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Aslan‐Üzel AS, Beier A, Kovář D, Cziegler C, Padhi SK, Schuiten ED, Dörr M, Böttcher D, Hollmann F, Rudroff F, Mihovilovic MD, Buryška T, Damborský J, Prokop Z, Badenhorst CPS, Bornscheuer UT. An Ultrasensitive Fluorescence Assay for the Detection of Halides and Enzymatic Dehalogenation. ChemCatChem 2020; 12:2032-2039. [PMID: 32362951 PMCID: PMC7188320 DOI: 10.1002/cctc.201901891] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2019] [Revised: 12/16/2019] [Indexed: 12/31/2022]
Abstract
Halide assays are important for the study of enzymatic dehalogenation, a topic of great industrial and scientific importance. Here we describe the development of a very sensitive halide assay that can detect less than a picomole of bromide ions, making it very useful for quantifying enzymatic dehalogenation products. Halides are oxidised under mild conditions using the vanadium-dependent chloroperoxidase from Curvularia inaequalis, forming hypohalous acids that are detected using aminophenyl fluorescein. The assay is up to three orders of magnitude more sensitive than currently available alternatives, with detection limits of 20 nM for bromide and 1 μM for chloride and iodide. We demonstrate that the assay can be used to determine specific activities of dehalogenases and validate this by comparison to a well-established GC-MS method. This new assay will facilitate the identification and characterisation of novel dehalogenases and may also be of interest to those studying other halide-producing enzymes.
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Affiliation(s)
- Aşkın S. Aslan‐Üzel
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Andy Beier
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - David Kovář
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Clemens Cziegler
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | - Santosh K. Padhi
- Biocatalysis and Enzyme Engineering Laboratory Department of Biochemistry School of Life SciencesUniversity of HyderabadGachibowli500046India
| | - Eva D. Schuiten
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Mark Dörr
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Dominique Böttcher
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Frank Hollmann
- Department of BiotechnologyDelft University of TechnologyDelft2629 HZ (TheNetherlands
| | - Florian Rudroff
- Institute of Applied Synthetic ChemistryTU WienVienna1060Austria
| | | | - Tomáš Buryška
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
| | - Jiří Damborský
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Zbyněk Prokop
- Loschmidt Laboratories Department of Experimental Biology and RECETOX Faculty of ScienceMasaryk UniversityBrno625 00Czech Republic
- International Clinical Research CenterSt. Anne's University Hospital BrnoBrno656 91Czech Republic
| | - Christoffel P. S. Badenhorst
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
| | - Uwe T. Bornscheuer
- Department of Biotechnology & Enzyme Catalysis Institute of BiochemistryGreifswald UniversityGreifswald17487Germany
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Schenkmayerova A, Pinto G, Marek M, Toul M, Hernychova L, Liskova V, Emond S, Bednar D, Prokop Z, Chaloupkova R, Hollfelder F, Bornscheuer U. Functional switching based on altered enzyme flexibility via InDel mutagenesis of a reconstructed ancestor. J Biotechnol 2019. [DOI: 10.1016/j.jbiotec.2019.05.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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3
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Pilát Z, Kizovský M, Ježek J, Krátký S, Sobota J, Šiler M, Samek O, Buryška T, Vaňáček P, Damborský J, Prokop Z, Zemánek P. Detection of Chloroalkanes by Surface-Enhanced Raman Spectroscopy in Microfluidic Chips. Sensors (Basel) 2018; 18:E3212. [PMID: 30249041 PMCID: PMC6210807 DOI: 10.3390/s18103212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 09/18/2018] [Accepted: 09/21/2018] [Indexed: 01/12/2023]
Abstract
Optofluidics, a research discipline combining optics with microfluidics, currently aspires to revolutionize the analysis of biological and chemical samples, e.g., for medicine, pharmacology, or molecular biology. In order to detect low concentrations of analytes in water, we have developed an optofluidic device containing a nanostructured substrate for surface enhanced Raman spectroscopy (SERS). The geometry of the gold surface allows localized plasmon oscillations to give rise to the SERS effect, in which the Raman spectral lines are intensified by the interaction of the plasmonic field with the electrons in the molecular bonds. The SERS substrate was enclosed in a microfluidic system, which allowed transport and precise mixing of the analyzed fluids, while preventing contamination or abrasion of the highly sensitive substrate. To illustrate its practical use, we employed the device for quantitative detection of persistent environmental pollutant 1,2,3-trichloropropane in water in submillimolar concentrations. The developed sensor allows fast and simple quantification of halogenated compounds and it will contribute towards the environmental monitoring and enzymology experiments with engineered haloalkane dehalogenase enzymes.
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Affiliation(s)
- Zdeněk Pilát
- Institute of Scientific Instruments of the CAS, v.v.i., Czech Academy of Sciences, Kralovopolska 147, 61264 Brno, Czech Republic.
| | - Martin Kizovský
- Institute of Scientific Instruments of the CAS, v.v.i., Czech Academy of Sciences, Kralovopolska 147, 61264 Brno, Czech Republic.
| | - Jan Ježek
- Institute of Scientific Instruments of the CAS, v.v.i., Czech Academy of Sciences, Kralovopolska 147, 61264 Brno, Czech Republic.
| | - Stanislav Krátký
- Institute of Scientific Instruments of the CAS, v.v.i., Czech Academy of Sciences, Kralovopolska 147, 61264 Brno, Czech Republic.
| | - Jaroslav Sobota
- Institute of Scientific Instruments of the CAS, v.v.i., Czech Academy of Sciences, Kralovopolska 147, 61264 Brno, Czech Republic.
| | - Martin Šiler
- Institute of Scientific Instruments of the CAS, v.v.i., Czech Academy of Sciences, Kralovopolska 147, 61264 Brno, Czech Republic.
| | - Ota Samek
- Institute of Scientific Instruments of the CAS, v.v.i., Czech Academy of Sciences, Kralovopolska 147, 61264 Brno, Czech Republic.
| | - Tomáš Buryška
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 62500 Brno, Czech Republic.
| | - Pavel Vaňáček
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 62500 Brno, Czech Republic.
| | - Jiří Damborský
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 62500 Brno, Czech Republic.
| | - Zbyněk Prokop
- Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University, Kamenice 5/A13, 62500 Brno, Czech Republic.
| | - Pavel Zemánek
- Institute of Scientific Instruments of the CAS, v.v.i., Czech Academy of Sciences, Kralovopolska 147, 61264 Brno, Czech Republic.
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Gross J, Prokop Z, Janssen D, Faber K, Hall M. Regio- and Enantioselective Sequential Dehalogenation of rac-1,3-Dibromobutane by Haloalkane Dehalogenase LinB. Chembiochem 2016; 17:1437-41. [PMID: 27223496 DOI: 10.1002/cbic.201600227] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2016] [Indexed: 11/06/2022]
Abstract
The hydrolytic dehalogenation of rac-1,3-dibromobutane catalyzed by the haloalkane dehalogenase LinB from Sphingobium japonicum UT26 proceeds in a sequential fashion: initial formation of intermediate haloalcohols followed by a second hydrolytic step to produce the final diol. Detailed investigation of the course of the reaction revealed favored nucleophilic displacement of the sec-halogen in the first hydrolytic event with pronounced R enantioselectivity. The second hydrolysis step proceeded with a regioselectivity switch at the primary position, with preference for the S enantiomer. Because of complex competition between all eight possible reactions, intermediate haloalcohols formed with moderate to good ee ((S)-4-bromobutan-2-ol: up to 87 %). Similarly, (S)-butane-1,3-diol was formed at a maximum ee of 35 % before full hydrolysis furnished the racemic diol product.
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Affiliation(s)
- Johannes Gross
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Zbyněk Prokop
- Department Experimental Biology, Faculty of Science, Masaryk University, Kamenice 5A13, 625 00, Brno, Czech Republic
| | - Dick Janssen
- Biomolecular Sciences and Biotechnology Institute, University of Groningen, Nijenborgh 4, 9747 AG, Groningen, NL
| | - Kurt Faber
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Mélanie Hall
- Department of Chemistry, University of Graz, Heinrichstrasse 28, 8010, Graz, Austria.
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Prokop Z, Nečasová A, Klánová J, Čupr P. Bioavailability and mobility of organic contaminants in soil: new three-step ecotoxicological evaluation. Environ Sci Pollut Res Int 2016; 23:4312-4319. [PMID: 26490898 DOI: 10.1007/s11356-015-5555-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2015] [Accepted: 10/05/2015] [Indexed: 06/05/2023]
Abstract
A novel approach was developed for rapid assessment of bioavailability and potential mobility of contaminants in soil. The response of the same test organism to the organic extract, water extract and solid phase of soil was recorded and compared. This approach was designed to give an initial estimate of the total organic toxicity (response to organic extractable fraction), as well as the mobile (response to water extract) and bioavailable fraction (response to solid phase) of soil samples. Eighteen soil samples with different levels of pollution and content of organic carbon were selected to validate the novel three-step ecotoxicological evaluation approach. All samples were chemically analysed for priority contaminants, including aromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs), hexachlorocyclohexane (HCH) and dichlordiphenyltrichloroethane (DDT). The ecotoxicological evaluation involved determination of toxicity of the organic, mobile and bioavailable fractions of soil to the test organism, bacterium Bacillus cereus. We found a good correlation between the chemical analysis and the toxicity of organic extract. The low toxicity of water extracts indicated low water solubility, and thus, low potential mobility of toxic contaminants present in the soil samples. The toxicity of the bioavailable fraction was significantly greater than the toxicity of water-soluble (mobile) fraction of the contaminants as deduced from comparing untreated samples and water extracts. The bioavailability of the contaminants decreased with increasing concentrations of organic carbon in evaluated soil samples. In conclusion, the three-step ecotoxicological evaluation utilised in this study can give a quick insight into soil contamination in context with bioavailability and mobility of the contaminants present. This information can be useful for hazard identification and risk assessment of soil-associated contaminants. Graphical Abstract New three-step ecotoxicological evaluation by using the same organism.
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Affiliation(s)
- Zbyněk Prokop
- Faculty of Science, RECETOX-Research Centre for Toxic Compounds in the Environment, Masaryk University, Kamenice753/5, 625 00, Brno, Czech Republic
| | - Anežka Nečasová
- Faculty of Science, RECETOX-Research Centre for Toxic Compounds in the Environment, Masaryk University, Kamenice753/5, 625 00, Brno, Czech Republic
| | - Jana Klánová
- Faculty of Science, RECETOX-Research Centre for Toxic Compounds in the Environment, Masaryk University, Kamenice753/5, 625 00, Brno, Czech Republic
| | - Pavel Čupr
- Faculty of Science, RECETOX-Research Centre for Toxic Compounds in the Environment, Masaryk University, Kamenice753/5, 625 00, Brno, Czech Republic.
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Biedermannová L, Prokop Z, Gora A, Chovancová E, Kovács M, Damborsky J, Wade RC. A single mutation in a tunnel to the active site changes the mechanism and kinetics of product release in haloalkane dehalogenase LinB. J Biol Chem 2012; 287:29062-74. [PMID: 22745119 DOI: 10.1074/jbc.m112.377853] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Many enzymes have buried active sites. The properties of the tunnels connecting the active site with bulk solvent affect ligand binding and unbinding and also the catalytic properties. Here, we investigate ligand passage in the haloalkane dehalogenase enzyme LinB and the effect of replacing leucine by a bulky tryptophan at a tunnel-lining position. Transient kinetic experiments show that the mutation significantly slows down the rate of product release. Moreover, the mechanism of bromide ion release is changed from a one-step process in the wild type enzyme to a two-step process in the mutant. The rate constant of bromide ion release corresponds to the overall steady-state turnover rate constant, suggesting that product release became the rate-limiting step of catalysis in the mutant. We explain the experimental findings by investigating the molecular details of the process computationally. Analysis of trajectories from molecular dynamics simulations with a tunnel detection software reveals differences in the tunnels available for ligand egress. Corresponding differences are seen in simulations of product egress using a specialized enhanced sampling technique. The differences in the free energy barriers for egress of a bromide ion obtained using potential of mean force calculations are in good agreement with the differences in rates obtained from the transient kinetic experiments. Interactions of the bromide ion with the introduced tryptophan are shown to affect the free energy barrier for its passage. The study demonstrates how the mechanism of an enzymatic catalytic cycle and reaction kinetics can be engineered by modification of protein tunnels.
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Affiliation(s)
- Lada Biedermannová
- Molecular and Cellular Modeling Group, Heidelberg Institute for Theoretical Studies, Schloss-Wolfsbrunnenweg 35, D-69118 Heidelberg, Germany.
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Gutteling EW, Doroszuk A, Riksen JAG, Prokop Z, Reszka J, Kammenga JE. Environmental influence on the genetic correlations between life-history traits in Caenorhabditis elegans. Heredity (Edinb) 2007; 98:206-13. [PMID: 17203010 DOI: 10.1038/sj.hdy.6800929] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Empirical evidence is mounting to suggesting that genetic correlations between life-history traits are environment specific. However, detailed knowledge about the loci underlying genetic correlations in different environments is scant. Here, we studied the influence of temperature (12 degrees C and 24 degrees C) on the genetic correlations between egg size, egg number and body mass in the nematode Caenorhabditis elegans. We used a quantitative trait loci (QTL) approach based on a genetic map with evenly spaced single nucleotide polymorphism markers in an N2 x CB4856 recombinant inbred panel. Significant genetic correlations between various traits were found at both temperatures. We detected pleiotropic or closely linked QTL, which supported the negative correlation between egg size and egg number at 12 degrees C, the positive correlation across temperatures for body mass, and the positive correlation between body mass and egg size at 12 degrees C. The results indicate that specific loci control the covariation in these life-history traits and the locus control is prone to environmental conditions.
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Affiliation(s)
- E W Gutteling
- Laboratory of Nematology, Wageningen University, Wageningen, The Netherlands
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Sato Y, Natsume R, Prokop Z, Senda M, Damborsky J, Nagata Y, Tsuda M, Senda T. Crystal structure of the haloalkane dehalogenase DbjA. Acta Crystallogr A 2005. [DOI: 10.1107/s0108767305091786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/03/2023] Open
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Streltsov VA, Prokop Z, Damborský J, Nagata Y, Oakley A, Wilce MCJ. Haloalkane Dehalogenase LinB from Sphingomonas paucimobilis UT26: X-ray Crystallographic Studies of Dehalogenation of Brominated Substrates. Biochemistry 2003. [DOI: 10.1021/bi0330141] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Prokop Z, Cupr P, Zlevorova-Zlamalikova V, Komarek J, Dusek L, Holoubek I. Mobility, bioavailability, and toxic effects of cadmium in soil samples. Environ Res 2003; 91:119-126. [PMID: 12584013 DOI: 10.1016/s0013-9351(02)00012-9] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Total concentration is not a reliable indicator of metal mobility or bioavailability in soils. The physicochemical form determines the behavior of metals in soils and hence the toxicity toward terrestrial biota. The main objectives of this study were the application and comparison of three approaches for the evaluation of cadmium behavior in soil samples. The mobility and bioavailability of cadmium in five selected soil samples were evaluated using equilibrium speciation (Windermere humic aqueous model (WHAM)), extraction procedures (Milli-Q water, DMSO, and DTPA), and a number of bioassays (Microtox, growth inhibition test, contact toxicity test, and respiration). The mobility, represented by the water-extractable fraction, corresponded well with the amount of cadmium in the soil solution, calculated using the WHAM (r(2)=0.96, P<0.001). The results of the ecotoxicological evaluation, which represent the bioavailable fraction of cadmium, correlated well with DTPA extractability and also with the concentration of free cadmium ion, which is recognized as the most bioavailable metal form. The results of the WHAM as well as the results of extraction experiments showed a strong binding of cadmium to organic matter and a weak sorption of cadmium to clay minerals.
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Affiliation(s)
- Z Prokop
- Research Centre for Environmental Chemistry and Ecotoxicology, Masaryk University, Kamenice 126/3, 625 00 Brno, Czech Republic.
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Prokop Z, Vangheluwe ML, Van Sprang PA, Janssen CR, Holoubek I. Mobility and toxicity of metals in sandy sediments deposited on land. Ecotoxicol Environ Saf 2003; 54:65-73. [PMID: 12547637 DOI: 10.1016/s0147-6513(02)00022-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
A times series of laboratory experiments were conducted to investigate the effect of land deposition of contaminated sediments on the bioavailability and mobility of metals. Four sandy sediments were sampled at sites expected to have elevated levels of cadmium and zinc. The physical and chemical characteristics and ecotoxicity of sediments, pore waters, and leachates were evaluated after periods ranging from 1 to 45 days of land deposition. Cd and Zn retardation and leaching potential were calculated and this simulation gave good predictions of subsequently observed Cd and Zn mobility. The mobility and leaching of Cd and Zn in the sediments increased with decreasing pH and with decreasing content of organic matter. During the deposition an increase in sediment toxicity to plants and an increase in eluate toxicity to invertebrates were observed. A high rate of water flow through the sediment resulted in a lower toxicity enhancement of the sediments and a higher toxicity enhancement of the eluates. This result suggests that water flow through the sediment reduces the actual toxicity of the upper layer of deposited sediment but at the same time intensifies the risk of groundwater contamination.
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Affiliation(s)
- Z Prokop
- Department of Environmental Chemistry and Exotoxicology, Masaryk University, Kotlarska 2, 602 00 Brno, Czech Republic.
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Setínek K, Prokop Z. Wirkung der funktionellen Gruppen eines Ionenaustauschers bei seiner Anwendung als eines festen Katalysators. Colloid Polym Sci 1978. [DOI: 10.1007/bf01639319] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Prokop Z, Setínek K. The catalytic activity of differently cross-linked standard sulphonated styrene-divinylbenzene copolymers. ACTA ACUST UNITED AC 1977. [DOI: 10.1135/cccc19773123] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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