References of "De Pauw, Edwin"
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See detailAn analytical pipeline for MALDI in-source decay mass spectrometry imaging
Zimmerman, Tyler ULg; Debois, Delphine ULg; Mazzucchelli, Gabriel ULg et al

in Analytical Chemistry (2011), 83(15), 6090-6097

In-source decay (ISD) fragmentation as combined with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry allows protein sequencing directly from mass spectra. Acquisition of MALDI-ISD ... [more ▼]

In-source decay (ISD) fragmentation as combined with matrix-assisted laser desorption/ionization (MALDI) mass spectrometry allows protein sequencing directly from mass spectra. Acquisition of MALDI-ISD mass spectra from tissue samples is achieved using an appropriate MALDI matrix, such as 1,5-diaminonaphthalene (DAN). Recent efforts have focused on combining MALDI-ISD with mass spectrometry imaging (MSI) to provide simultaneous sequencing and localization of proteins over a thin tissue surface. Successfully coupling these approaches requires the development of new data analysis tools, but first, investigating the properties of MALDI-ISD as applied to mixtures of protein standards reveals a high sensitivity to the relative protein ionization efficiency. This finding translates to the protein mixtures found in tissues and is used to inform the development of an analytical pipeline for data analysis in MALDI-ISD MS imaging, including software to identify the most pertinent spectra, to sequence protein mixtures, and to generate ion images for comparison with tissue morphology. The ability to simultaneously identify and localize proteins is demonstrated by using the analytical pipeline on three tissue sections from porcine eye lens, resulting in localizations for crystallins and cytochrome c. The variety of protein identifications provided by MALDI-ISD-MSI between tissue sections creates a discovery tool, and the analytical pipeline makes this process more efficient. [less ▲]

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See detailNovel comprehensive approach for accessible biomarker identification and absolute quantification from precious human tissues
Turtoi, Andrei ULg; Dumont, Bruno ULg; Greffe, Yannick et al

in Journal of Proteome Research (2011), 10(7), 3160-82

The identification of specific biomarkers obtained directly from human pathological lesions remains a major challenge, because the amount of tissue available is often very limited. We have developed a ... [more ▼]

The identification of specific biomarkers obtained directly from human pathological lesions remains a major challenge, because the amount of tissue available is often very limited. We have developed a novel, comprehensive, and efficient method permitting the identification and absolute quantification of potentially accessible proteins in such precious samples. This protein subclass comprises cell membrane associated and extracellular proteins, which are reachable by systemically deliverable substances and hence especially suitable for diagnosis and targeted therapy applications. To isolate such proteins, we exploited the ability of chemically modified biotin to label ex vivo accessible proteins and the fact that most of these proteins are glycosylated. This approach consists of three successive steps involving first the linkage of potentially accessible proteins to biotin molecules followed by their purification. The remaining proteins are then subjected to glycopeptide isolation. Finally, the analysis of the nonglycosylated peptides and their involvement in an in silico method increased the confident identification of glycoproteins. The value of the technique was demonstrated on human breast cancer tissue samples originating from 5 individuals. Altogether, the method delivered quantitative data on more than 400 potentially accessible proteins (per sample and replicate). In comparison to biotinylation or glycoprotein analysis alone, the sequential method significantly increased the number (≥30% and ≥50% respectively) of potentially therapeutically and diagnostically valuable proteins. The sequential method led to the identification of 93 differentially modulated proteins, among which several were not reported to be associated with the breast cancer. One of these novel potential biomarkers was CD276, a cell membrane-associated glycoprotein. The immunohistochemistry analysis showed that CD276 is significantly differentially expressed in a series of breast cancer lesions. Due to the fact that our technology is applicable to any type of tissue biopsy, it bears the ability to accelerate the discovery of new relevant biomarkers in a broad spectrum of pathologies. [less ▲]

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See detailMALDI mass spectrometry imaging of secreted lipopeptides in a bacterial biofilm colonizing plant roots
Debois, Delphine ULg; Jourdan, Emmanuel ULg; Ongena, Marc ULg et al

Conference (2011, June 06)

During the aggression of a plant by a pathogen, different immune reactions may occur. "Induced Systemic Resistance” (ISR) is triggered by the specific interaction between plant and non-pathogenic ... [more ▼]

During the aggression of a plant by a pathogen, different immune reactions may occur. "Induced Systemic Resistance” (ISR) is triggered by the specific interaction between plant and non-pathogenic microorganism. The first step (of three) consists in the perception by plant cells of elicitors produced by the inducing agents that initiates the phenomenon. One class of known elicitors is antibiotics including surfactin- and fengycin-type lipopeptides. Recent studies in biology, genetics or biochemistry allowed a better understanding of the interactions between plants and microorganism but few has been done at the molecular level. MALDI MS imaging has been used to study the nature of the secreted lipopeptides, their relative quantity and their distribution in the root’s environment. Disinfected tomato seeds were first incubated at 28°C in sterile conditions for germination. Germinated seeds were then treated with freshly-grown cells of Bacillus amyloliquefaciens S499 and placed in Petri dish on ITO glass slide recovered with a thin layer of plant nutritive solution (Hoagland) containing 1,75% of agar. Petri dishes were finally incubated vertically in phytotron during 10 days (28°C, photoperiod 16h). For MALDI imaging experiments, the ITO slide was removed from the agar and dried in a dessiccator under vacuum. The matrix solution (9-aminoacridine) was applied with an ImagePrep automated sprayer (Bruker Daltonics). An UltraFlex II TOF/TOF mass spectrometer was used to record molecular cartographies. 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. Only the surfactins have been detected when working with the S499 strain. The most abundant surfactins were those with longer fatty acyl chain lengths, such as C14- and C15-homologues. Such a surfactin signature is interesting since homologues with the longest acyl chains are also the more active biologically. The distribution of surfactins showed a gradient representing the diffusion of the molecules during the root growth. The more the fatty acyl chain is long, the more the surfactin is detected near the root. Other compounds detected during the analysis showed a clear anti-colocalization with the surfactins. Future work will be focused on the influence of the plant species (tobacco, salad, Arabidopsis thaliana) on the secretion of lipopeptides (type, concentration…) and the influence of the strain of Bacillus amyloliquefaciens regarding its ability to selectively produce specific lipopeptide families (overproducing or repressed mutants). This MS imaging technique thus appears to be a very powerful method to study in situ production of bioactive lipopeptides by bacteria developing on roots. This is crucial for a better understanding of the molecular dialogue governing perception of beneficial Bacillus strains by the host plant. This study provides a first analysis over a long root section of lipopeptides secreted by a bacterial biofilm colonizing plant. [less ▲]

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See detailInvestigation of Ion Mobility coupled with mass spectrometry (IMMS) for the screening of pesticide residues in food
Goscinny, Séverine ULg; Touilloux, Romain; Joly, Laure et al

Conference (2011, June)

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See detailStudy on the susceptibility of the bovine milk fat globule membrane proteins to enzymatic hydrolysis and organization of some of the proteins
Vanderghem, Caroline ULg; Francis, Frédéric ULg; Danthine, Sabine ULg et al

in International Dairy Journal (2011), 21(5), 312-318

Isolated milk fat globules were subjected to enzyme hydrolysis by a specific protease (trypsin) and a nonspecific protease (pronase E) to study the asymmetric arrangement of milk fat globule membrane ... [more ▼]

Isolated milk fat globules were subjected to enzyme hydrolysis by a specific protease (trypsin) and a nonspecific protease (pronase E) to study the asymmetric arrangement of milk fat globule membrane (MFGM) proteins. The remaining proteins on the globules after proteolysis were resolved by two-dimensional gel electrophoresis and identified by mass spectrometry. By this proteomic approach, the results confirmed different susceptibility of the MFGM proteins to proteolysis by enzymes. Butyrophilin and adipophilin were completely digested by trypsin and by pronase E, whereas lactadherin and xanthine dehydrogenase/oxidase were almost resistant to hydrolysis by trypsin and partially attacked by pronase E. Based on our results and recent bibliographic data, an up-dated model of the organization of some MFGM proteins is proposed and discussed. (c) 2011 Elsevier Ltd. All rights reserved. [less ▲]

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See detailDisulfide bonds assignment and folding characterization of peptide toxins by Ion Mobility Mass Spectrometry
Echterbille, Julien ULg; Quinton, Loïc ULg; De Pauw, Edwin ULg et al

Conference (2011, April 29)

Main component of animal venoms is peptide toxins, which are highly structured by several disulfide bridges. Disulfide bridges fill different roles as increasing the toxins efficiency by lowering their ... [more ▼]

Main component of animal venoms is peptide toxins, which are highly structured by several disulfide bridges. Disulfide bridges fill different roles as increasing the toxins efficiency by lowering their immunogenicity or providing the adequate conformation to efficiently bind to the biological receptor. The sequencing and the determination of the cysteine pairing is still challenging and therefore an important step in structural analysis. In this work, we present a new strategy to sequence structured toxins and assign S-S bridges using ion mobility resolved MS/MS. The method relies on the analysis of partially reduced multiple-disulfide peptide. The mixture of the different forms is resolved by ion mobility, followed by MS/MS acquisition on each mobility separated species. The proof of concept has been successfully conducted on α-CnI, a toxin purified from the venom of Conus consors marine snail. The toxin’s sequence contains four cysteines linked together with two disulfide bridges. α-CnI was partially reduced by a small excess of tris(carboxyethyl)phosphine (10:1). The resulting mixture was purified before analysis by infusion nanoESI-Synapt-G2. Fragmentation was performed after the mobility cell, to obtain specific fragments of each species. Partial reduction of α-CnI results in a mixture of oxidized (the two disulfides are formed), reduced (the two disulfides have been reduced) and partially reduced forms (one of the two disulfides has been reduced). The arrival time distribution of triply charged ions reveals the presence of 4 different species, characterized by different relative cross sections in the gas-phase. Mass matching allows identifying the species: the first mobility (the most compact structure) was identified to be the oxidized folded toxin (M). The latest peak, corresponding to the larger cross-section, was identified as the fully reduced toxin (M+4Da). The second and the third mobility peaks were attributed to the two partially reduced forms in which only one disulfide bridge was reduced (M+2Da). The change in ion mobility depends on which S-S bridge is reduced. Ion mobility separated species give characteristic fragment ions upon fragmentation in the transfer cell (i.e. after ion mobility separator). Interestingly, fragment ions coming from partially reduced species, especially the C-S or S-S bond cleavages, clearly indicates that the disulfide linkage of α-CnI is (Cys1-Cys3) and (Cys2-Cys4) as expected from literature. The method is now being applied with success to more complex systems containing 3 or 4 disulfide bridges. The influence of the charge state on the mobility separation is systematically analyzed in terms of structural implications. [less ▲]

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See detailMass spectrometry applied to biomolecules analysis
Far, Johann ULg; Mazzucchelli, Gabriel ULg; Meuwis, Marie-Alice ULg et al

Conference (2011, March 31)

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See detailBIOMARKER FOR OSTEOARTHRITIS AND/OR OTHER AGEING-RELATED DISEASES, AND USE THEREOF
Henrotin, Yves ULg; Gharbi, Myriam; Deberg, Michelle et al

Patent (2011)

The invention relates to the identification of abiomarker whose abundance in biological sampleis changed in subjects with osteoarthritis and/or other ageing-related diseases. Thebiomarker hasapplications ... [more ▼]

The invention relates to the identification of abiomarker whose abundance in biological sampleis changed in subjects with osteoarthritis and/or other ageing-related diseases. Thebiomarker hasapplications in the diagnosis of osteoarthritis and/or other ageing-related diseases, in determining the prognosis for an individual diagnosed with osteoarthritis and/or other ageing-related diseases, and in monitoring the efficacy of treatment for osteoarthritis and/or other ageing-related diseases. [less ▲]

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See detailBIOMARKER FOR OSTEOARTHRITIS AND/OR OTHER AGEING-RELATED DISEASES, AND USE THEREOF
Henrotin, Yves ULg; Gharbi, Myriam; Deberg, Michelle et al

Patent (2011)

The invention relates to the identification of abiomarker whose abundance in biological sampleis changed in subjects with osteoarthritis and/or other ageing-related diseases. Thebiomarker hasapplications ... [more ▼]

The invention relates to the identification of abiomarker whose abundance in biological sampleis changed in subjects with osteoarthritis and/or other ageing-related diseases. Thebiomarker hasapplications in the diagnosis of osteoarthritis and/or other ageing-related diseases, in determining the prognosis for an individual diagnosed with osteoarthritis and/or other ageing-related diseases, and in monitoring the efficacy of treatment for osteoarthritis and/or other ageing-related diseases. [less ▲]

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See detailIncreased risk of non-Hodgkin lymphoma and serum organochlorine concentrations among neighbors of a municipal solid waste incinerator
Viel, Jean-François; Floret, Nathalie; Deconinck, Eric et al

in Environment International (2011), 37(2), 449-453

Organochlorine chemicals may contribute to an increased risk of non-Hodgkin lymphoma (NHL) within nonoccupationally exposed populations. Among these chemicals, dioxins and furans were mainly released by ... [more ▼]

Organochlorine chemicals may contribute to an increased risk of non-Hodgkin lymphoma (NHL) within nonoccupationally exposed populations. Among these chemicals, dioxins and furans were mainly released by municipal solid waste incinerators (MSWIs) until a recent past in France, a source of exposure that is of public concern. We investigated organochlorines and the risk of NHL among neighbors of a French MSWI with high levels of dioxin emissions (Besançon, France), using serum concentrations to assess exposure. The study area consisted of three electoral wards, containing or surrounding the MSWI. Pesticides, dioxins, furans, and polychlorinated biphenyls (PCBs) were measured in the serum of 34 newly diagnosed NHL cases (2003– 2005) and 34 controls. Risks of NHL associated with each lipid-corrected serum concentration were estimated using exact logistic regression. The pesticides β-hexachlorocyclohexane (odds ratio [OR]=1.05, 95% confidence interval [CI]=1.00–1.12, per 10 ng/g lipid) and p,p' dichloro-diphenyl-trichloroethane (DDT) (OR=1.20, 95% CI=1.01-1.45, per 10 ng/g lipid) were associated with NHL risk. Evidence indicated an increased NHL risk associated with cumulative WHO1998-toxic equivalency factor (TEQ) concentrations (dioxins, OR=1.12, 95% CI=1.03–1.26; furans, OR=1.16, 95% CI=1.03–1.35; dioxin-like PCBs, OR=1.04, 95% CI=1.00–1.07; and total TEQ, OR=1.04, 95% CI=1.01–1.05), as well as with non dioxin-like PCBs (OR=1.02, 95% CI=1.01–1.05, per 10 ng/g lipid). Most congener-specific associations were statistically significant. This study provides strong and consistent support for an association between serum cumulative WHO1998-TEQ concentrations, at levels experienced by people residing in the vicinity of a polluting MSWI, and risk of NHL. [less ▲]

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