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Sensitive Layers for Optical Biosensors and Protein Chips
Rodriguez Emmenegger, César ; Brynda, Eduard (advisor) ; Lynn, Nicholas Scott (referee) ; Shukurov, Andrey (referee)
Sensitive layers for optical biosensors and protein chips The goal of this thesis was the development of sensitive surfaces for optical affinity biosensors detecting in complex biological media. The practical application of these surface-based technologies has been hampered by protein fouling from biological media, in particular blood plasma, where the vast majority of relevant analytes are present. The work of the thesis was centred in three main foci: Design and preparation of antifouling and non-fouling surfaces Evaluation and conceptualisation of their resistance to fouling from blood plasma and serum as well as other biological fluids Preparation of sensitive layers for detection in complex biological media Three approaches were used to prepare protein resistance surfaces, i) ω-functional self-assembled monolayers (SAM), ii) end-tethered polymers and iii) polymer brushes prepared by surface initiated controlled radical polymerisation. Investigation of proteins in the blood plasma deposits on PEG- based surfaces revealed that some fouling is unavoidable in PEG-based surface modifications. A novel type of non-fouling polymer brushes based on poly[N-(2-hydroxypropyl) methacrylamide] challenged the accepted ideas for the design of protein resistant surfaces. For the first time a...
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Multifunctional biomolecular assemblies for parallelized analysis of biomolecular interactions
Bocková, Markéta ; Homola, Jiří (advisor) ; Brynda, Eduard (referee) ; Procházka, Marek (referee)
Title: Multifunctional biomolecular assemblies for parallelized analysis of biomolecular interactions Author: Markéta Bocková Department / Institute: Institute of Physics, Charles University Supervisor of the doctoral thesis: Prof. Jiří Homola, Ph.D., DSc., Institute of Photonics and Electronics, The Czech Academy of Sciences Abstract: Surface plasmon resonance (SPR) biosensors represent the most advanced optical method for the direct, real-time monitoring of biomolecular interactions without the need for labelling. This doctoral thesis aims to advance the SPR biosensor method and to expand its utility in the investigation of biomolecular interactions. This encompasses activities on two major fronts of SPR biosensor research - immobilization methods and biosensing methodologies. Methods for the immobilization of biomolecules were researched with the aim of enabling the immobilization of a broad range of biomolecules on the SPR biosensor surface in a spatially controlled manner. The development of novel biosensing methodologies was pursued in order to address the current limitations of SPR biosensors associated with non-specific adsorption and limited analyte transport, and thus to improve the accuracy and robustness of SPR biosensor measurements. Finally, advances in the development of immobilization...
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Adhesion and growth of adipose tissue-derived stem cells on fibrin assemblies with attached growth factors for tissue engineering of heart valves
Filová, Elena ; Trávníčková, Martina ; Knitlová, Jarmila ; Matějka, Roman ; Kučerová, Johanka ; Riedelová, Zuzana ; Brynda, Eduard ; Bačáková, Lucie
Currently used xenogeneic biological heart valve prostheses are decellularized and crosslinked with glutaraldehyde. These grafts usually undergo degeneration and calcification. Pericardium-based heart valve prostheses, re-seeded with autologous cells, i.e. Adipose tissue-derived cells (ASCs) and endothelial cells, could have longer durability and biocompatibility. In order to improve the adhesion of cells and their ingrowth into decellularized pericardium, various fibrin (Fb) layers were developed, i.e. Fb, Fb with covalently bound heparin (H), Fb with either vascular endothelial growth factor (VEGF) or fibroblast growth factor 2 (FGF) in various concentrations (1 ng/ml, 10 ng/ml, 100 ng/ml) or with both VEGF and FGF (100 ng/ml). Growth factors were attached onto Fb via heparin or were adsorbed. ASCs were seeded on theses layers in a DMEM medium supplemented with 2 % of fetal bovine serum, TGFβ1 and BMP-4 (both 2.5 ng/ml), and with ascorbic acid. Cell adhesion and growth/viability was assessed by counted cell number/MTS evaluation. ASCs were stained for differentiation markers of smooth muscle cells, such as alpha-actin, calponin, and myosin heavy chain. On day 7, ASCs on Fb-H-VEGF layers produced both calponin and alpha-actin. An increased FGF concentration caused reduced calponin staining of ASCs. Lack of heparin in fibrin assemblies with growth factors inhibited the production of both alpha-actin and calponin in ASCs. The highest ASCs density/viability was found on Fb-H-VEGF-FGF layer. The proper formulation of fibrin coatings could be favorable for ASCs growth and differentiation and could subsequently support endothelialization of cardiovascular prostheses with endothelial cells.
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Bioactive interfaces between synthetic surfaces and biological fluids
de los Santos Pereira, Andrés ; Brynda, Eduard (advisor) ; Shukurov, Andrey (referee) ; Šubr, Vladimír (referee)
Title: Bioactive interfaces between synthetic surfaces and biological fluids Author: Andrés de los Santos Pereira Institute: Institute of Macromolecular Chemistry, Czech Academy of Sciences Supervisor of the doctoral thesis: RNDr. Eduard Brynda, CSc., Institute of Macromolecular Chemistry, Czech Academy of Sciences Abstract: The application in medicine of label-free affinity biosensors, advanced implants, and blood-contacting devices requires that their surfaces resist non-specific protein adsorption (fouling) and associated complications in blood-derived fluids while displaying immobilized bioreceptors that provide specific biofunctionality. The aim of this thesis was to explore the strategies for the preparation of these antifouling bioactive surfaces. Various types of recently developed antifouling polymer brushes were synthesized and evaluated in terms of their ability to prevent fouling from blood plasma (obtained from various commercial sources and individual donors) as well as thrombus formation when contacted with whole blood. Moreover, single-cell force spectroscopy was utilized to characterize the bacterial adhesion force and energy on these polymer brushes, which were significantly reduced in comparison to various reference substrates. The immobilization of bioreceptors was tackled by means of a...
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In situ study of nuclear acids interactions key for gene expression and therapy based on its silencing
Špringer, Tomáš ; Štěpánek, Josef (advisor) ; Brynda, Eduard (referee) ; Vorlíčková, Michaela (referee)
In this doctoral thesis we study novel analogues based on R06 aptamers and targeting TAR hairpins of the HIV virus by means of surface plasmon resonance biosensor, which allows for sensitive and real-time monitoring of molecular interactions. We investigate seven different modifications placed at nine different positions on the R06 aptamer in order to find out their applicability in the construction of efficient and stable anti-TAR oligonucleotides. We also determine which positions are suitable for substitutions with a modification and interpret the results in the context of the local nucleotide geometries and interactions in the TAR/anti-TAR complex. In this doctoral thesis we further develop a new fluidic system. This fluidic system eliminates sample dispersion and intermixing effects and thus enables accurate monitoring of molecular interactions on the surface of an SPR chip. We also characterize experimental conditions on the surface of an oligonucleotide chip and their relations towards bio-molecular assays. Specifically, we study the shielding effect of monovalent and divalent cations, which are crucial for the interaction of negatively charged oligonucleotides.
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Surface plasmons in optical microstructures and their sensor applications
Adam, Pavel ; Homola, Jiří (advisor) ; Brynda, Eduard (referee) ; Richter, Ivan (referee)
Title: Surface plasmons in optical microstructures and their sensor applications Author: Pavel Adam Institute: Institute of Photonics and Electronics AS CR, v.v.i., Department of Optical Sensors Supervisor of the doctoral thesis: doc. Ing. Jiří Homola, CSc., DSc. Abstract: This work is focused on the study of surface plasmon resonance (SPR) sensor platforms based on wavelength division multiplexing (WDM) of multiple surface plasmons (SPs). These sensors are based on advanced diffraction gratings supporting either conventional or Bragg-scattered SPs, which are simultaneously excited at different wavelengths. These SPs are studied both analytically and numerically using rigorous coupled-wave analysis and an integral approach. WDM of two and three SPs is presented and followed by the method for the analysis of the resolution, noise and cross-sensitivity. This method is employed to analyze the ability of different SPR sensor platforms (supporting WDM of two SPs) to discriminate refractive index (RI) changes in a thin layer at the sensor surface from background RI changes. The WDM SPR sensors based on advanced diffraction gratings prepared by interferometric holography are developed and tested in a model biosensing experiment consisting of the layer-by-layer growth of protein multilayers. The linear WDM of two...
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Sensitive Layers for Optical Biosensors and Protein Chips
Rodriguez Emmenegger, César ; Brynda, Eduard (advisor) ; Lynn, Nicholas Scott (referee) ; Shukurov, Andrey (referee)
Sensitive layers for optical biosensors and protein chips The goal of this thesis was the development of sensitive surfaces for optical affinity biosensors detecting in complex biological media. The practical application of these surface-based technologies has been hampered by protein fouling from biological media, in particular blood plasma, where the vast majority of relevant analytes are present. The work of the thesis was centred in three main foci: Design and preparation of antifouling and non-fouling surfaces Evaluation and conceptualisation of their resistance to fouling from blood plasma and serum as well as other biological fluids Preparation of sensitive layers for detection in complex biological media Three approaches were used to prepare protein resistance surfaces, i) ω-functional self-assembled monolayers (SAM), ii) end-tethered polymers and iii) polymer brushes prepared by surface initiated controlled radical polymerisation. Investigation of proteins in the blood plasma deposits on PEG- based surfaces revealed that some fouling is unavoidable in PEG-based surface modifications. A novel type of non-fouling polymer brushes based on poly[N-(2-hydroxypropyl) methacrylamide] challenged the accepted ideas for the design of protein resistant surfaces. For the first time a...
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