|
|
Classification of Small Noncoding RNAs
Žigárdi, Tomáš ; Martínek, Tomáš (referee) ; Vogel, Ivan (advisor)
This masters's thesis contains description of designed and implemented tool for classification of plant microRNA without genome. Properties of mature and star sequences in microRNA duplexes are used. Implemented method is based on clustering of RNA sequences (with CD-HIT) to mainly reduce their count. Selected representants from each clusters are classified using support vector machine. Performance of classification is more than 96% (based on cross-validation method using the training data).
|
|
|
The role of small RNAs in transgenerational plant stress memory
Jaklová, Veronika ; Marková, Hana (advisor) ; Lipavská, Helena (referee)
Plants are constantly affected by various abiotic and biotic stresses, which cause a whole range of reactions.The resultcanbe increasedplantresistance tovariousstressfactorssuchasherbivoryattack or lack of water. Additionally, this resistance can also be passed on to subsequent generations through epigeneticmechanisms.Small RNAsservingas signaling moleculesof the plant's rapid response tostress can play a large part in the formationof intergenerationalandmultigenerationalstressmemory.MiRNAs are mainly regulators of gene expression,throughtheirinhibitory and degradative activitiesthey control the transcription of genes and the translation of a large number of proteins. SiRNAs could participate in the transfer of transcriptional memory through the mechanism of RNA-directed DNA methylation (RdDM). DNA methylation and histone modifications together act as chromatin marks that can be epigeneticallytransferredtosubsequentgenerations.Basedonthis,plants derivedfromstressedparent plants show large changes in gene expression compared to plants with non-stressed parents. These changesthenpersistfor varyinglengthsof time,dependingon whethergene expressionisagain induced bythe stressfactoror not.Interestinunderstandingthe mechanismsof transgenerationalstressmemory has recently grown considerably, and this...
|
|
|
Biofyzikální studium malých RNA
Šmerková, Kristýna
Thanks to the prove of connection between the aberrant occurrence of small RNA and various diseases and their potential in diagnostics and treatment led to discovery of new methods and materials facilitating their detection and targeted transport during gene therapy. This work summarizes present knowledge about chosen groups of small RNA, their significance in medical science and the possibilities of their detection. This work primarily concentrates on combination of magnetic separation with electrochemical detection. Magnetic particles (MPs) with different surface modifications were used for isolation. Non-specific isolation was carried out using silanol-coated MPs; streptavidin-coated MPs modified with specific biotinylated probe were used for specific separation. Square wave voltammetry (SWV) was used as a very sensitive electrochemical detection method. Optimized method based on specific magnetic separation with SWV was able to reach nanomolar detection limit (4 nM) with microRNA. The method was applied on human embryonic cells for specific isolation and detection of miR-124. The CdTe quantum dots (QDs) were studied as a nanomaterial tool for nucleic acid detection. The QDs were modified with streptavidin for their bioconjugation with biotinylated molecules were used. Interaction of QDs with nucleic acids was studied using capillary electrophoresis.
|
|
|
Clinico-pathological characteristics of mucin-producing colorectal carcinoma
Sojka, Ladislav ; Levý, Miroslav (advisor) ; Boublíková, Ludmila (referee) ; Klos, Dušan (referee)
Colorectal carcinoma (CRC) is one of the most common malignancies worldwide with persistently high mortality. As a consequence, high demands are placed on research into this disease. The aim of this study was to evaluate the epidemiology of colorectal carcinoma in the Czech Republic in comparison with worldwide data. We focused on the evaluation of the latest findings in screening and diagnosis, investigated prognostic factors, and also focused on the therapeutic options of CRC. Furthermore, mucin-producing carcinomas are described in detail and mucin itself was confirmed as a risk factor for the prognosis of CRC patients. The experimental part of the study focused on gene mucin MUC13 and the MUC13 - miR-4647 axis, which is associated with adverse prognosis in CRC patients. Samples of CRC and samples of adjacent non-malignant mucosa tissue were used. The samples were collected from patients who underwent surgery at the General University Hospital in Prague, at the Thomayer University Hospital in Prague and at the University Hospital in Pilsen (Czech Republic). The collection of samples took place between 2011 and 2015. The total of 187 samples were collected from patients with sporadic colorectal cancer. The subjects of the study all provided information on their lifestyle habits, body mass index...
|
|
|
The role of microRNAs in regulation of mammalian oocyte and embryo development
Marcollová, Kateřina ; Procházka, Radek (advisor) ; Svoboda, Petr (referee)
Cumulus-oocyte complex (COCs) is crucial for mammalian reproduction. Cumulus cells not only nurture the oocyte; they also represent important communicational nodes for mediating information towards and from the oocyte. The non-coding miRNAs can modulate posttranscriptional events they might serve as a useful biomarker for evaluating cell conditions. Based on the COCs staining with vital Lissamine Green B stain we divided cumulus cells into high- and low-quality ones. Furthermore, we implemented division based on the maturation stage, the GV and MII. Sequencing data analysis showed that DE miRNAs from qualitatively different stages donot significantly vary. Nonetheless, significantly DE miRNAs were detected between two developmentally different stages. We identified e.g. ssc-miR-183, ssc-miR-182, and ssc-miR-21-5p to be highly downregulated when comparing GV to MII stage. Among the highly expressed miRNAs from all samples were members of let-7 family (let-7c, let-7a, let- 7f-5p), ssc-miR-16, ssc-miR-21-5p, and ssc-miR-125a. Targeted genes by the DE miRNAs were involved in ErbB, TGF-β, MAPK, FoxO, gap junction and cGMP signalling pathways. We conclude that single miRNAs in cumulus cells probably cannot be used as a reliable oocyte quality marker. On the other hand,changes in the miRNA expression in...
|
|
|
miRNA analysis of small extracellular vesicles isolated from plasma after diet intervention
Kratochvílová, Michala ; Koc, Michal (advisor) ; Šrámek, Jan (referee)
The aim of this thesis was to establish a protocol for the isolation of small extracellular vesicles (sEVs) from human plasma. Plasma samples were collected from 44 healthy women who underwent a 60-hour dietary intervention in the form of fasting as part of a clinical trial. These women were divided into two groups based on their BMI - lean and obese. Plasma was collected from each participant before and after the dietary intervention and sEVs were isolated using the polyethylene glycol precipitation method. Each sample was then characterized by the size of sEVs and their concentration. The amount of sEVs in plasma before the dietary intervention was the same for both groups and did not change with dietary intervention. However, the 60-hour fasting resulted in a change in sEVs size in the lean group. Another goal of this thesis was to analyze miRNA expression in sEVs. There were differences found in the expression of certain miRNA between the two groups. More specifically, differences were observed in the expression of hsa-miR-17-5p, hsa-miR-20a-5p and hsa-let-7b-5p. The 60-hour fasting period resulted in an increased expression of hsa-miR-5100 in the lean group and hsa- miR-27a-3p and hsa-miR-27b-3p in the obese group. However, these changes induced by the dietary intervention were not evaluated...
|
|
|
Small extracellular vesicles as microRNA carriers and their role in neural cell regeneration
Šprincl, Vojtěch ; Romanyuk, Natalyia (advisor) ; Kriška, Ján (referee)
Acute spinal cord injury is a serious type of injury, the treatment of which still represents a challenge for contemporary medicine. Neural stem cells (NSCs) transplantation is one of many promising ways to contribute to the regeneration of damaged tissue. NSCs communicate with the rest of the tissue by means of small extracellular vesicles (sEVs), in which their regenerative potential is thus assumed. The aim of this thesis is to verify the antiapoptotic effect of sEVs isolated from the culture medium of two types of NSCs in an rat in vitro model of spinal cord injury. To meet this goal, different methods of isolating sEVs from the culture medium were tested. Subsequently, sEVs were characterized according to their size and the presence of surface markers. This thesis includes an PCR analysis of the cargo of sEVs, which showed an abundance of neuroprotective and antiapoptotic miRNAs. Fluorescent staining of sEVs proved that sEVs penetrate into the cytoplasm of stem cells. Finally, sEVs were applied to a rat in vitro model of spinal cord injury and their neuroprotective effect was demonstrated using the immunoblotting method. Keywords Small extracellular vesicles, exosomes, acute spinal cord injury, regeneration of nervous tissue, miRNA, microRNA, neural stem cells
|
|
|
The role of exosomes in chronic myeloid leukemia
Březinová, Lenka ; Krijt, Matyáš (advisor) ; Holada, Karel (referee)
Exosomes are extracellular vesicles of a size range 30-150 nm whose function has been explored in chronic myeloid leukemia (CML) due to their role in proliferation of CML cells, remodelling the bone marrow niche, angiogenesis and resistance to treatment with tyrosin- kinase inhibitors (TKIs). Although BCR-ABL kinase is effectively targeted by TKIs, 20-30 % of patients remain resistant to treatment. Resistance of CML cells to TKIs treatment is supported by exosomes. Exosomes transport proteins, nucleic acids, chemokines and small molecules that stimulate anti-apoptotic or suppress pro-apoptotic processes in leukemic cells. Anti-apoptotic processes are especially enhanced by upregulated protein levels: TGF- β1, USP6 and FGF2 and various types of RNA: miR-365, miR-21, Hsa_circ_0058493 and mRNA for BCR-ABL. In contrast leukemic cells tend to reduce the number of pro-apoptotic molecules, including miR-320, miR-328 and miR-146a-5p. Leukemic cells modify the bone marrow microenvironment through exosomes in the way to support their survival and also in order to adjust expression of adhesion and pro- angiogenic molecules. An important role in those processes play miR-126, miR-210 and miR- 92a. Neither the number of processes affected by CML exosomes nor their potential use in the treatment of CML is...
|
|
|
The role of miRNA in injury and regeneration of spinal cord tissue
Šprincl, Vojtěch ; Romanyuk, Natalyia (advisor) ; Mrózková, Petra (referee)
MicroRNAs are small non-coding RNA molecules of a length about 20-24 nucleotides, that regulate gene expression post-transcriptionally. They interfere mRNA molecules via base- pairing with complementary sequences. Recently it was shown that they play an important role in injury and regeneration of nervous tissue. The aim of this bachelor thesis is to describe possible role of miRNAs in central nervous system injury with focus on spinal cord injury.
|
|
|
RNA interference in plants
Čermák, Vojtěch ; Fischer, Lukáš (advisor) ; Kulich, Ivan (referee)
The process of RNA interference allows cells to regulate functions of their genes. This process is usually initiated by the presence of double-stranded RNA within a cell. Such double-stranded RNA is diced by a specific protein called Dicer into duplexes of small RNAs, usually 20-25 nucleotides long. Single-stranded small RNAs, released from the duplexes, are the heart of RNA interference and they can be categorize into several groups according to their biogenesis. There are two groups of small RNAs in plants: miRNA and siRNA. Small RNAs can associate with a protein called Argonaut and guide it to the target molecule on the bases of sequence complementarity. The Argonaut-small RNA complex can act on itself or it can interact with other proteins in a wide spectrum of processes. The complex can slice the target mRNA (which can be handled by the sole Argonaut and small RNA), it can suppress translation or it can direct chromatin modifications. The phenomena of RNA interference can be found in almost all Eukaryotes where it can serve many functions, for example it can control cell differentiation, participate in stress responses, direct changes in chromatin and defend the organism against viruses. A diverse set of operating modes of RNA interference can be found in plants, which we are only at the...
|
guest ::
