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Daems E (2021) Shaping up oligonucleotides : aptamer-target recognition investigated by native mass spectrometry. 235 p
Abstract: Aptamers are short, synthetic DNA or RNA molecules that are characterized by a specific 3D conformation which enables specific target recognition. Aptamers are promising tools in many application fields from sensing to therapeutics. One of the major challenges in the aptamer field is understanding the relationship between the sequence and what determines the higher-order structure and specific interactions with targets. Therefore, this PhD thesis focuses on the use of different mass spectrometry (MS) based approaches to characterize aptamers and their interactions. Several of these approaches are already widely applied to study other biomolecules, such as proteins, but are still largely unexplored for aptamers and oligonucleotides in general. A first focus was put on obtaining information on the higher-order structure and conformational stability of aptamers using a combination of MS and with ion mobility (IM) spectrometry by performing collision-induced unfolding (CIU) experiments. CIU was shown to hold great promise to analyze the conformational dynamics and gas-phase stabilities of aptamers. Next, the capabilities and limitations of native IM-MS for the analysis of noncovalent interactions of aptamers were demonstrated. The conformational behavior and interactions of cocaine-binding aptamers were studied and it was found that relative binding affinities of aptamers that only differ slightly in sequence and structure can be determined using native MS. Moreover, native IM-MS allowed the detection of small conformational changes upon binding of a target, which were found to be dependent on the binding mode of the aptamer. An adaptive binding mechanism was suggested for flexible aptamers that require more reorganization upon binding. In the final part of this thesis, the importance of thoroughly characterizing and validating aptamer-target interactions before using them in an application was emphasized. Moreover, the gathered insights were applied in our own development of a proof-of-concept aptamer-based sensor. This was shown by investigating the interactions of ampicillin aptamers which were found to not bind the target they were selected for in the first place. A multi-analytical approach combining complementary techniques was used for this purpose since no single technique is generally applicable to characterize all aptamers and their interactions and to obtain a comprehensive picture of the aptamer-target interactions. Furthermore, such multi-analytical approach was used to characterize a testosterone-binding aptamer while developing an aptamer-based electrochemiluminescent sensing strategy for this target. This shows the importance of native MS, in combination with other techniques, to thoroughly understand the aptamer-target interactions in the development of a designed application.
Keywords: Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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Piñ,era Herná,ndez I (2014) Simulation of atom displacements induced by photons and electrons in solids. 137 p
Keywords: Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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Amiri-Aref M (2015) Utilization of magnetic nanoparticles and carbon nanotubes to fabrication electrochemical sensors for determination of some important biological and pharmaceutical compounds. 137 p
Keywords: Doctoral thesis; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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van der Snickt G (2012) James Ensor's pigments studied by means of portable and synchrotron radiation-based X-ray techniques : evolution, context and degradation. 501 p
Keywords: Doctoral thesis; Art; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“L'analyse des eaux géothermales par spectrométrie de masse à, étincelles”. Vandelannoote R, Blommaert W, van Grieken R, Gijbels R, Spectra 2000: la revue de l'instrumentation 53, 66 (1979)
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Analysis of geothermal waters by spark source mass spectrometry”. Vandelannoote R, Blommaert W, Gijbels R, van Grieken R, Fresenius' Zeitschrift für analytische Chemie 309, 291 (1981). http://doi.org/10.1007/BF00488604
Abstract: Although the analysis of thermal water by spark-source mass spectrometry (SSMS) is rather timeconsuming, it allows the detection of about 20 elements of geochemical interest down to the ppb-level. A physical preconcentration is proposed in order to collect elements having quite different chemical properties, e.g. alkalis, transition elements, and elements occurring in anionic form. The relative sensitivity factors appear to be rather independent of the salt content of the graphite electrodes. Contrary to neutron activation analysis, SSMS has a quite uniform elemental sensitivity, and allows to determine elements for which neutron activation is not suitable, e.g. Sn and Pb. The precision of SSMS is however by a factor of about 2 worse than that obtained for neutron activation.
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Times cited: 8
DOI: 10.1007/BF00488604
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“Relative evaluation of neutron activation, X-ray fluorescence and spark source mass spectrometry for multi-element analysis of geothermal waters”. Blommaert W, Vandelannoote R, Van 't dack L, Gijbels R, van Grieken R, Journal of radioanalytical chemistry 57, 382 (1980)
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Statistical grouping and controlling factors of dissolved trace elements in a surface water system”. Vandelannoote R, Blommaert W, Van 't dack L, Gijbels R, van Grieken R, Environmental technology letters 4, 363 (1983). http://doi.org/10.1080/09593338309384219
Abstract: Sensitive multi‐element analytical techniques were applied to determine 24 dissolved trace components in 25 different water samples from a 10 km2 zone in Brittany, France. Correspondence factor and multiple regression analyses showed that the elements considered are influenced mainly by the presence of: Fe‐Mn oxide accumulations, a local poly‐metallic sulfide mineralization, and non‐mineralized host rocks, agricultural activity and abundant organic material in local swamps. Via these numerical techniques the location of the poly‐metallic ore body can be derived from the data set.
Keywords: A3 Journal article; Plasma Lab for Applications in Sustainability and Medicine – Antwerp (PLASMANT); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
Times cited: 1
DOI: 10.1080/09593338309384219
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“Increased erythrocyte glutathione peroxidase activity in psoriatics consuming high-selenium drinking water at the dead-sea psoriasis treatment center”. Shani J, Livshitz T, Robberecht H, Van Grieken R, Rubinstein N, Even-Paz Z, Pharmacological research communications 17, 479 (1985). http://doi.org/10.1016/0031-6989(85)90083-9
Abstract: Erythrocyte selenium-dependent glutathione peroxidase activity was measured in psoriatic Danes, before and after their four-week balneological therapy at the Ein-Bokek International Psoriasis Treatment Center, on the Dead-Sea shore in Israel. The drinking water in Ein-Bokek was found to be rich in selenium, a trace element with anticarcinogenic properties and of great importance in human nutrition and health. The most reliable biological parameter for increase in selenium bioavailability is the erythrocytes' glutathione-peroxidase activity. As psoriasis is a proliferative skin disease, the activity of this enzyme was assayed in 35 psoriatic Danes and in 25 long-term local hotel workers, as well as in 34 volunteers drinking low-selenium water. The glutathione peroxidase activity in the psoriatic patients increased significantly during their four-week stay in Ein-Bokek. Erythrocyte glutathione peroxidase activity in the hotel workers was 50% higher than that in the healthy volunteers consuming low-selenium water. A possible role of selenium in psoriasis is suggested.
Keywords: A3 Journal article; Pharmacology. Therapy; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/0031-6989(85)90083-9
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“Laser microprobe mass analysis (LAMMA) to study lead intoxication at the subcellular level”. Vandeputte DF, Verbueken AH, Jacob WA, Van Grieken RE, Acta pharmacologica et toxicologica 59, 617 (1986). http://doi.org/10.1111/J.1600-0773.1986.TB02840.X
Keywords: A3 Journal article; Pharmacology. Therapy; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1111/J.1600-0773.1986.TB02840.X
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“Selenium gehalten van levensmiddelen geconsumeerd in België”. Robberecht H, Deelstra H, vanden Berghe D, Van Grieken R, Revue des fermentations et des industries alimentaires 37, 188 (1983)
Keywords: A3 Journal article; Pharmacology. Therapy; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Skin penetration of minerals in psoriatics and guinea-pigs bathing in hypertonic salt solutions”. Shani J, Barak S, Levi D, Ram M, Schachner ER, Schlesinger T, Robberecht H, Van Grieken R, Avrach WW, Pharmacological research communications 17, 501 (1985). http://doi.org/10.1016/0031-6989(85)90123-7
Abstract: Penetration of electrolytes through the human skin was measured in healthy volunteers and in psoriatic patients after bathing in the Dead-Sea or in simulated bath-salt solutions. Significant increases in the levels of serum Br, Rb, Ca and Zn were noticed only in the psoriatic patients after daily bathing in the Dead-Sea for a 4-week regimen. Guinea-pigs bathed in simulated Dead-Sea bath-salt solutions containing radionuclides of Ca, Mg, K and Br. Traces of each radionuclide were detected in the blood and in some internal organs after 60 minutes of bathing. The radionuclides showed a physiological pattern in their organ distribution. Even though the whole investigation was carried out in hypertonic solutions, there is a definite penetration of salts through healthy (human and guinea-pigs) and damaged (psoriatic) epidermis. This finding suggests that improvement of the psoriatic condition after bathing in the Dead-Sea, may be partly attributed (in addition to ultraviolet irradiation) to the minerals' effect on the psoriatic skin.
Keywords: A3 Journal article; Pharmacology. Therapy; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
DOI: 10.1016/0031-6989(85)90123-7
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“Assessment of atmospheric particles emitted from sugar cane burning in Southeast Brazil”. Godoi RHM, Godoi AFL, Andrade SJ, Santiago-Silva M, de Hoog J, Worobiec A, Van Grieken R, Journal od aerosol science , S749 (2003)
Keywords: A3 Journal article; Laboratory Experimental Medicine and Pediatrics (LEMP); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Badanie składu powietrza w zabytkowych kościołach”. Samek L, Worobiec A, Spolnik Z, Van Grieken R, Analytika , 26 (2006)
Keywords: A3 Journal article; Laboratory Experimental Medicine and Pediatrics (LEMP); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Characterization of atmospheric aerosol particles over Lake Balaton, Hungary, using X-ray emission methods”. Osán J, Alföldy B, Kurunczi S, Török S, Bozó, L, Worobiec A, Injuk J, Van Grieken R, Idöjárás: quarterly journal of the Hungarian Meteorological Service 105, 145 (2001)
Keywords: A3 Journal article; Laboratory Experimental Medicine and Pediatrics (LEMP); AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Applications of laser microprobe mass analysis in medicine”. Verbueken AH, van de Vijver FL, de Broe ME, Van Grieken RE, CRC critical reviews in clinical laboratory sciences 24, 263 (1987)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
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“Characterization of air pollutants observed in three European cathedrals: is the protective glazing really effective?”.Kontozova V, Godoi RHM, Spolnik Z, Worobiec A, Deutsch F, Van Grieken R, Rivista della Stazione sperimentale del vetro 3, 13 (2005)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
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“Laser microprobe mass spectrometry of platinum in dog kidney after cisplatin adminstration”. Verbueken AH, Van Grieken RE, Paulus GJ, Verpooten GA, de Broe ME, Biomedical mass spectrometry 11, 159 (1984). http://doi.org/10.1002/BMS.1200110404
Abstract: By means of laser microprobe mass analysis (LAMMA) platinum was detected in the renal proximal tubular cells of a dog that had been intravenously adminstered the antitumor drug cisplatin (5 mg per kg body weight). No definite subcellular localization of the heavy metal was obtained. Sample prparation and analytical features are examined to increase spatial resolution of analysis while maintaining sufficient detection efficiency. The LAMMA method is destructive, but the amount and type of evaporated material can readily be determined when using LAMMA in combination with transmission electron microscopy. Instrumental optimization and standardization of mass signals is possible by using platinum-loaded, ion chelating resin beads embedded and sectioned with the tissue.
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
DOI: 10.1002/BMS.1200110404
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“X ray fluorescence in member states: Belgium: integration of analysis techniques of different scales using X ray induced and electron induced X ray spectrometry for applications in preventive conservation and environmental monitoring”. Van Grieken R, Potgieter-Vermaak S, Darchuk L, Worobiec A, XRF newsletter , 9 (2009)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Laboratory Experimental Medicine and Pediatrics (LEMP)
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“XRS activities at the Micro &, Trace Analysis Centre (MiTAC), University of Antwerp, Belgium”. Padilla R, Janssens K, van Espen P, Van Grieken R, IAEA XRF newsletter 12, 13 (2006)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Chemometrics (Mitac 3)
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“Background aerosol composition at Gobabeb, South West Africa”. Annegarn H, Van Grieken R, van Espen P, von Blottnitz F, Sellschop J, Winchester J, Maenhaut W, Madoqua , 107 (1976)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Chemometrics (Mitac 3)
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“Does leaf micro-morphology influence the recognition of particles on SEM images?”.Muhammad S, Wuyts K, De Wael K, Samson R, International Journal of Environmental Pollution and Remediation 9, 22 (2021). http://doi.org/10.11159/IJEPR.2021.003
Abstract: Scanning electron microscopy (SEM) remains a popular approach to determine the shape, size, density and elemental composition of particles collected on leaf surfaces, but the effect of leaf micro-morphology on particle counts is not very well known. In this study, leaves of sixteen urban plant species were examined for particle density in June and September 2016 using SEM. The investigated plant species differed in leaf micro-morphology involving trichomes, raised stomata, epicuticular wax crystals and convex epidermal cells forming deep grooves between cells. The particle density on leaves of the investigated plant species was estimated by particle size fraction and leaf side. Particle density was significantly higher on the adaxial (AD) leaf side compared to the abaxial (AB) leaf side and higher for fine-particles than coarse-particles. The effect of trichome density on particle density of the AB and the AD leaf side was indicated to be significant and positive for both coarse and fine-particles in June but not in September. The successive repeated measurements elucidated that features constructing the topography of a leaf surface such as trichomes, stomata, and epidermal cells frequently contributed towards the edge enhancement effect, resulting in exaggerated particle counts. Besides, the mechanical drift contributed to the disparity in particle density measurements. Lastly, the reduction in particle density between successive measurements were imputed on the charging effect. These results enable us to suggest that in addition to characterization of micro-morphological features on a leaf surface, SEM will continue to be a useful approach for determining the particle: shape, size, elemental composition and density of the deposited particles. Nonetheless, the disparity in particle density measurements can occur due to abnormal particle recognition. Based on the results of September, we recommend that within-session successive repeated measurements (~ n ≥ 5) need to be performed to remove measurement uncertainties and obtain reliable quantitative data of particle counts using SEM.
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation); Antwerp Electrochemical and Analytical Sciences Lab (A-Sense Lab)
DOI: 10.11159/IJEPR.2021.003
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“Analiza pierwiastkowa zabytkowych obiektów szklanych”. Wagner B, Nowak A, Bulska E, Kunicki-Goldfinger J, Schalm O, Janssens K, Nauka i Zabytki , 71 (2008)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“A chemical investigation of altered jade art objects”. Aerts A, Janssens K, Adams F, Orientations , 79 (1995)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“A compact μ-XRF spectrometer for (in-situ) analyses of cultural heritage and forensic materials”. Vittiglio G, Bichlmeier S, Klinger P, Heckel J, Fuzhong W, Vincze L, Janssens K, Engström P, Rindby A, Dietrich K, Jembrih-Simbürger D, Schreiner M, Denis D, Lakdar A, Lamotte A, Nuclear instruments and methods in physics research B 213, 693 (2004)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Comparison of synchrotron X-ray microanalysis with electron and proton microscopy for individual particle analysis”. Janssens KH, Adams FC, van Langevelde F, Vis RD, Jones KW, Rivers M, Sutton S, Advances in X-ray analysis 35, 1265 (1992)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Composition of 15-17th century archaeological glass vessels excavated in Antwerp, Belgium”. Janssens K, de Raedt I, Vincze L, Vekemans B, Adams F, Haller M, Knöchel A, HASYLAB Jahresbericht 1997 1, 937 (1998)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Cultural heritage research in “The Micro and Trace Analysis Center&rdquo, of the University of Antwerp”. Godoi RHM, Kontozova V, Godoi AFL, Bencs L, Spolnik Z, Janssens K, Van Grieken R, Coalition 7, 11 (2004)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Echt of namaak? Venetiaans glas uit het oude Antwerpen”. de Raedt I, Janssens K, Veeckman J, De wetenschappelijke bibliotheek 67, 58 (1999)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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“Evaluation of a Monte Carlo simulation for EDXRF spectrometers at beamline BW5, HASYLAB”. Vincze L, Vekemans B, Janssens K, Adams F, Lippmann T, HASYLAB Jahresbericht 1997 1, 1043 (1998)
Keywords: A3 Journal article; AXES (Antwerp X-ray Analysis, Electrochemistry and Speciation)
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