Biotehnoloogia magistritööd - Master's theses

Selle kollektsiooni püsiv URIhttps://hdl.handle.net/10062/72745

Sirvi

Nüüd näidatakse 1 - 20 60

Enzymatic Oxidation of Biorefinery Lignin
(Tartu Ülikool, 2021) Khan, Sharib; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Lignocellulosic biomass is the main source of renewable chemicals in the future. Biorefinery methods can be used to separate the three major components, which are cellulose, hemicel-lulose and lignin. Treatment methods, where the polysaccharides are hydrolyzed, resulting in the production of hydrolysis lignin (HL). In order to valorize HL further enzymatic treat-ment is promising and can be a game changer in the biorefinery approach. The goal of the present work was to investigate possibilities to use enzymatic oxidation in valorization of HL. For the first time, the treatment of industrially fractionated HL with enzymes was used. Four different laccases and a peroxidase were tested. All enzymes showed activity in most conditions for different HL-s. A positive result was the observation of enzyme activity in conditions with several times higher HL content than previously described.
The use of phospho-degrons for controlled protein expression in the cell cycle
(Tartu Ülikool, 2021) Bulatovic, Luka; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Cyclin-dependent kinases (Cdks) are the master regulators of the cell cycle, which together with their activating cyclin subunits, phosphorylate hundreds of targets to govern the cell cycle progression. The precise substrate targeting mechanisms of the Cdk complex have led to a hypothesis that the Cdk machinery could be used to control the expression and cellular concentration of any desired protein by fusion with different phospho-regulation modules. The modules consist of barcodes of linear motifs including phosphorylation sites and cyclins docking motifs. These barcodes are scanned by the Cdk complex and depending on the bar-code, the machinery will differentially regulate the protein in the cell cycle. This work shows that one such module, the Far1 degron, can be used to control the cellular concentration of different proteins. We also demonstrate that different versions of the degron allow us to fine-tune the cellular concentration of the targeted protein in different cell cycle phases.
Enzyme-constrained genome-scale metabolic model of Rhodotorula toruloides
(Tartu Ülikool, 2021) Rekena, Alina; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Rhodotorula toruloides is a non-conventional, oleaginous yeast able to naturally accumulate high amounts of microbial lipids when grown on various carbon substrates, including from a lignocellulosic origin. Its unique metabolic characteristics, which make lipid synthesis possible, are not fully understood. With genome-scale models (GEMs) it is possible to systematically study cellular metabolism using metabolic flux predictions in silico. Enzyme-constrained genome-scale modelling approach has been demonstrated to improve cell phenotype predictions in model organisms, including yeasts. In this work, enzyme-constrained genome-scale metabolic model of R. toruloides was developed, incorporating cell physiology and absolute proteomics data on three different carbon substrates (xylose, glucose, acetic acid) under exponential growth and lipid accumulation phases. The generated model could predict experimental rates measured in all conditions, except for the gases on glucose. Further, predicted intracellular flux patterns demonstrated the differences in R. toruloides metabolism under different carbon substrates and the importance of cofactor balance (NADPH) during the lipid accumulation. These results and the developed genome-scale model can be further used for the design of efficient microbial cell factories and various metabolic studies
HPV L2 protein derived endosomal escape enhancers
(Tartu Ülikool, 2021) Mammadova, Sabina; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Delivery of macromolecular therapeutics, and specifically their endosomal escape is one of the challenges in the medicine. Although there are several delivery methods developed, there is still a need to overcome the challenges associated with endosomal entrapment. In this work HPV16 L2 protein and peptides derived from this protein were applied for in-creasing transfection efficacy of CPP mediated delivery of nucleic acid. For this, peptides derived from HPV L2 protein specific regions, that are responsible for L2 mediated endo-somal trafficking of viral DNA were tested. Both L2 protein and new synthesised peptides showed promising results for applying them as additives to the CPP/NA nanoparticles for therapeutic use and protein production in the future.
Characterization of ligand binding to Dopamine D3 receptor using fluorescence anisotropy and radioligand binding
(Tartu Ülikool, 2021) Thoondee, Lakshmi; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
There are five subtypes of dopamine receptors that play a role in the dopaminergic system. Due to their limited distribution and involvement in cognitive and emotional functions, Dopamine D3 receptors are attractive pharmacological targets for treatment of drug addiction and neuropsychiatric disorders. D3 receptor ligands have been labelled with a fluorescent dye or a radioisotope for direct monitoring of ligand binding to the receptor. However, there are not many fluorescent ligands that are available for studying D3 receptor. A2-TAMRA is a novel fluorescent ligand with high affinity for D3 receptor. Binding of [3H]-methylspiperone to D3R was studied in parallel to validate results from A2-TAMRA binding to D3R. The D3 receptor ligands had similar affinities in inhibiting A2-TAMRA and [3H]-methyl spiperone binding to D3 receptor, since a very good correlation (R2 = 0.94) was obtained between both methods. The affinities for the known antagonists had a good correlation with previously published data. Selectivity of A2-TAMRA towards two different subtypes was also studied and we found that A2-TAMRA prefers D3 receptor over D1 receptor.
Cell cycle independent signaling by modified Clb5- Cdk1 complex
(Tartu Ülikool, 2021) Agerova, Alissa; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
A eukaryotic cell contains a robust regulatory network that controls the ordered sequence and timing of distinct cell cycle events. In budding yeast this is mainly regulated by the growing activity of cyclin-dependent kinases (Cdks) during the cell cycle. Post-translational modifications, particularly protein phosphorylation is a powerful mechanism regulating stability, localization, activity and interactions of proteins. Building synthetic circuits based on protein phosphorylation has remained a riddle due to the overlapping specificity of protein kinases. To tackle this issue it was aimed to obtain a cell cycle independent cyclin-Cdk1 input that could target substrates created specifically for this particular cyclin-Cdk1 complex. By manipulating the Cdk1 specificity of phospho-degron and -localization modules it was anticipated to design orthogonal Cdk circuits that respond to the modified Clb5-Cdk1 complex.
Analysis of the docking interaction between Sld2 and Clb5 in budding yeast
(Tartu Ülikool, 2021) Mikhailova, Valentina; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
The cell cycle of Saccharomyces cerevisiae is governed by cyclin dependent kinases (Cdks), which are activated by periodically synthesized and degraded cyclins. The substrate target-ing by a cyclin-Cdk complex is mediated by the active site on the Cdk and the cyclin docking pocket. Docking interactions between short linear motifs (SLiMs) in target proteins and cy-clin-dependent kinases are shown to be critical regulators of different cell cycle events. SLiMs function in almost every pathway due to their role in regulatory function and signal transduction.
Optimization of Sic1-Cln2-based phosphodegron tag for inducible protein degradation
(Tartu Ülikool, 2021) Panfilova, Aleksandra; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Precise regulation of protein abundance in the cell would be instrumental in both research and industry. A variety of tools exists for the regulation of protein expression at the transcriptional level. However, there is a shortage of tools that would allow control over already expressed proteins. In this study, we exploit the native cell cycle regulation system of Saccharomyces cerevisiae to develop a system for targeted inducible protein degradation. Using sequence elements that modulate cyclin-dependent kinase (CDK) substrate specificity, we generated a set of phosphodegron tags that have diverse effects on degradation rates of the tagged proteins. The control over the system is provided by conditional expression of the stabilized version of cyclin Clb3, which drives CDK-dependent phosphorylation of the tag, and F-box protein Grr1, which recognizes phosphorylated tag and label it for further degradation. In the course of this work, we have designed a set of phosphodegron tags that can be used for the regulation of the protein abundance in the cell and its maintenance at desirable levels that can be useful for the industrial production of value-added products. In addition, we discovered that Cks1 priming effect on the multisite phosphorylation is not only distance-, but, likely, also context-dependent which might be of interest for fundamental research.
The effect of binding sites for POU-HD pro-teins (Oct-1) on the replication of HPV18
(Tartu Ülikool, 2021) Joseph, Michael; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Human papillomaviruses (HPV) are known to infect the basal cells of the epithe-lia. Infection caused by certain type of HPVs are known to lead to cancer. Therefore, under-standing the viral life cycle could be a key to develop novel therapeutic strategies to inhibit viral infection. The regulation of HPV genome replication depends upon the certain viral factors and various cellular factors which could potentially have a positive or a negative effect on the viral replication. The upstream regulatory region (URR) of the HPV genome has motifs for these viral and cellular factors. One such cellular factor, Oct-1 has multiple binding sites located in this region. Based on a previous study it has been shown that Oct-1 binding does have a negative effect on the HPV18 minimal origin. Since, the URR could be filled with a lot of potential motifs for Oct-1 factors, it is important to understand the effect of these specific motifs on the HPV genome replication. This thesis aims to observe the impact of such binding sites on HPV18 replication by performing mutational analysis.
Predicting Off-target Effects in CRISPR-Cas9 System using Graph Convolutional Network
(Tartu Ülikool, 2021) Vinodkumar, Prasoon Kumar; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
CRISPR-Cas9 is a powerful genome editing technology that has been widely applied in target gene repair and gene expression regulation. One of the main challenges for the CRISPR-Cas9 system is the occurrence of unexpected cleavage at some sites (off-targets) and predicting them is necessary due to its relevance in gene editing research. Very few deep learning models have been developed so far that predict the off-target propensity of single guide RNA (sgRNA) at specific DNA fragments by using artificial feature extract operations and machine learning techniques. Unfortunately, they implement a convoluted process that is difficult to understand and implement by researchers. This thesis focuses on developing a novel graph-based approach to predict off-target efficacy of sgRNA in CRISPR-Cas9 system that is easy to understand and replicate by researchers. This is achieved by creating a graph with sequences as nodes and by performing link prediction using Graph Convolutional Network (GCN) to predict the presence of links between sgRNA and off-target inducing target DNA sequences. Features for the sequences are extracted from within the sequences.
A preclinical trial of Bisdemethoxycurcumin in a mouse model of Alzheimer's disease
(Tartu Ülikool, 2022) Mansouri, Seyedeh Elnaz Sadat; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Bioelectrochemical system for oil pollution remediation in marine sediments
(Tartu Ülikool, 2022) Ugoezue, Samuel Tochukwu; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Familial hypercholesterolemia: enhancing actionability through the recall-by-genotype experience
(Tartu Ülikool, 2022) Nurm, Miriam; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
The role of ATR in G1 phase DNA damage response
(Tartu Ülikool, 2022) Matiyevskaya, Frida; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
CRISPR/nCas9 deletion of genes linked to the C1-fixing gene cluster in a gas-fermenting acetogen
(Tartu Ülikool, 2022) Nwaokorie, Ugochi Jennifer; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Role of MPK12 in stomata movement
(Tartu Ülikool, 2022) Kuusk, Katarina-Liyza; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Efficient peptide-mediated delivery of oligonucleotides into mammalian cells
(Tartu Ülikool, 2022) Emenike, Chimdi Raphael; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
In vitro and in silico epitope-paratope mapping
(Tartu Ülikool, 2022) Jermakovs, Klavs; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Growth and phenotype characterization of laboratory evolved gas-fermenting acetogen strains
(Tartu Ülikool, 2022) Yar Saqib, Asfand; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut
Investigation of Dopamine-mediated Toxicity in Parkinsonian Sensory Neurons
(Tartu Ülikool, 2022) Olaoye, Oyedele John; Tartu Ülikool. Loodus- ja täppisteaduste valdkond; Tartu Ülikool. Tehnoloogiainstituut

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