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The role of alternative splicing in plants
Földi, Marek ; Klodová, Božena (advisor) ; Fischer, Lukáš (referee)
Alternative splicing is a mechanism of gene expression regulation that maintains, regulates, and creates genomic diversity and tissue specificity in plants. It involves the differential joining of exons in precursor mRNAs, leading to multiple mRNA isoforms from a single gene. The formation of these isoform variants and their subsequent translation leads to subfunctionalization of proteins, generating diversity in structure and function. Therefore, alternative splicing is often important in various biological processes in plants, such as development, stress response, immunity, and reproduction. Key types of alternative splicing events include intron retention, exon skipping, alternative 5'/3' splice sites, and mutually exclusive exons. Regulation of alternative splicing involves cis-regulatory elements and trans- acting protein factors such as serine/arginine-rich (SR) proteins and heterogeneous nuclear ribonucleoproteins (hnRNPs). This thesis aims to summarise the mechanisms and consequences of alternative splicing in plant development, including maturation of male and female gametophytes, meiosis, stress, and cell differentiation. It also describes methodological approaches that allow for a genome-wide study of alternative splicing, including microarrays, RNA-seq, and PCR. A better understanding of...
Electrochemical determination of DNA using flow injection analysis
Jasenovský, Marek ; Dejmková, Hana (advisor) ; Fischer, Jan (referee)
6 Abstract The aim of this work was to create a method for electrochemical detection of DNA in a flow system and subsequently evaluate its functionality and usability. Prior to actual measurement in the flow system, an evaluation of a suitable type of working electrode was performed in a batch measurement, where a basal plane pyrolytic graphite electrode (BPPGE) was selected from the evaluated types of working electrodes. For signaling the sample zone on the surface of the working electrode in the flow arrangement, the recording of the dependence of the first derivative of current response with respect to time (dI/dt) was tested. For this measurements, a flow rate of 0,4 ml·min−1 was evaluated as optimal conditions, using a 0,35 mm-thick PTFE spacer film with a volume of 1,5 µl above the working electrode and a time delay prior stopping the flow 0,5 s after exceeding the set threshold of the dependence of dI/dt with respect to time. During the repeatability check of the procedure for automatic stopping of the sample zone on BPPGE, instability of acetate buffer noise (pH 5) was found, which greatly complicated long-term use of the procedure, and an alternative method of dispensing was therefore sought. For this purpose, a new 3D printed electrochemical cell with a dispensing hole directly into the cell...
Risk assessment and prediction of natural fires in the immediate vicinity\nsurface sources of drinking water.
Trnka, Miroslav ; Kudláčková, Lucie ; Čermák, P. ; Balek, Jan ; Novotný, Jan ; Homolová, Lucie ; Semerádová, Daniela ; Brovkina, Olga ; Štěpánek, Petr ; Zahradníček, Pavel ; Skalák, Petr ; Bláhová, Monika ; Benáček, Patrik ; Fischer, Milan ; Sedlák, Pavel ; Janouš, Dalibor ; Žalud, Zdeněk ; Marek, Michal V. ; Možný, M. ; Hájková, L. ; Chuchma, F. ; Knozová, G. ; Beranová, J. ; Zatloukal, V. ; Albert, J. ; Mašková, R. ; Cienciala, E. ; Vizina, A. ; Nesládková, M. ; Melišová, E. ; Hanel, M.
The methodology formulates a procedure for assessing the risks of the occurrence and spread of natural fires in the immediate vicinity of surface sources of drinking water. The methodology\nproposes methods for estimating the consequences of natural fires on surface water quality, forecasting the change in the risk of fires due to climate change and the procedure for determining the risk of secondary pollution of reservoirs due to changes in run off after a natural fire. On this basis, the methodology proposes and diversifies preventíve and operational measures.The measures were designed in connection to modeling results for the Hadce pilot síte near the Švihov reservoir and the experience with the adverse effects of extensive deforestation on the water quality in the Vranov and Vír reservoirs.
Role of sequence context in DNA methylation
Polák, Jan ; Fischer, Lukáš (advisor) ; Širl, Marek (referee)
Cytosine methylation of DNA is a pivotal epigenetic mark, which contributes to the regulation of the gene expresion, silencing of transposable elements, and co-defines chromatine state. There are three cytosine contexts: CG, CHG and CHH (where H stands for C, A, or T). Arabidopsis thaliana (and plants in general) has an arsenal of molecular mechanisms capable of cytosine methylation in all of its contexts. That said, there are two tasks at hand: maintaining of pre-existing methylation and if need be, creating new methylated spots. The actual process of maintaining of the methylation depends on the cytosine context. Methylation of symmetrical contexts of CG and CHG can utilize the information about the methylation pattern from the second DNA strand. The aymmetrical context of CHH, and also CHG need to look for this information elsewhere: in the methylation of the lysine 9 of H3 histone. This creates a self-reinforcing loop and a crosstalk between two epigenetic mechanisms. Maintaince of methylation of CHH is also navigated by small RNA complementary to the locus in question. This mechanism of enzyme navigating by RNA is also used in establishing a new methylated site for all of the contexts. CG methylation is most prevalent in both heterochromatine and euchromatine. It also has a special functions...
Utilization of biotechnological method in growing of technical hemp
Širl, Marek ; Zelenková, Sylva (advisor) ; Fischer, Lukáš (referee)
Hemp (Cannabis sativa L.) is a multi-use crop, able to provide fibre celulose and hurds for industrial treatment biomass for energy conversion and produces secondary metabolites useful for pharmaceutical application. For its resistence to stress and ability to accumulate high concentration of heavy metals it can be potentialy used for phytoremediation. The aim of current research is the development of new strains, with specialy improved qualities and the enhancement of its applicability. Besides traditional breeding methods, genetic manipulation might be the possible tool. What is currently discussed is finding optimal conditions allowing efective in vitro cultivation as a basic assumption of genetic manipulation. Hemp transformation via Agrobacterium tumefaciens co-cultivation might be the appropriate technic.
Leaf area index development and radiation use efficiency of a poplar short rotation coppice culture
Tripathi, Abishek ; Fischer, Milan ; Trnka, Miroslav ; Orság, Matěj ; Vanbeveren, S. ; Marek, Michal V.
Leaf area index (LAI) is the most appropriate parameter for analyzing canopy structure and crop productivity. LAI and radiation use efficiency (RUE) were estimated to evaluate the productivity of a short rotation coppice culture of a poplar clone. RUE was calculated as the ratio between total aboveground woody biomass and available photosynthetic active radiation (PAR) accumulated during one growing season. Prior to coppicing, LAI reached a maximum value of 7.3 (in 2009), whereas the maximum LAI after coppicing was 6.8 (in 2012). The maximum RUE reached prior to coppicing was 0.25 g mol−1 (in 2009), while after coppicing it was 0.20 g mol−1 (in 2012), which did not represent a significant difference (p > 0.05).
The Construction and Use of the Time Input-Output Tables in context of the Semi-dynamic Input-Output Model
Zbranek, Jaroslav ; Fischer, Jakub (advisor) ; Hronová, Stanislava (referee) ; Rojíček, Marek (referee)
The aim of the dissertation thesis is to develop a methodology of the compilation of symmetric Time Input-Output tables under the conditions of the Czech Republic. The following aim is to create an input-output model which is based on the compiled symmetric Time Input-Output tables. For the practical applications of this model it is crucial to link the created Input-Output model with the Semi-Dynamic Input-Output model. Semi-Dynamic Input-Output model in the conception of the submitted dissertation thesis takes into account several multiplier effects and presents more comprehensive tool for the use of the Input-Output analyses in this way. The first chapter focuses on the development of the issues linked to the Input-Output tables and analyses on the territory of the Czech Republic and in the world as well. The second chapter which is also theoretical is focused on mapping of different kinds of Input-Output analyses which are done in the world using Physical, Time or Hybrid Input-Output tables. The third chapter is a purely methodological because here it is described the methodology of the compilation of symmetric Time Input-Output tables as well as methodological approach to the various sensitivity analyses. The fourth chapter focuses on the creation Semi-Dynamic Input-Output model and on the formal linking with the Input-Output model based on the Time Input-Output tables. The last fifth chapter is focused analytically. Methods described in the third chapter are applied on the official published data on the Czech economy. The analytical chapter is perceived in the submitted dissertation thesis as a tool for the sensitivity analysis in the sense of validation of the quality of the compiled Time Input-Output tables.
Estimation of above ground woody biomass of SRC hybrid poplar clone J-105 in different fertilizer treatments in Czech-Moravian highland
Tripathi, A.M. ; Trnka, Miroslav ; Fischer, Milan ; Orság, Matěj ; Fajman, M. ; Marek, Michal V. ; Žalud, Zdeněk
Short rotation coppice poplar hybrid clone J-105 (Populus nigra x P. maximowiczii) is studied as an alternative source of bio-energy in the region of Czech-Moravian Highland. The plantation was established in 2001 at the locality Domanínek in the vicinity of Bystřice nad Pernštejnem (Czech Republic, 49o32’N, 16o15’E and altitude 530 m a. s. l.) where mean annual rainfall of 609 mm and mean annual temperature of 7.2oC was recorded between 1981 and 2010. The total area planted with the clone was close to 1.5 ha with total plantation area being close to 3.5 ha. The plantation with planned density of 9,216 trees ha-1was established on the former agricultural land and the length of the rotation cycle was set to 6-8 years. At the beginning of the second rotation period i.e. in spring 2009 (following winter harvest), the plantation was divided into four randomized blocks with different nutrient treatments and three replicates (4×3). These treatments comprised of application of mineral NPK fertilizer (nitrogen 305 kg ha-1, phosphorous 154 kg ha-1 and potassium 291 kg ha-1), sewage sludge (4200 kg/ha-1) and ash (1000kg ha-1) and lime (5 ton ha-1), while control was with natural nutrients content only (deposition and leaves mineralization). The objectives of the study were to estimate the above ground annual yields (based on allometry and stem inventory), the mortality and the shoot to stump ratio as the main productivity characteristics.
Potřeba kvalitativních změn norem se blíží
Marek, Pavel ; Laurie Kennedy, D.J. ; Fischer, Ondřej
A review of the increasing complexity of existing standards (Codes) for structural design shows that a disparity exists between them and the increasingly sophisticated assessment process that utilizes the full potential of computer technology.
Basic information serving to developed qualitatively new codes corresponding to probabilistic assessment exposed to dynamic loaded structures
Pirner, Miroš ; Fischer, Ondřej ; Marek, Pavel ; Urushadze, Shota
The first condition for a reliable structure is a well-judged design, correctly and carefully calculated, and based on authentic input values. So fare we were used to take these values from the Codes and in the case that they can very accidentally, this variability can be respected by means of a coefficient. A more realistic approach is to take into account directly the random nature of the property in question, and to describe it in probabilistic terms (by a histogram). This can be done with the use of SBRA (Simulation Based Reliability Assessment) method. Here some considerations are shown, how the actual Czech Codes should be reorganized for probabilistic design, in the case of dynamic civil engineering problems. In this paper the problems of loading are treated; the problems of structural response and some special examples are shown in the full text on CD.

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See also: similar author names
2 Fischer, Martin
2 Fischer, Michael
2 Fischer, Michal
3 Fischer, Milan
2 Fischer, Monika