|
|
Construction and evaluation of a novel protein mechanosensor
Kolomazníková, Veronika ; Rösel, Daniel (advisor) ; Novotný, Ivan (referee)
The protein p130Cas (human ortholog BCAR1) is a major substrate for phosphorylation by the Src family kinase and plays a central role in oncogenic transformation. Increased level of BCAR1 correlates with primary tumour growth and cancer progression. Localized to focal adhesion, p130Cas serves as a mechanosensor and mediates key interactions with the extracellular environment. The structure of p130Cas is crucial for its function, mainly the anchoring domains SH3 and CCH, together with the substrate domain which is extended when under tension. This Master's thesis presents a newly developer FRET mechanosensor based on the structure of p130Cas. The sensor utilizes the anchoring domains of p130Cas for proper localization to focal adhesions, where it can detect tension in living cells. Key words: p130CAS, FRET, focal adhesions, mechanosensing
|
|
|
Real-time monitoring of cellular processes - current approaches
Švecová, Iva ; Hodný, Zdeněk (advisor) ; Groušl, Tomáš (referee)
This thesis aims to provide an overview of real-time live-cell imaging methods with a focus on the signalling pathways. The first, most thorough section is about fluorescence methods and is followed by sections about bioluminescence and label-free methods. In the fluorescence section, we will at first introduce the types of fluorophores and respective labelling approaches. Subsequently, we will go through the individual techniques, starting with single-fluorophore and FRET biosensors, continuing with kinetic modelling approaches, a FLIM method used to detect changes in the cellular environment, and ending with two methods used to improve the resolution. With each technique, we will shortly explain the working principle and look at the examples at which this method was used. Finally, we will look at the example of live-cell imaging of one signalling cascade.
|
|
|
Stability of vesicular systems using fluorescence spectroscopy techniques
Máčala, Jakub ; Venerová, Tereza (referee) ; Mravec, Filip (advisor)
This thesis is focused on possibility of studying stability and fusion of catanionic vesicles with Förster resonance energy transfer. The mainly used technique was Time-Correlated single photon counting. Firstly, excitation and emission spectra of chosen probes were measured and donor-acceptor pairs were suggested: 5-hexadecanoylaminofluorescein with Octadecyl Rhodamine B, Bodipy 493/503 with rhodamine or DiI, perylene with fluorescein, DiO with DiI. Then, time-resolved measurements of suggested pairs from environment of catanionic vesicles with different content of cholesterol were made in order to track the FRET associated with fusion of vesicles. It was found out, that it is not possible to use DiO as a donor because of it’s inefficient solubilisation into vesicles. It is also not possible for Bodipy to be used as a donor, because of it‘s excimer formation. In case of using fluorescein as a donor, it was found, that there is ongoing homo-fret between fluorescein molecules. Thanks to this, fusion was tracked by addition of unstained vesicles. It was also possible to track fusion in longer period of time. Also perylene-fluorescein pair was found to be capable of tracking the fusion, but with the exception of vesicles with content of cholesterol of 43 mol. %, tracking of fusion was possible only in short period of time.
|
|
|
Construction and evaluation of a novel protein mechanosensor
Kolomazníková, Veronika ; Rösel, Daniel (advisor) ; Novotný, Ivan (referee)
The protein p130Cas (human ortholog BCAR1) is a major substrate for phosphorylation by the Src family kinase and plays a central role in oncogenic transformation. Increased level of BCAR1 correlates with primary tumour growth and cancer progression. Localized to focal adhesion, p130Cas serves as a mechanosensor and mediates key interactions with the extracellular environment. The structure of p130Cas is crucial for its function, mainly the anchoring domains SH3 and CCH, together with the substrate domain which is extended when under tension. This Master's thesis presents a newly developer FRET mechanosensor based on the structure of p130Cas. The sensor utilizes the anchoring domains of p130Cas for proper localization to focal adhesions, where it can detect tension in living cells. Key words: p130CAS, FRET, focal adhesions, mechanosensing
|
|
|
Genetically encoded biosensors of cellular tension and their use in cellular biology
Pelantová, Markéta ; Rösel, Daniel (advisor) ; Lánský, Zdeněk (referee)
1 Abstract and key words Mechanical forces have great impact on the life of cells. They influence cell proliferation, migration or differentiation and defects in cellular mechanosensing were reported to be the cause of various diseases, such as deafness, atherosclerosis or cancer. However, mechanisms of mechanical sensing are not thoroughly examined and not many tools for doing such research are available. Genetically encoded FRET-based biosensors are one of the existing methods for studying transfer of mechanical signal in cells. It is a non-invasive method allowing to observe changes in mechanical tension across proteins in living cells. In this thesis, different types of existing genetically encoded FRET-based tension biosensors are introduced together with the process of their development and knowledge gained by their use in research. Key words: mechanical force, mechanosensing, FRET, tension sensor, biosensor development
|
|
|
Advanced Fluorescence Techniques in Research on Micellar Systems and Their Interactions with Biopolymers
Holínková, Petra ; Burgert, Ladislav (referee) ; Táborský, Petr (referee) ; Pekař, Miloslav (advisor)
The dissertation thesis deals with study of advanced steady-state and time-resolved fluorescence techniques, which can be used for study of micellar systems properties. Selected fluorescence techniques were used for characterization of Septonex and CTAB cationic micellar systems and theirs interactions with hyaluronan. Fluorescent probe pyrene was used for determination of critical micelle concentration (CMC) and micellar aggregation number of these surfactants. The changes of fluorescence behaviour of fluorescein and prodan were studied in wide concentration range of Septonex. Next chapter of thesis deals with study of Förster resonance energy transfer between perylene and fluorescein in Septonex and CTAB micellar solutions and the effect of hyaluronan addition to these systems. Also steady-state and time-resolved fluorescence anisotropy studies were used for research of the effect of hyaluronan addition to micellar solutions. The last chapter of this thesis is focused on photophysical behaviour of Prodan in different solutions (water, Septonex solutions below CMC, hyaluronan solution, Septonex micellar solution and Septonex micellar solution with hyaluronan), which was discussed on the basis of time-resolved emission spectra.
|
|
|
Influence of lipid composition and model peptides on lateral organization of lipid layers
Veľas, Lukáš ; Heřman, Petr (advisor) ; Malínský, Jan (referee)
Oxidized phospholipids (OxPLs) are known to be present in living organisms due to oxidative stress. However, the physiological function of OxPLs is still not fully understood. They have been shown to be present in many inflammatory diseases such as atherosclerosis and neurodegenerative diseases like Parkinson's and Alzheimer's disease. In this work we present the influence of two truncated OxPLs on the lateral heterogeneity of a model lipid membrane. Specifically, we studied the effect of 1-palmitoyl-2-(5'-oxo-valeroyl)-sn-glycero-3- phosphocholine (POVPC) and 1-palmitoyl-2-glutaryl-sn-glycero-3-phosphocholine (PGPC) on the formation of nanodomains present in giant unilamellar vesicles containing 1,2- dioleoyl-sn-glycero-3-phosphocholine (DOPC), cholesterol and sphingomyelin. Only few techniques are capable of detecting nanometer-sized domains in the membrane with high resolution. Time resolved Förster resonance energy transfer (TR-FRET) combined with Monte Carlo (MC) simulations provide a strong tool not only to detect lateral heterogeneities but also characterize them with the resolution of 2 nm. Profound effects on the nanodomain size were observed in the presence of both studied OxPLs and differences were detected, as PGPC with a carboxylic group drives formation of larger nanodomains than POVPC...
|
|
|
Využití simulace jako komplementární metody pro interpretaci experimentálních dat ve výzkumu fluorescence jednotlivých molekul
CARDA, Zdeněk
Fluorescence single-molecule methods represent mighty tools for researchers in the field of structural and molecular biology. These methods are bringing in many advantages when compared to the statistical data processing of multi-molecular species. We can directly compare true statistical distributions and their kinetics. Here belongs fluorescence correlation spectroscopy, FRET and burst variance analysis. As the research advances, new methods are being developed which at the very beginning do not have proper analytical relations for data interpretation and which experimental limits we can't tell. That is the moment when the computer simulations can be used to our advantage. They can help us to specify the right direction of the future research, which is a great money-saver, while opening new perspectives and insights into the explored matter. Correct interpretation of the simulations results is key for the consequent defining of new theoretical models.
|
|
|
Spliceosome assembly
Hausnerová, Viola ; Staněk, David (advisor) ; Chalupníková, Kateřina (referee)
Pre-mRNA splicing is a process in which introns are removed from eukaryotic transcripts and exons are ligated together. Splicing is catalyzed by spliceosome, a large ribonucleoprotein complex composed of five small nuclear RNAs and more than 100 additional proteins, which recognizes 5' splice site, branch point site and 3' splice site and performs two transesterification reactions to produce mRNA molecules. 5' splice site is recognized by U1 snRNP and U2 auxiliary factor (U2AF) is involved in branch point and 3' splice site recognition in the early splicing complex. There is some evidence of splice sites cooperation during intron recognition in vitro but little is known about the situation in vivo. Using Fluorescence resonance energy transfer (FRET) and RNA immunoprecipitation (RIP) methods, we have investigated the early stages of spliceosome assembly. We have employed splicing reporters based on -globin gene and MS2 stem loops to detect interactions of proteins on RNA molecule directly in the cell nucleus. Results of FRET indicate that intact 5' splice site is required for U2AF35 interaction with 3' splice site and that U1C recruitment to 5' splice site is partially limited upon 3' splice site mutation. We have also confirmed by RIP that U2 snRNP association with pre-mRNA molecule requires presence of 5'...
|
|
| |
guest ::
