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Module for a Lecture Browser for Correcting the Output of Speech Recognizer
Srb, Pavel ; Schwarz, Petr (referee) ; Fapšo, Michal (advisor)
The core of my work is a browser upgrade, which contains user based transcript-correction from speech recognizer, including creation of transcription storage and sharing server. Introduction of my work mentions motivation for multimodal usage in computer science sphere. Further in text is list of speech recognition reasearch categories from Faculty of Information Technology. The main attention is given to description of multimodal browser used for browser technology testing and presentation. In future, the multimodal browser is supposed to be used as a study-utility or common user multimodal player. Required features of this player, concepts, realization description and whole C++, wxWidgets, XML, HTTP based architecture is defined.
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Dynamical Behaviour of Matrix Proteins from Mason-Pfizer Monkey Virus
Srb, Pavel ; Lang, Jan (advisor) ; Žídek, Lukáš (referee) ; Brus, Jiří (referee)
Title: Dynamical behaviour of matrix proteins from Mason-Pfizer Monkey Virus Author: Pavel Srb Department: Department of Low temperature physics Supervisor: doc. RNDr. Jan Lang, PhD. Abstract: We studied the oligomeric properties of betaretroviral nonmyristoylated ma- trix protein (MA) and its R55F mutant from the Mason-Pfizer monkey virus in solution by means of NMR spectroscopy. We have proven that the wild- type (WT) MA forms oligomers in solution. The final model of oligomeriza- tion of the WT MA was derived by concerted use of chemical shift mapping and diffusion-ordered spectroscopy measured on a set of protein samples with varying concentrations. We found that the Mason-Pfizer monkey virus WT MA exists in a monomer-dimer-trimer equilibrium in solution. Further a combination of NMR relaxation measurements and advanced analysis of molecular dynamics simulation trajectory provided an unprecedentedly de- tailed insight into internal mobility of matrix proteins of the Mason-Pfizer monkey virus. Strong evidence have been obtained that the oligomerization capacity of the wild-type matrix protein is closely related to the enhanced dynamics of several parts of its backbone on a nanosecond time scale. In- creased flexibility has been observed for two regions: the loop between he- lices α2 and α3 and the C-terminal...
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Structural properties and stability of DNA hairpins characterized by NMR spectroscopy
Socha, Ondřej ; Římal, Václav (advisor) ; Srb, Pavel (referee)
CArG box is a highly conservative DNA motif found in Serum Response Element (SRE), which regulates expression of c-fos gene. In this thesis, short oligodeoxynucleotides containing CArG box were measured using nuclear magnetic resonance spectroscopy to evaluate their ability to preferentially form hairpin over duplex. 1H spectra were measured at temperature range (274-360) K. We acquired thermodynamic parameters of the transition between hairpin and single strand by fitting the temperature- dependent chemical shifts. The hairpin structure of our oligonucleotide samples was confirmed by non- B-DNA patterns in NOESY spectra, absence of concentration dependence of melting, and other pieces of evidence. Thus, occurrence of unusual DNA conformation of CArG box in native DNA, potentially even cruciform is highly possible. This could explain the high affinity between SRE and its transcription factor. Powered by TCPDF (www.tcpdf.org)
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The presence and stability of DNA mini-hairpins
Bušková, Hana ; Římal, Václav (advisor) ; Srb, Pavel (referee)
The secondary structure of DNA is variable and depends on the sequence of nu- cleotides in a strand. While DNA can form duplexes, formations of three, four, or even a single strand have been observed in vivo and in vitro as well. In this thesis, we study the effect of small changes of oligonucleotide sequences on the stability of hairpins formed by DNA heptamers by 1 H nuclear magnetic resonance (NMR) spectroscopy. Suitable DNA sequences were selected based on symmetry rules and stability prediction by near- est neighbor model. Two-dimensional 1 H -1 H NOESY spectra were used to assign the 1 H resonances of aromatic hydrogens. Variable-temperature 1D spectra served for ob- taining melting curves, from which the thermodynamic properties of the hairpins were determined. The presence of hairpins in the solutions was confirmed by the character of the NOESY spectra, independence of melting temperature on oligonucleotide concen- tration, and comparison of competing melting-curve models of duplex and hairpin. Our results point out the importance of the order of the stem base pairs and contribute to the description of the extraordinary stability of DNA mini-hairpins. 1
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Structural properties and stability of DNA hairpins characterized by NMR spectroscopy
Socha, Ondřej ; Římal, Václav (advisor) ; Srb, Pavel (referee)
CArG box is a highly conservative DNA motif found in Serum Response Element (SRE), which regulates expression of c-fos gene. In this thesis, short oligodeoxynucleotides containing CArG box were measured using nuclear magnetic resonance spectroscopy to evaluate their ability to preferentially form hairpin over duplex. 1H spectra were measured at temperature range (274-360) K. We acquired thermodynamic parameters of the transition between hairpin and single strand by fitting the temperature- dependent chemical shifts. The hairpin structure of our oligonucleotide samples was confirmed by non- B-DNA patterns in NOESY spectra, absence of concentration dependence of melting, and other pieces of evidence. Thus, occurrence of unusual DNA conformation of CArG box in native DNA, potentially even cruciform is highly possible. This could explain the high affinity between SRE and its transcription factor. Powered by TCPDF (www.tcpdf.org)
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Studium teplotně citlivých porfyrinů a jejich supramolekulárních komplexů
Hrubovský, Martin ; Kouřilová, Hana (advisor) ; Srb, Pavel (referee)
Study of thermoresponsive porphyrins and their supramolecular complexes Abstract: We studied the water-soluble artificial compound meso-tetrakis{3,4,5-tris[2-(2-(2- methoxyethoxy)ethoxy)ethoxy]phenyl}porphyrin prepared at NIMS, Japan, using the high-resolution NMR spectroscopy experimental method. We observed its LCST-type phase separation and applied the Flory-Huggins theory of polymer solutions in order to find its phase diagram (binodal and spinodal curves of the phase separation) and we also obtained molar enthalpies, entropies and critical temperatures of its phase separation; from the Flory-Huggins theory we discovered that its molecules form dimers in aqueous solutions. We also studied its host-guest interactions with the S-camphorsulfonic acid; we learned that the porphyrin binds cations and the porphyrin dimers break down when dissolved cations are available for complexation. We observed no phase separation in chloroform. We obtained no proof of the existence of molecular stacks larger than dimers. 1
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Dynamical Behaviour of Matrix Proteins from Mason-Pfizer Monkey Virus
Srb, Pavel ; Lang, Jan (advisor) ; Žídek, Lukáš (referee) ; Brus, Jiří (referee)
Title: Dynamical behaviour of matrix proteins from Mason-Pfizer Monkey Virus Author: Pavel Srb Department: Department of Low temperature physics Supervisor: doc. RNDr. Jan Lang, PhD. Abstract: We studied the oligomeric properties of betaretroviral nonmyristoylated ma- trix protein (MA) and its R55F mutant from the Mason-Pfizer monkey virus in solution by means of NMR spectroscopy. We have proven that the wild- type (WT) MA forms oligomers in solution. The final model of oligomeriza- tion of the WT MA was derived by concerted use of chemical shift mapping and diffusion-ordered spectroscopy measured on a set of protein samples with varying concentrations. We found that the Mason-Pfizer monkey virus WT MA exists in a monomer-dimer-trimer equilibrium in solution. Further a combination of NMR relaxation measurements and advanced analysis of molecular dynamics simulation trajectory provided an unprecedentedly de- tailed insight into internal mobility of matrix proteins of the Mason-Pfizer monkey virus. Strong evidence have been obtained that the oligomerization capacity of the wild-type matrix protein is closely related to the enhanced dynamics of several parts of its backbone on a nanosecond time scale. In- creased flexibility has been observed for two regions: the loop between he- lices α2 and α3 and the C-terminal...
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Module for a Lecture Browser for Correcting the Output of Speech Recognizer
Srb, Pavel ; Schwarz, Petr (referee) ; Fapšo, Michal (advisor)
The core of my work is a browser upgrade, which contains user based transcript-correction from speech recognizer, including creation of transcription storage and sharing server. Introduction of my work mentions motivation for multimodal usage in computer science sphere. Further in text is list of speech recognition reasearch categories from Faculty of Information Technology. The main attention is given to description of multimodal browser used for browser technology testing and presentation. In future, the multimodal browser is supposed to be used as a study-utility or common user multimodal player. Required features of this player, concepts, realization description and whole C++, wxWidgets, XML, HTTP based architecture is defined.
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