References of "De Pauw, Edwin"
     in
Bookmark and Share    
Full Text
Peer Reviewed
See detailMALDI-FTICR MS Imaging as a Powerful Tool to Identify Paenibacillus Antibiotics Involved in the Inhibition of Plant Pathogens
Debois, Delphine ULg; Ongena, Marc ULg; Cawoy, Hélène ULg et al

in Journal of the American Society for Mass Spectrometry (2013), 24(8), 1202-1213

Nowadays, microorganisms are more and more often used as biocontrol agents for crop protection against diseases. Among them, bacteria of Bacillus and Paenibacillus genders are already used as commercial ... [more ▼]

Nowadays, microorganisms are more and more often used as biocontrol agents for crop protection against diseases. Among them, bacteria of Bacillus and Paenibacillus genders are already used as commercial biocontrol agents. Their mode of action is supposed to be related to their production of antibiotics, such as cyclic lipopeptides, which exhibit great antimicrobial activities. We chose to work with a Paenibacillus polymyxa strain (Pp56) very resistant to various microorganisms. The bacteria were grown simultaneously with Fusarium oxysporum and we applied matrix-assisted laser desorption/ionization-Fourier transform ion cyclotron resonance (MALDI-FTICR) mass spectrometry to identify the antibiotics compounds present in the fungus growth inhibition area. We, therefore, identified fusaricidins A, B, and C and numerous members of the LI-F antibiotics family. MALDIFTICR mass spectrometry imaging was then used to follow the diffusion of lipopeptides involved in the inhibitory activity over time. We analyzed the molecular content of the inhibitory area at different Pp56 and Fusarium incubation durations and concluded that some lipopeptides such as fusaricidin B and a mixture of LI-F05b/06b/08a were mainly involved in the defense mechanism of Pp56. Our study confirms that MALDI imaging may be a powerful tool to quickly determine which molecular species is involved in an antagonism with another microorganism, avoiding time-consuming steps of extraction, purification, and activity tests, which are still commonly used in microbiology. [less ▲]

Detailed reference viewed: 36 (13 ULg)
Full Text
Peer Reviewed
See detailIn-Source Decay during Matrix-Assisted Laser Desorption/Ionization Combined with the Collisional Process in an FTICR Mass Spectrometer
Asakawa, Daiki; Calligaris, David; Zimmerman, Tyler et al

in Analytical Chemistry (2013), 85

The type of ions detected after in-source decay (ISD) in a MALDI source differs according to the ion source pressure and on the mass analyzer used. We present the mechanism leading to the final ISD ions ... [more ▼]

The type of ions detected after in-source decay (ISD) in a MALDI source differs according to the ion source pressure and on the mass analyzer used. We present the mechanism leading to the final ISD ions for a Fourier transform-ion cyclotron resonance mass spectrometer (FTICR MS). The MALDI ion source was operated at intermediate pressure to cool the resulting ions and increase their lifetime during the long residence times in the FTICR ion optics. This condition produces not only c′, z′, and w fragments, but also a, y′, and d fragments. In particular, d ions help to identify isobaric amino acid residues present near the Nterminal amino acid. Desorbed ions collide with background gas during desorption, leading to proton mobilization from Arg residues to a less favored protonation site. As a result, in the case of ISD with MALDI FTICR, the influence of the Arg residue in ISD fragmentation is less straightforward than for TOF MS and the sequence coverage is thus improved. MALDI-ISD combined with FTICR MS appears to be a useful method for sequencing of peptides and proteins including discrimination of isobaric amino acid residues and site determination of phosphorylation. Additionally we also used new software for in silico elimination of MALDI matrix peaks from MALDI-ISD FTICR mass spectra. The combination of high resolving power of an FTICR analyzer and matrix subtraction software helps to interpret the low m/z region of MALDI-ISD spectra. Finally, several of these developed methods are applied in unison toward a MALDI ISD FTICR imaging experiment on mouse brain to achieve better results. [less ▲]

Detailed reference viewed: 10 (1 ULg)
Peer Reviewed
See detailInnovative analytical strategy using ion-mobility shifting additive for isobaric selenium compound identification in selenomethionine standards by IMS
Kune, Christopher ULg; Far, Johann ULg; Eppe, Gauthier ULg et al

Conference (2013, July 09)

Selenium (Se) is a trace element which is both essential and toxic depending on its concentration and its chemical form. Selenomethionine (SeMet) is one of the widely used selenium standard during ... [more ▼]

Selenium (Se) is a trace element which is both essential and toxic depending on its concentration and its chemical form. Selenomethionine (SeMet) is one of the widely used selenium standard during Selenium speciation studies. This work was focused on the elaboration of an analytical strategy for the detection and the structural elucidation of an isobaric Se interference, which is found in standard solutions of SeMet by high resolution mass spectrometry (Rm/Δm > 20.000). The structural elucidation of these compounds requires the isolation of the respective parent ion. Nevertheless, the mass difference between SeMet and its interference is less than 0.02Da which is well below the window selection of conventional techniques in mass spectrometry (Quadripole, ion trap). The empirical formula and double bound equivalent (DBE) of these ions suggest different tridimensional structures which lead to a discrimination depending on the ion mobility. This separation is observed, both in gaseous and liquid phase, by Ion Mobility Spectrometry (IMS), Capillary Electrophoresis (CE) and Liquid Chromatography (LC) which are hyphenated to mass spectrometry as detector. The separation efficiency of these ions by IMS and CE is improved by using specific shifting agents (18-Crown-6 Ether) selective to only one of these ions. This strategy has successfully separated the two isobaric ions present and leads to the structural elucidation of the isobar contaminant of SeMet. [less ▲]

Detailed reference viewed: 38 (22 ULg)
Peer Reviewed
See detailInnovative analytical strategy using ion-mobility for structural or functional selenium isomers identification by ion mobility spectrometry
Far, Johann ULg; Kune, Christopher ULg; Lobinski, Ryszard et al

Poster (2013, July)

Selenium (Se) is a trace element which is both essential and toxic depending on its concentration and its chemical form. Se-rich yeast is one of the most popular Se source for supplementation. The ... [more ▼]

Selenium (Se) is a trace element which is both essential and toxic depending on its concentration and its chemical form. Se-rich yeast is one of the most popular Se source for supplementation. The classical method of speciation is related to multidimensional liquid chromatography (LC) hyphenated to mass spectrometry (MS) Recent advances in Se speciation led to greatly improve the Se speciation in these samples but isomers identification and quantification remain challenging. This work focuses on the elaboration of an innovative analytical strategy for the detection and the structural elucidation of isobaric selenium compounds present in Se-rich yeast. A specific complex formation agent acts as a chemical probe for the detection of chemical function. The addition of a complexing agent can improve the discrimination between structural or functional Se isomers using ion mobility techniques as Ion Mobility Spectrometry (IMS) by increasing the molecular weight (i.e. the m/z ratio in MS) and the collision cross section of a target ion after selective complexation. This Ion Mobility orthogonal separation improves the structural elucidation. Crown ethers used as shifting agents can specifically form complexes with primary amines. The addition of crown ether to different low molecular weight fractions obtained by multidimensional LC of a water extract from Se-rich yeast permitted to detect Se isomers and confirmed their structure using IMS. [less ▲]

Detailed reference viewed: 16 (4 ULg)
Full Text
Peer Reviewed
See detailIsolation and Cultivation of a Xylanolytic Bacillus subtilis Extracted from the Gut of the Termite Reticulitermes santonensis
Tarayre, Cédric ULg; Brognaux, Alison ULg; Brasseur, Catherine ULg et al

in Applied Biochemistry and Biotechnology (2013)

The aim of this work was the isolation of xylanolytic microorganisms from the digestive tract of the termite Reticulitermes santonensis. The reducing sugars released after the hydrolysis of xylans can be ... [more ▼]

The aim of this work was the isolation of xylanolytic microorganisms from the digestive tract of the termite Reticulitermes santonensis. The reducing sugars released after the hydrolysis of xylans can be further fermented to provide bioethanol. A xylanolytic strain of Bacillus subtilis was isolated from the hindgut of the termite and displayed amylase and xylanase activities. The bacterium was grown on media containing agricultural residues: wheat bran, wheat distiller’s grains, and rapeseed oil cake. Wheat bran led to the highest induction of xylanase activity, although the development of the strain was less fast than in the other media. It was possible to reach maximal xylanase activities of 44.3, 33.5, and 29.1 I.U./ml in the media containing wheat bran, wheat distiller’s grains, and rapeseed oil cake, respectively. Mass spectrometry identified a wide range of xylose oligomers, highlighting an endoxylanase activity. The enzyme was stable up to 45 °C and displayed an optimal pH close to 8. [less ▲]

Detailed reference viewed: 48 (30 ULg)
Full Text
Peer Reviewed
See detailDistribution and identification of molecular interactions between tomato roots and bacterial biofilms
Debois, Delphine ULg; Jourdan, Emmanuel; Smargiasso, Nicolas ULg et al

Poster (2013, June 12)

Some non-pathogenic microorganisms evolving in the root micro-environment can trigger a positive effect on plant, increasing host defense against disease or/and directly inhibiting growth of pathogen in ... [more ▼]

Some non-pathogenic microorganisms evolving in the root micro-environment can trigger a positive effect on plant, increasing host defense against disease or/and directly inhibiting growth of pathogen in soil (1). To initiate both phenomena leading to biocontrol activity, microorganisms use plant exudates to grow on roots and to produce in-situ active compounds. In Bacilli, cyclic lipopeptides of the surfactin, iturin and fengycin families represent important antibiotics involved in biocontrol (2). Recent studies in microbiology allowed a better understanding of plant microorganism interactions but few has been done at the molecular level. In this study, MALDI MS imaging has been used to study the nature of the secreted lipopeptide molecules, their relative quantity and their distribution in the root’s environment.Disinfected tomato seeds were first germinated at 28°C in sterile conditions for germination. Seedlings were then placed in Petri dish on ITO glass slide recovered with a thin layer of plant nutritive solution containing 1,75% of agar and treated with freshly-grown cells of Bacillus amyloliquefaciens S499. Petri dishes were incubated at 28°C with a 16h photoperiod. Different growth / incubation durations were studied: 10/3; 13/7; 21/14 and 39/32. For MALDI imaging experiments, the ITO slide was removed from the agar and dried in a dessiccator under vacuum. (HCCA, 5mg/mL in ACN/0.2% TFA 70:30) was used as matrix. UltraFlex II TOF/TOF and Solarix FT-ICR mass spectrometers were used to record molecular cartographies and perform MS/MS experiments for structural analysis purposes. The average mass spectra recorded around the tomato root (2-3 mm on both sides of the root) showed that lipopeptides were major compounds detected on the agar. The relative intensity of lipopeptides families varied with respect to the age of the root/biofilm system. In the 10/3 system, 3 homologues of surfactins were essentially detected (C13, C14 and C15), with very few iturins and fengycins. Their localizations were identical, whatever the considered homologue. Then the production of iturin and fengycin families increases in older systems (13/7 and 21/14) and a novel homologue of surfactin is detected (C12). Some variations in localizations within families may be observed (around the root or at the close vicinity of it in function of the considered homologue or alkali adduct). Then for the oldest system we studied, iturins and fengycins are not detected anymore and the localization of surfactins is less precise. In the 39/32 system, we also detected unknown compounds at 986.6, 1000.6, 1014.7 and 1028.7 m/z. The mass range of these compounds allied to the mass difference between two consecutive ion peaks let us think that these unknown compounds could be a new lipopeptide family. Tandem mass spectrometry experiments, performed on the dried culture medium, allowed to partially sequence these new lipopeptides. MS/MS results allied to exact mass measurements and isotopic pattern simulation give good confidence in the chemical structure we suggest. Nevertheless, to fully identify these new variants of surfactin, micro-extractions followed by (LC)-nano-ESI-MS/MS using a LESA module are in progress. MALDI Mass Spectrometry Imaging becomes a tool to decipher inter-species molecular communication. [less ▲]

Detailed reference viewed: 60 (11 ULg)
Full Text
Peer Reviewed
See detailDe novo sequencing of unusual non tryptic peptides thanks to 4-sulfophenylisothiocyanate derivatization by post-source decay MALDI-MS.
Echterbille, Julien ULg; Quinton, Loïc ULg; Escoubas, Pierre et al

Poster (2013, June 11)

Introduction Due to the specificity of trypsin, tryptic peptides contain basic residues on the C-terminal side. This feature provides good ionization efficiency, and facilitates fragmentation processes ... [more ▼]

Introduction Due to the specificity of trypsin, tryptic peptides contain basic residues on the C-terminal side. This feature provides good ionization efficiency, and facilitates fragmentation processes. In the case of non tryptic peptides, the absence of basic residues at one extremity implicates lower fragmentation ratio and poor MS/MS spectra. Several methods have been developed to circumvent this drawback. Derivatization of peptides with compounds containing positive charge has been studied; Chen et al. (RCMS, 2004, 18, 191) demonstrated the simplification of CID spectra of tryptic peptides modified by 4-sulfophenylisothiocyanate. The result is a predominance of y-type ions. In this work, we evaluate the potential of SPITC for the de novo sequencing of unknown non-tryptic peptides containing disulfide bridges, i.e. peptide toxins from animal venoms. Methods 2µL of peptide solution (100 µM) were diluted in 6µL NH4HCO3 50mM (pH 8.7). As peptide toxins often contain disulfide bridges, reduction (2µL DTT 50mM, 1h at 56°C) and alkylation (2µL IAA 500mM, 1h in darkness at RT) of peptides were performed before the derivatization reaction. Peptides were then adsorbed on a C18 ZipTip micro-column followed by 10 µL of 4-sulfophenylisothiocyanate (SPITC) 50mM. The column was then incubated for 6h at 56°C. Peptides were washed by TFA 0.2% and eluted in 10µL 50/50 ACN/FA 0.1%, before being spotted in 2,5-DHB. MS experiments were performed using a Bruker Ultraflex II MALDI-TOF/TOF. FlexControl 3.0, FlexAnalysis 3.0, BioTools 3.2 and SequenceEditor 3.2 softwares (Bruker Daltonics, Bremen) were used for data acquisition and interpretation. Preliminary data According to our first results, SPITC derivatization allows in positive mode to direct the fragmentation thanks to the acidic character of the sulfonate moiety present on the modified molecule. Indeed, a large series of y-type ions is found in the CID spectra allowing determining easily large sequence tags. Moreover, the number of C-terminus ions (b- and a-type ions) decreases, which improve the simplification of MS/MS spectra. Due to this fragmentation pattern, SPITC derivatization is clearly valuable for the sequencing of peptides that are not described in databases (de novo sequencing). For example, animal venoms are composed of several hundreds of peptides that are poorly studied, up to now. These peptides display a high importance for pharmaceutical applications and their sequencing is, as a consequence, of prime interest. Peptide toxins, which are not resulting from an enzymatic digestion, are however difficult to sequence by classical MS/MS methods. In this work, we demonstrate that the modification of peptide toxins with SPITC reagent is suitable for “real” de novo sequencing. The method was applied to isolated peptides as well as chromatographic fractions that contain up to 30 toxins. The perspectives of this work rest on the study of the SPITC modified peptides in negative mode. We expect to obtain a better sensitivity due to the presence of the negative sulfonic acid group at the N-terminus extremity, and also interesting MS/MS spectra including mainly a- or b-type ions. The final challenge will be the application of the protocol to high throughput sequencing of peptide toxins from a large variety of animal venoms. Novel aspect De novo sequencing of unusual non-tryptic peptides thanks to 4-sulfophenylisothiocyanate derivatization by post-source decay MALDI-MS [less ▲]

Detailed reference viewed: 65 (12 ULg)
Full Text
Peer Reviewed
See detailIsolation and cultivation of cellulolytic and xylanolytic bacteria and molds extracted from the gut of the termite Reticulitermes santonensis (3DV.1.14)
Tarayre, Cédric ULg; Bauwens, Julien ULg; Mattéotti, Christel et al

Poster (2013, June)

Biofuel production can be based on the use of agro-residues, consisting in a complex lignocellulosic structure which is not easily hydrolysable. The digestive tract of the termite Reticulitermes ... [more ▼]

Biofuel production can be based on the use of agro-residues, consisting in a complex lignocellulosic structure which is not easily hydrolysable. The digestive tract of the termite Reticulitermes santonensis contains a diversified microflora able to hydrolyze the wood components. Bacteria, molds and protists form efficient consortia, able to break the lignocellulosic complex by producing enzymes, such as xylanases and cellulases. Our purpose is the isolation of microbial strains from termite guts in order to evaluate their potential for hydrolysis of lignocellulosic materials. Termites were fed using different diets chosen to improve the xylanolytic and cellulolytic microflora: wood, microcristalline cellulose (added with lignin or not), α-cellulose (added with lignin or not) and birchwood xylan. Then, dissections were realized to isolate the potential xylanolytic and cellulolytic strains. This approach led us to isolate and to study several strains of bacteria (Bacillus sp. strain CTGx and Chryseobacterium sp. strain CTGx) and molds (Trichoderma virens strain CTGx and Sarocladium kiliense strain CTGx). These microorganisms were able to hydrolyze starch, xylan, cellulose, carboxymethylcellulose, esculin, β-glucan and Whatman® filter paper. They can produce glucose and xylose monomers and oligomers which can be further fermented to produce bioethanol. [less ▲]

Detailed reference viewed: 53 (10 ULg)
Full Text
See detailResearch of New Enzyme Producing Strains in the Gut of the Termite Reticulitermes santonensis
Tarayre, Cédric ULg; Bauwens, Julien ULg; Mattéotti, Christel et al

Poster (2013, June)

Termites contain a complex microflora inside of their guts. Inferior termites contain bacteria, mycetes and protists that interact to degrade vegetable components. These strains act as consortia to break ... [more ▼]

Termites contain a complex microflora inside of their guts. Inferior termites contain bacteria, mycetes and protists that interact to degrade vegetable components. These strains act as consortia to break natural materials by secreting various enzymes. Our aim was the isolation and cultivation of microorganisms in order to produce new enzymes that can be further used in green chemistry. Termites were fed with different diets: pinewood, microcristalline cellulose (added with lignin or not), α-cellulose (added with lignin or not) and birchwood xylan. Then, dissections were realized to isolate interesting strains. All the microorganisms were subjected to enzyme assays. That technique allowed us to isolate and to cultivate various strains of bacteria, molds and protists. Three strains of bacteria, two strains of molds and one strain of protist were isolated and displayed different enzymatic activities. The bacteria Bacillus subtilis strain ABGx, Bacillus sp. strain CTGx and Chryseobacterium sp. strain CTGx displayed amylase, cellulase and xylanase activities. The molds Trichoderma virens strain CTGx and Sarocladium kiliense strain CTGx were also able to produce those enzymes. However, the protist Poterioochromonas sp. was found to produce only amylase. In conlusion, the termite gut is a complex culivation medium that provides a habitat for many microorganisms that show interesting enzymatic activities. [less ▲]

Detailed reference viewed: 41 (8 ULg)
Full Text
See detailDevelopment of a quantitative approach to measure phospholipids in dried drops by Raman spectroscopy
Malherbe, Cédric ULg; Jadoul, Laure ULg; Gilbert, Bernard ULg et al

Poster (2013, May 24)

Phospholipids, PL, such as the phosphatidylcholine PC(18:0/18:1), play a role in the structure of living cells and are suspected to be part of the development of some diseases, for example cancers. Mass ... [more ▼]

Phospholipids, PL, such as the phosphatidylcholine PC(18:0/18:1), play a role in the structure of living cells and are suspected to be part of the development of some diseases, for example cancers. Mass spectrometry enables the structural analysis of PL in complex biological media but imaging mass spectrometry by MALDI-MS is rather limited for quantification purposes. Complementarily, Raman spectroscopy as a non invasive and non destructive method is a potential candidate to quantify and visualise the spatial distribution of the PL by molecular imaging. Unfortunately, the lack of specific chemical function in PL, compared to others biomolecules, limits the use of Raman spectroscopy in the identification process of those PL in complex biological samples. The results presented here belong to a first study of the application of the Raman analyses on dried residues of PL and mice brain tissue performed in the lab. [less ▲]

Detailed reference viewed: 27 (10 ULg)
Full Text
See detailLes venins d'animaux, nouvelle panacée?
Echterbille, Julien ULg; Quinton, Loïc ULg; De Pauw, Edwin ULg

in Athena (2013)

Araignées, serpents, scorpions,… autant d’animaux ayant une place particulière dans l’imaginaire collectif. Fascinants, horripilants voire même terrifiants, les adjectifs ne manquent pas pour qualifier ... [more ▼]

Araignées, serpents, scorpions,… autant d’animaux ayant une place particulière dans l’imaginaire collectif. Fascinants, horripilants voire même terrifiants, les adjectifs ne manquent pas pour qualifier les réactions qu’ils suscitent auprès des populations. Que dire alors de la peur engendrée par leur venin. Une simple piqûre, morsure ou contact peut s’avérer extrêmement dangereux voire létal... [less ▲]

Detailed reference viewed: 54 (25 ULg)
Full Text
See detailIntraocular lenses with functionalized surfaces by biomolecules in relation with lens epithelial cell adhesion
Huang, Yi-Shiang ULg; Alexandre, Michaël ULg; Bozukova, Dimitriya et al

Poster (2013, April 25)

A cataract is pathology opacity of the lens or capsule of the eye, causing impairment of vision or even blindness. Surgery, with lens extraction and intraocular lens implantation, is still the only ... [more ▼]

A cataract is pathology opacity of the lens or capsule of the eye, causing impairment of vision or even blindness. Surgery, with lens extraction and intraocular lens implantation, is still the only currently available treatment. The most common complication after implantation of intraocular lenses (IOLs) is the posterior capsular opacification (PCO) or secondary cataract. This is the result of lens epithelial cells (LECs) proliferation and their transition to mesenchymal cells. In 1997, a Sandwich theory was proposed to elucidate the developmental process of PCO. [1] According to this model, an IOL with higher affinity to LECs will induce a less PCO. In our research, the pHEMA (Poly(2-hydroxyethyl methacrylate)) based acrylic hydrophilic polymer is subjected to the surface modification by conjugating with the bioactive peptides. The RGD sequence, known for its excellent biocompatibility, is designed to stimulate the biointegration between the LECs and the polymer implant. [2]. From our research, The RGD peptide immobilized onto pHEMA surfaces significantly facilitates the adhesion of the porcine LEC. The peptide immobilized surface retains its biological function even after 10 times of autoclave. On the other hand, the immobilized peptide does not alter the hydrophobicity of the surface, the light transmission, as well as the cytotoxicity of the material. This functionalized biomaterial would possibly prevent the formation of PCO. [1] J Cataract Refract Surg. 1997 Dec;23(10):1539-42 [2] Trends Biotechnol. 2008 Jul;26(7):382-92 [less ▲]

Detailed reference viewed: 29 (6 ULg)