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Modification of the focusing part of the table-top setup for Laser Induced Breakdown Spectroscopy (LIBS)
Borovský, Ján ; Prochazka, David (referee) ; Samek, Ota (advisor)
This bacheolor thesis solves functional modifications of the foccusing part of the table-top setup for laser induced breakdown spectroscopy LIBS. Main requirements for modified draft includes increasing view field of the navigation camera, increasing the setup’s aperture and prevention of the camera destruction by radiation of plasma. These requirements were fulfilled in new draft of optical stand including possible solution as enlarging focusing lens, new dielectric mirror and mechanical iris shutter. Some elements of proposed solution will be used in suggestion of Tescan company‘s new interaction chambers for LIBS analysis.
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Optical micromanipulation and Raman spectroscopy of cells in microfluidic systems
Klementová, Tereza ; Samek, Ota (referee) ; Mravec, Filip (advisor)
This diploma thesis deals with optimization of analysis process and measuring antibiotics induced changes in E. coli cells via Raman spectroscopy, LTRS and microfluidic systems. Optical micromanipulation by a laser beam allows noncontact and noninvasive manipulation of objects on scale 10^-5–10^-8 m, for example bacterial cells. Microfluidic device consists of microchannels and microchambers in transparent polymer and it is used for isolation, observation and cultivation of bacterial cells. Combination of these methods gives an effective tool for observation, manipulation and analysis of microorganisms. E. coli is a microorganism potentially pathogenic for humans and faster detection of its sensitivity to antibiotic treatment would make the whole process of diagnostics and treatment easier. We performed laser tweezer-Raman spectroscopy and conventional Raman spectroscopy of bacterial cells and cells under antibiotic stress and collected Raman spectra and characteristic areas were compared with literature to establish the reliability and usefulness of this method.
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Evolutionary engineering of cyanobacteria with respect to PHA accumulation
Vašířová, Kristýna ; Slaninová, Eva (referee) ; Samek, Ota (advisor)
The aim of this diploma thesis was to subject selected cyanobacterial strains to adaptive evolution and subsequently investigate the properties of the resulting adapted strains, especially their changes related to polyhydroxyalkanoates (PHA) accumulation. The theoretical part of the work describes in more detail the issue of cyanobacteria, PHA and their interconnection in the field of evolutionary engineering. Cyanobacterial strains Synechocystis sp 6803 and. Synechocystis salina CCALA 192 were used for evolutionary experiments. Selection pressures of hydrogen peroxide and copper. were applied to selected representatives. The resulting cultures and their ability to accumulate PHA were subsequently assessed by gas chromatography. Both of these selection pressures proved to be unsuitable, as strong growth inhibition was observed after their application to cultures, which did not allow the application of evolutionary engineering methods. In the second half of the experimental part, the provided adapted strains to 6% NaCl were monitored. Adaptation has been shown to have a positive effect on microorganisms, as they have a higher biomass content, better stress resistance and a slight increase in PHA accumulation.
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Design of optomechanical module for chemical mapping using Laser-Induced Breakdown Spectroscopy
Švábíková, Anna ; Samek, Ota (referee) ; Pořízka, Pavel (advisor)
Tato diplomová práce se zabývá návrhem optomechanického modulu pro chemické mapování metodou spektroskopie laserem buzeného plazmatu (LIBS). Cílem je vyvinout modul, který bude umožňovat analýzu spektrálních čar zinku v ultrafialové (UV) oblasti. V práci jsou popsány teoretické základy metody LIBS a následně je provedena rešerše zaměřená na problematiku dálkové LIBS analýzy. V diplomové práci jsou prezentovány možné optické návrhy fokusační a sběrné optiky, z nichž jsou vybrané následně otestovány. Výsledkem práce je konstrukční návrh modulu.
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Multi-element analysis of soft tissues in paraffin by laser induced breakdown spectroscopy
Kopřivová, Hana ; Samek, Ota (referee) ; Pořízka, Pavel (advisor)
This thesis deals with the analysis of paraffin-embedded soft tissues using laser-induced breakdown spectroscopy (LIBS) and the complementary technique of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Specifically, the work focuses on optimizing soft tissue LIBS measurement parameters for femtosecond and nanosecond pulsed laser ablation at different wavelengths on mouse kidneys as a soft tissue model matrix. In addition, elemental analyses were performed on several samples of the most commonly occurring human skin cancers (malignant melanoma, basal cell carcinoma, and squamous cell carcinoma) using the above-mentioned analytical methods. Maps of the spatial distributions of biogenic elements were obtained. Aim of this work is to show a potential of new analytical methods that are not intended to replace the classical histological examination completely. However, these techniques could be used for preliminary screening of tumor tissue or purely as a complementary technique for histologists to diagnose cancers. Both methods could offer a completely new perspective on soft tissue cancer diagnosis in the future.
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Analysis of secondary metabolites from Streptomyces by Raman spectroscopy in vivo
Mikulová, Adéla ; Petříčková, K. ; Bobek, J. ; Chroňáková, Alica ; Samek, Ota ; Pilát, Zdeněk
The work deals with the study of Raman spectra of secondary metabolites of bacteria of the genus Streptomyces, especially polyene antifungal agents. Purified isolates and commercial standards of these compounds were used to obtain reference spectra from which spectral markers characterizing specific details of the chemical structure were derived. Verification of the observed markers was performed using in silico Raman spectra predictions. Subsequently, these findings were used for the spectroscopic characterization of the composition of secondary metabolites in vivo, directly in bacteria growing on a solid medium. The developed methodologies will help to optimize the conditions for the biotechnological production of antibiotics.
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SERS-TAGS: Selective immobilization and detection of bacteria using specific antibodies and surface-enhanced Raman scattering
Benešová, Markéta ; Bernatová, Silvie ; Samek, Ota ; Pokorná, Zuzana ; Mika, Filip ; Kizovský, Martin ; Pilát, Zdeněk
Raman spectroscopy is a non-destructive instrumental analytical technique based on Raman scattering, which is the inelastic scattering of photons that occurs when interacting with electrons in chemical bonds. With the help of Raman spectroscopy, chemical compounds, their mixtures and biological samples, including living organisms, can be analyzed very quickly, non-contactly and non-destructively. The performed measurements can be compared with spectra databases. A problem with Raman spectroscopy is that samples sometimes give a weak signal that is often overlaid by intense fluorescence. SERS (surface-enhanced Raman spectroscopy) is used to amplify Raman scattering.
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Development and optimization of laser assisted spark discharge optical emission spectroscopy
Kleštinec, Róbert ; Samek, Ota (referee) ; Pořízka, Pavel (advisor)
This master's thesis addresses the improvement of the detection capability and sensitivity of the LIBS method through the utilization of a secondary energy source in the form of spark discharge. The use of spark discharge for plasma excitation significantly extends its lifetime and provides an opportunity to enhance the analytical properties of the existing LIBS system. In the experimental part, both conductive and non-conductive samples were analyzed. In cement paste samples, chlorine was successfully detected without the need for additional rare gas atmosphere.
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Multi-element analysis of soft tissues in paraffin by laser induced breakdown spectroscopy
Kopřivová, Hana ; Samek, Ota (referee) ; Pořízka, Pavel (advisor)
This thesis deals with the analysis of paraffin-embedded soft tissues using laser-induced breakdown spectroscopy (LIBS) and the complementary technique of laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS). Specifically, the work focuses on optimizing soft tissue LIBS measurement parameters for femtosecond and nanosecond pulsed laser ablation at different wavelengths on mouse kidneys as a soft tissue model matrix. In addition, elemental analyses were performed on several samples of the most commonly occurring human skin cancers (malignant melanoma, basal cell carcinoma, and squamous cell carcinoma) using the above-mentioned analytical methods. Maps of the spatial distributions of biogenic elements were obtained. Aim of this work is to show a potential of new analytical methods that are not intended to replace the classical histological examination completely. However, these techniques could be used for preliminary screening of tumor tissue or purely as a complementary technique for histologists to diagnose cancers. Both methods could offer a completely new perspective on soft tissue cancer diagnosis in the future.
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Raman microspectroscopy of living cells and biological tissues
Moudříková, Šárka ; Mojzeš, Peter (advisor) ; Matthäus, Christian (referee) ; Samek, Ota (referee)
Title: Raman microspectroscopy of living cells and biological tissues Author: Šárka Moudříková Department / Institute: Institute of Physics of Charles University Supervisor of the doctoral thesis: doc. RNDr. Peter Mojzeš, CSc., Institute of Physics of Charles University Abstract: Raman microscopy combines Raman spectroscopy with optical confocal microscopy and thus provides information on chemical composition of a sample with a µm3 resolution. In this thesis, Raman microscopy has been used to study microalgae-unicellular photosynthetic organisms that are greatly relevant for the Earth's environment as well as for biotechnological applications. Raman microscopy of photosynthetic organisms struggles with a highly intensive background of the spectra, which is formed by fluorescence of cellular photosynthetic apparatus. In this thesis, we have developed a fast and reliable photobleaching method that suppresses the unwanted background; this method has enabled us to study intracellular distribution of algal biomolecules such as proteins, starch, lipids and polyphosphate. We have investigated an evolution of these structures during a cell cycle of a model microalga Desmodesmus quadricauda. Next, we have developed a method for quantitative analysis of polyphosphate in a cellular culture of a microalga Chlorella...
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