to mass spectrometry (IM-MS) with computational chemistry support allows the structural conformation monitoring (as Collisional Cross Section or CCS) and the elucidation of interactions of the non-covalent complexes. Nonetheless such determinations suppose/assume that desolvation steps and gas phase transfer during MS detection do not modify the tridimensional structure of these systems or the magnitude order of the involved interactions (dipole-dipole, dipole-ion, ion-ion, hydrophobic interactions). Further studies (Circular Dichroism, Nuclear Magnetic resonance, UV-Visible spectra …) are generally required to confirm the MS data but there are unfortunately time consuming. This project proposes the coupling of Capillary Electrophoresis (CE) to IM-MS in order to obtain in one injection the quantitative and qualitative data of non-covalent complexes and the monitoring of tridimensional conformation modification between the liquid and gas phase. Indeed CE allows the determination of numerous physicochemical properties (dissociation constant, pK values, hydrodynamic radius determination …). The structural data (i.e. hydrodynamic radius and CCS) are compared to the data obtained by IM-MS as a proof of concept using tryptic digest of Bovine Serum Albumine (BSA). [less ▲]

Detailed reference viewed: 12 (4 ULg)
Peer Reviewed
See detailContribution of ion mobility for structural analysis and analytical chemistry: Use of selective IMS shift reagents (SSR)
Kune, Christopher ULg; Far, Johann ULg; Delvaux, Cédric ULg et al

Poster (2014, June 19)

Ion mobility is a gas phase separation technique based on the Collisional Cross Section (CCS) of ions. It discriminates isobaric and isomeric ions provided their CCS difference is larger than the ... [more ▼]

Ion mobility is a gas phase separation technique based on the Collisional Cross Section (CCS) of ions. It discriminates isobaric and isomeric ions provided their CCS difference is larger than the instrumental resolution. This work proposes a new method to overcome this limitation while providing additional structural information. A Selective Shift Reagent (SSR) is a ligand specifically modifying the CCS of ions. Indeed specific non-covalent complexes can be form with a suitable SSR to reach the required selectivity and the CCS induced shift. A CID dissociation of the complex may be used after IMS separation to produce specific MS/MS spectra of the targeted analyte. This concept paves the way for new analytical strategies by ion mobility based on non-covalent complex formation. [less ▲]

Detailed reference viewed: 43 (10 ULg)
Full Text
Peer Reviewed
See detailMALDI Mass Spectrometry Imaging: a new tool to decipher the antibiome of Bacillus amyloliquefaciens
Debois, Delphine ULg; Jourdan, Emmanuel; Cawoy, Hélène et al

Conference (2014, June 05)

Soil Bacillus isolates may devote up to 8% of their genome to nonribosomal synthesis of lipopeptide (LP)- and polyketide (PK)-type antibiotics. LPs from surfactin, iturin and fengycin families are known ... [more ▼]

Soil Bacillus isolates may devote up to 8% of their genome to nonribosomal synthesis of lipopeptide (LP)- and polyketide (PK)-type antibiotics. LPs from surfactin, iturin and fengycin families are known to exert different actions on the wellness of the producing strain such as fungitoxicity (iturin, fengycin) or motility, root colonization and immune stimulating agent (surfactin). Nevertheless, few is reported about the actual antibiome secreted in situ by Bacillus cells during confrontation with phytopathogens or plant root colonization. We developed a method mimicking the conditions prevailing in the rhizosphere and, taking advantage of the versatility of Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging, we were able to localize and identify antibiotics produced in situ by bacterial cells. First, we applied this new methodology to bioassays in which Bacillus amyloliquefaciens 98S were grown together with Fusarium oxysporum, with the aim of deciphering the role of the different LP families during the phytopathogen growth inhibition. Our results showed that the three LP families were readily produced in different proportions. Especially, images of surfactins, iturins and fengycins demonstrated that iturins are the antibiotic family actually involved in the antagonism against Fusarium oxysporum. In a second approach, we used a “in planta” model in which Bacillus amyloliquefaciens S499 was simultaneously grown with Tomato and Arabidopsis thaliana roots. Imaging results, obtained during a time course analysis, showed that surfactin is always the major lipopeptide detected. In further experiments involving a refined time-window, we observed that surfactin is actually produced as soon as 24h post inoculation. These results were the starting point of a wider study showing that the early accumulation of surfactin is a complex phenomenon involving, among other mechanisms, cell-well components recognition by bacteria, and that this interaction is a win-win association for both plant and bacterial cells. [less ▲]

Detailed reference viewed: 32 (1 ULg)
See detailDesign of a sprayer that makes CE-ESI-MS easy and robust
Far, Johann ULg; De Pauw, Edwin ULg; Falmagne, Jean-Bernard et al

Conference (2014, May 28)

Presentation of a CEMS interface design for easy and robust coupling of Capillary Electrophoresis with Mass Spectrometry equipped with a nanospray source. Principles and specification were presented.

Detailed reference viewed: 18 (0 ULg)
Full Text
Peer Reviewed
See detailSpatiotemporal monitoring of the antibiome secreted by Bacillus biofilms on plant roots using MALDI mass spectrometry imaging
Debois, Delphine ULg; Jourdan, Emmanuel; Smargiasso, Nicolas ULg et al

in Analytical Chemistry (2014), 86(9), 4431-4438

Some soil Bacilli living in association with plant roots can protect their host from infection by pathogenic microbes and are therefore being developed as biological agents to control plant diseases. The ... [more ▼]

Some soil Bacilli living in association with plant roots can protect their host from infection by pathogenic microbes and are therefore being developed as biological agents to control plant diseases. The plant protective activity of these bacteria has been correlated with the potential to secrete a wide array of antibiotic compounds upon growth as planktonic cells in isolated cultures under laboratory conditions. However, in situ expression of these antibiotics in the rhizosphere where bacterial cells naturally colonize root tissues is still poorly understood. In this work, we used Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry Imaging (MALDI MSI) to examine spatio-temporal changes in the secreted antibiome of B. amyloliquefaciens developing as biofilms on roots. Non-ribosomal lipopeptides such as the plant immunity elicitor surfactin or the highly fungitoxic iturins and fengycins were readily produced albeit in different time-frames and quantities in the surrounding medium. Interestingly, MS/MS experiments performed directly from the gelified culture medium, also allowed to identify a new variant of surfactins released at later time points. However, no other bioactive compounds such as polyketides were detected at any time, strongly suggesting that the antibiome expressed in planta by B. amyloliquefaciens does not reflect the vast genetic arsenal devoted to the formation of such compounds. This first dynamic study reveals the power of MALDI MSI as tool to identify and map antibiotics synthesized by root-associated bacteria and more generally, to investigate plant-microbe interactions at the molecular level. [less ▲]

Detailed reference viewed: 15 (2 ULg)
Full Text
Peer Reviewed
See detailProbing the conformational changes during desolvation of ions using orthogonal mobility methods (CE-IMS)
Far, Johann ULg; Kune, Christopher ULg; Delvaux, Cédric ULg et al

Poster (2014, April 08)

The transfer of ions from the solution to the gas phase is a critical step to produce « native species ». Coming from a highly solvating medium, ionic species will tend to find a new equilibrium ... [more ▼]

The transfer of ions from the solution to the gas phase is a critical step to produce « native species ». Coming from a highly solvating medium, ionic species will tend to find a new equilibrium conformation in the gas phase. The pathway to reach the thermodynamically stable conformation involves crossing potential barriers of different heights. When these barriers are too high compared to the internal energy of the ions, it will result in “partial memories” (as structural preservation) of the conformation in solution. In order to evaluate the effect of the solvent evaporation and of the various collision processes encountered by the ions in the mass spectrometer. The strategy consists in comparing in a single experiment the shape of the ions in solution and in the gas phase. Data are obtained by coupling capillary electrophoresis with Ion Mobility Mass Spectrometry. Drift times in solution and in the gas phase are directly compared. Deviations from their correlation points out changes in folding upon desolvatation. Preliminary results show that among peptides issued from tryptic digest of BSA some of them clearly change their conformation during desolvatation. This work intends to evaluate the extent of conformational “memory” of the ions of different nature for best experimental condition allowing “native mass spectrometry”. [less ▲]

Detailed reference viewed: 27 (10 ULg)
Full Text
See detailImaging MS: strategies for the identification of analytes
Debois, Delphine ULg; Smargiasso, Nicolas ULg; Jourdan, Emmanuel et al

Scientific conference (2014, April 04)

Detailed reference viewed: 27 (5 ULg)
Full Text
Peer Reviewed
See detailOrganized proteomic heterogeneity in colorectal liver metastases and implications for therapies
Turtoi, Andrei ULg; Blomme, A; Debois, Delphine ULg et al

in Acta Gastro-Enterologica Belgica (2014, March), 77(1), 07

Detailed reference viewed: 7 (1 ULg)
Full Text
Peer Reviewed
See detailNew mass spectrometry based methodology to sequence a whole snake venom
Echterbille, Julien ULg; Boulanger, Madeleine; Degueldre, Michel ULg et al

Poster (2014, February 10)

Animal venoms are complex chemical cocktails, comprising wide ranges of biologically active reticulated peptides that target with high selectivity and efficacy varieties of membrane receptors. Assuming ... [more ▼]

Animal venoms are complex chemical cocktails, comprising wide ranges of biologically active reticulated peptides that target with high selectivity and efficacy varieties of membrane receptors. Assuming the fact that each of the 170,000 venomous species reported can produce more than 250 bioactive toxins, at least 40,000,000 bioactive peptides and proteins may be discovered. Among the four described species of mambas, Eastern Jameson’s mamba (Dendroaspis jamesonii kaimosae) venom is the less characterized since only 9 peptides are referenced in database. This work aims at developing a new strategy devoted to the deep analysis of animal venoms. Our approach consists in a first separation of the venom using cation exchange chromatography. Each primary fraction is then purified a second time by classical RP-HPLC. A total of 328 fractions, containing amongst 1 and 4 toxins, are finally collected. MALDI-MS analysis of each fraction is done in order (1) to obtain information about masses and (2) to obtain sequences of toxins thanks to MALDI-In Source Decay (ISD) dissociation coupled with on MALDI target plate reduction of the peptides. ISD has already been demonstrated efficient for toxin sequencing, and especially when using 1,5-DAN as reducing matrix. ISD yields to sequences that cover more than 50% of peptide sequences by series of singly charged c-type ions. Thanks to this methodology, we were able to obtain 85% of satisfactory results i.e. spectra giving quite long tags of amino acids (up to 20 residues). As a way to validate our method, a tag coming from ISD spectrum interpretation has found a match in database for an Eastern Jameson’s mamba toxin. The global sequence has then been obtained by extrapolation on the ISD spectrum. Since ISD spectra are simpler than classical MS/MS spectra, automation of spectra interpretation, difficult with other fragmentation techniques (CID, ETD…), is implementable. In the near future, sequences obtained with this approach will be used to direct tests of biological activity through sequence homologies with already known ligands for different kinds of membrane receptors. [less ▲]

Detailed reference viewed: 37 (6 ULg)
Full Text
Peer Reviewed
See detailIsolation of an amylolytic chrysophyte, Poterioochromonas sp. from the digestive tract of the termite R. santonensis
Tarayre, Cédric ULg; Bauwens, Julien ULg; Brasseur, Catherine ULg et al

in Biotechnologie, Agronomie, Société et Environnement = Biotechnology, Agronomy, Society and Environment [=BASE] (2014), 18(1),

The aim of this work was the isolation and cultivation of amylolytic protists living in the digestive tract of the termite Reticulitermes santonensis (Feytaud). A chrysophyte identified as ... [more ▼]

The aim of this work was the isolation and cultivation of amylolytic protists living in the digestive tract of the termite Reticulitermes santonensis (Feytaud). A chrysophyte identified as Poterioochromonas sp. was isolated in a special medium containing rice grains as a source of carbon and nitrogen. Then, the protist was grown in a medium containing starch as a carbon source, tryptone, and a phosphate buffer at different pH values (5, 6 and 7). Yeast extract was added or not. Ciprofloxacin was used to avoid the bacterial development. Other antibiotics were also tested but showed an inhibitive effect on the growth of Poterioochromonas sp. Yeast extract allowed reaching 1.9 (pH 5), 2.3 (pH 6) and 2.2 (pH 7) times higher final cell concentrations, and 2.8 (pH 5), 2.8 (pH 6) and 2.2 (pH 7) times higher biomass yields. The starch concentration did not decrease in the medium until 3 and 4 days of culture, with and without yeast extract, respectively. Eight days of culture were necessary for hydrolyzing the starch completely, with and without yeast extract. Maltose and maltotriose were detected in the culture media and were hydrolyzed progressively. Maximal maltose concentrations were 0.68, 0.66 and 0.51 g.l-1 in the medium containing yeast extract. Maltotriose concentrations were only 0.17, 0.14 and 0.12 g.l-1. Other glucose oligomers were also detected but in lower quantities. It was determined that the protist developed a weak amylase activity, particularly at a weakly acidic pH (5-6). Such a pH also allowed a better growth of the protist. A maximal amylase activity of 112 nkat.l-1 was measured with yeast extract at pH 5. No other enzymatic activity (protease, cellulase or xylanase) was detected except amylase. The degradation products of starch which were obtained by enzymatic hydrolysis allow the identification of α-amylase, amyloglucosidase and possibly β-amylase activities. [less ▲]

Detailed reference viewed: 39 (13 ULg)
See detailInnovative analytical strategies for small molecules analysis by ion-mobility mass spectrometry
Eppe, Gauthier ULg; Goscinny, Séverine; Far, Johann ULg et al

Conference (2014, January)

Detailed reference viewed: 33 (11 ULg)
Full Text
Peer Reviewed
See detailBioactive Intraocular Lens – A Strategy to Control Secondary Cataract
Huang, Yi-Shiang ULg; Bertrand, Virginie ULg; Bozukova, Dimitriya et al

in IFMBE Proceedings (2014), 41

Cataract is the opacity of the lens, causing impairment of vision or even blindness. Today, a surgery is still the only available treatment. The intraocular lens (IOL) is a polymer implant designed to ... [more ▼]

Cataract is the opacity of the lens, causing impairment of vision or even blindness. Today, a surgery is still the only available treatment. The intraocular lens (IOL) is a polymer implant designed to replace the natural lens in the cataract surgery. However, the bioinert materials could not satisfy the unmet need in the secondary cataract control. Posterior capsular opacification (PCO, or Secondary Cataract), characterized by a thick and cloudy layer of lens epithelial cells (LECs), is the most common postoperative complication. In our research, a bioactive molecule is immobilized onto the conventional acrylic hydrophilic polymer pHEMA (Poly(2-hydroxyethyl methacrylate)) using oxygen plasma treatment followed by deposition. The RGD peptide sequence, being well-known for its ability to promote cellular attachment by binding to integrin receptors, is designed to stimulate the adhesion of LECs on the IOL. Our data show the peptide immobilized biomaterial not only exhibits similar optical property, but also reveals enhanced biological properties in cell adhesion and cell morphology maintenance. By means of surface functionalization of IOL to stimulate LECs adhesion, the secondary cataract could be controlled. [less ▲]

Detailed reference viewed: 39 (14 ULg)
See detailAdvances in proteomics for the FP7 Venomics project - Disulfide bridge assignement task
Massonnet, Philippe ULg; Upert, Gregory; Pastor, Alexandra et al

Scientific conference (2013, December 18)

Detailed reference viewed: 24 (6 ULg)
Full Text
Peer Reviewed
See detailTandem MS of -new- antibiotics from Bacillus guided by MALDI Mass Spectrometry Imaging
Debois, Delphine ULg; Jourdan, Emmanuel; Cawoy, Hélène ULg et al

Conference (2013, December 05)

Generally, an antibiotic is thought to have a role in antagonism simply because the producing strain is known to exhibit a potential for pathogen growth inhibition. Some genetic approaches such as PCR ... [more ▼]

Generally, an antibiotic is thought to have a role in antagonism simply because the producing strain is known to exhibit a potential for pathogen growth inhibition. Some genetic approaches such as PCR using specific primers or genome mining using known sequence data of close relatives are also used. Nevertheless, none of these methods allows stating for a link between a specific compound and the observed antagonism. Yet MALDI Mass Spectrometry Imaging (MSI) is a powerful tool to decipher the chemical messengers exchanged by two protagonists [1,2,3;]. Tandem mass spectrometry (MS/MS) may be also used, either on extracts [2,3] or directly on the microbial colonies [4]. The presentation will thus be focused on two examples of application of MALDI MSI combined to in situ tandem mass spectrometry. The first presented case will be the antagonism between soilborne strain Paenibacillus polymyxa Pp56 and the fungal phytopathogen Fusarium oxysporum. Using MALDI MSI, we were able to precisely localize each detected antibiotic, allowing discriminating which LI-F lipopeptides (fusaricidin) were really active against the pathogen progression. Besides, the use of in situ MS/MS allowed us to sequence the peptide moiety of several LI-F lipopeptides, showing that some of them are actually a mixture of several forms. The second example concerns the metabolites that are released by Bacillus amyloliquefaciens S499 cells following their inoculation on 7 days old tomato roots. We developed specific bioassays for time-course monitoring by MALDI MSI. First analyses revealed an efficient secretion of surfactin by Bacillus cells after 3 days when colonization as biofilm-structured populations is well established. Even if the composition of antibiotic mixture does not greatly evolve over time, after long incubation periods (32 or 35 days post inoculation), new series of compounds are detected in the tomato root -surrounding medium. Structural analysis based on exact mass measurements and MS/MS experiments, performed directly on the semi-solid agar medium, allowed us to identify these compounds as new variants of surfactins. [1] Barger, S., et al., Anton Leeuw Int J G, 2012, 102, 435-445. [2] Hoefler, B. C., et al,. Natl Acad Sci USA, 2012, 109, 13082-13087. [3] Moree, W. J., et al., Natl Acad Sci USA, 2012, 109, 13811-13816. [4] Debois, D., et al., J Am Soc Mass Spectrom. 2013, 24, 1202-1213 [less ▲]

Detailed reference viewed: 35 (5 ULg)
Full Text
Peer Reviewed
See detailAttribution of Cysteine Connectivities in small toxins - New Prospects Based on Partial Oxidation/Reduction Experiments and Ion-Mobility Mass Spectrometry
Quinton, Loïc ULg; Massonnet, Philippe ULg; Echterbille, Julien ULg et al

Conference (2013, December)

Disulfide bonds are post-translational modifications often found in biological compounds and especially in animal toxins. Disulfide bonds participate in the formation of specific folding of peptides and ... [more ▼]

Disulfide bonds are post-translational modifications often found in biological compounds and especially in animal toxins. Disulfide bonds participate in the formation of specific folding of peptides and proteins, directly related to their biological activity. Cystein pairing determinations are primordial for the synthesis of chemical homologous displaying the same bioactivity than the natural compound. This task appears already difficult when the cysteine pairings have to be determined from large proteins. The combination of physical and chemical techniques such as NMR, enzymatic proteolysis, liquid chromatography and mass spectrometry, is needed to circumvent this difficulty. However, when the work concerns small compounds such as conotoxins, the problem is much more complex due to the low amount of available compound and to the lack of enzymatic cleavage sites between cysteines. In this study, we investigate the case of small peptides that contain two disulphide bonds. The idea is to determine the cystein pairings in such compounds by a chemical partial reduction (or oxidation) of the peptides, followed by the separation of the generated species by ion-mobility mass spectrometry, and their characterisation by tandem mass spectrometry. Up to now, we have investigated the partial reduction not only in solution (with DTT and TCEP) but also in the gas-phase (Electron transfer dissociation), and partial oxidation in solution (with 3-CPBA). The results demonstrate an unexpected complexity of the data, including low fragmentation ratios of peptides and disulfide scramblings. [less ▲]

Detailed reference viewed: 24 (10 ULg)