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Proteomics for beginners
Hubálek, Martin ; Vrbacký, M. ; Křenková, Alena
Proteomic tutorial for the beginners will summarise and present current methods to analyse and evaluate proteomic samples. The tutorial will be divided into two parts. The first part will focus on data accquisition process and interpretation of spectra. The second part will focus on protein quantification.
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Structural characterization of dsDNA and transcription factor interactions
Kadavá, Tereza ; Novák, Petr (advisor) ; Hubálek, Martin (referee)
Transcription factors from TEAD protein family play an important role in various eukaryotic regulatory processes. They are partly responsible for cell differentiation and apoptosis due to their involvement in the Hippo signalling pathway. Scientific interest in this protein family is mainly because they are associated with carcinogenesis. DNA-binding domain of TEAD transcription factors interacts with M-CAT element of double-stranded DNA, which is present also in enhancer and exon of C-MYC gene. Interaction between TEAD1 DNA-binding domain and C-MYC dsDNA was investigated in this bachelor's thesis mainly by ion mobility in connection with mass spectrometry using native nESI ionization. For the further analysis of TEAD1-DBD and its complexes with dsDNA, the protein was firstly recombinantly expressed by the optimized protocol in our laboratory. Investigation of TEAD1-DBD and its complexes was done using two IM-MS activations. Firstly, the collision-induced unfolding was performed and afterwards perturbation of the sample by preheating nESI emitter was done. The first activation led to the collision- induced unfolding of some charge states of TEAD1-DBD protein and both protein-DNA complexes. The second activation performed by heating of nESI emitters led to temperature melting of both dsDNA and...
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Optimization of lipopeptide analysis by LC-MS
Kadeřábková, Marta ; Hubálek, Martin (advisor) ; Novák, Petr (referee)
Modification of proteins by lipid structure is relatively common post-translational modification that affects the properties of proteins directly and has a forthright effect on the binding of modified proteins to cell membranes. Some lipoproteins play key role in various pathological processes. Before the proteomic analysis of these proteins, the sample of interest is digested using a protease. The resulting hydrolysate contains both unmodified peptides and peptides bearing a lipid modification. During the subsequent chromatographic separation, the lipopeptides differ significantly from the unmodified peptides. For this reason, the analysis of lipopeptides, lipoproteins respectively, is problematic in terms of separation and detection. The subject of the study of this diploma thesis was the optimization of the method of lipoprotein analysis using liquid chromatography and mass spectrometry. The procedures were tested on lipoprotein Cya A (bifunctional adenylate-cyclase toxin from Bordetella pertussis) and MMTV (matrix protein of mouse mammary tumour virus). First, various sample preparation procedures involving proteolytic cleavage were tested. When enzymatic digestion using trypsin on filter (eFASP) was used, the lipid modification was detected with high degree of reliability. In the next step,...
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Structural characterization of dsDNA and transcription factor interactions
Kadavá, Tereza ; Novák, Petr (advisor) ; Hubálek, Martin (referee)
Transcription factors from TEAD protein family play an important role in various eukaryotic regulatory processes. They are partly responsible for cell differentiation and apoptosis due to their involvement in the Hippo signalling pathway. Scientific interest in this protein family is mainly because they are associated with carcinogenesis. DNA-binding domain of TEAD transcription factors interacts with M-CAT element of double-stranded DNA, which is present also in enhancer and exon of C-MYC gene. Interaction between TEAD1 DNA-binding domain and C-MYC dsDNA was investigated in this bachelor's thesis mainly by ion mobility in connection with mass spectrometry using native nESI ionization. For the further analysis of TEAD1-DBD and its complexes with dsDNA, the protein was firstly recombinantly expressed by the optimized protocol in our laboratory. Investigation of TEAD1-DBD and its complexes was done using two IM-MS activations. Firstly, the collision-induced unfolding was performed and afterwards perturbation of the sample by preheating nESI emitter was done. The first activation led to the collision- induced unfolding of some charge states of TEAD1-DBD protein and both protein-DNA complexes. The second activation performed by heating of nESI emitters led to temperature melting of both dsDNA and...
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Možnosti fixace vzorků pro měření obsahu DNA u ryb průtokovou cytometrií
HUBÁLEK, Martin
This thesis aims to assess the possibility of the usage of various biological fixatives for fish cell and tissues samples in order to extend its storage for later flow cytometric measurement of DNA content. The model species chosen were sterlet and tench, from which three types of samples were obtained: blood and fin tissue of subadult / adult individuals and tail tissue of hatched larvae. Altogether 13 fixation methods were tested for each type of sample of both model species. Methods were chosen based upon their easy feasibility and low time-consumption. The samples were measured on flow cytometer in native state immediately after sampling and placing in physiological saline and after 1, 5 and 10 days of fixation during which they were stored in a fridge or in a freezer at -80 ?C. Their analysis was carried out simultaneously with standards native cells from tench fin tissue when investigating sterlet samples, and commercially available fixed trout erythrocytes for tench samples. A fluorochrome used was 4',6-diamidine-2'-phenylindole dihydrochloride (DAPI; with excitation/emission maxima 358 / 461 nm). Based on the evaluation of coefficients of variation (CV) of fixed samples and the changes in their fluorescence levels in comparison with native state, optimal procedures for extended storage of all types of samples from both model species are suggested.
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Induction of gynogenesis in sterlet
HUBÁLEK, Martin
This bachelor thesis deals with the induction of gynogenesis in sturgeons. Theoretical part of thesis describes general basics of the induction of gynogenesis in fish and focuses on the published results of gynogenesis in sturgeon. It recapitulates the methods used and the different steps of gynogenesis induction and, last but not least, the importance of its practical use. Practical part of thesis acquaints with the results of experimental induction of mitotic gynogenesis in sterlet. It recapitulates the effectiveness of different steps, concludes on correctness of the performed process, compares the obtained results and brings one of the first information about optimization of the mitotic gynogenesis protocol in sturgeons.
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