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Abstracts of PhD projects for academic year 2015/2016 offered by Faculty Print option in slimbox / lytebox? (info)
Friday, 22 July 2016 13:32

Regulation of Cd-dependent Zn root-to-shoot translocation

Supervisor:
Prof. dr hab. Danuta Maria Antosiewicz
Dept. Plant Anatomy and Cytology
Inst. Plant Experimental Biology and Biotechnology
phone: (48 22) 55 42 105
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Scope: Zn and Cd translocation from roots to shoots is under tight control. The efficiency of translocation is a decisive factor in providing proper amount of micronutrients to shoots, protecting from their toxic excess, thus determining the level of accumulation also toxic Cd. Cd present in edible plant parts enters the food chain leading to health risk. To design strategies for excluding Cd from shoots and increase contents of the related metal Zn, we need to know more about biological processes that govern uptake and root-to-shoot translocation of both metals. It is known that between them exists competitive interactions. This project contributes to dissect processes underlying Zn-Cd cross-homeostasis mechanisms in tobacco (Nicotiana tabacum) thus to the regulation of the efficiency of Zn and Cd root-to-shoot translocation. Our recent study showed that ZIP genes (ZRT-IRT-like Protein) could be a part of the regulation of the Zn/Cd-concentration dependent translocation to shoots of both metals. The role in this process of NtZIP1 and NtZIP4 (both genes have been recently cloned) and  the interplay between various ZIP genes will be examined. Moreover, the role of the apical and basal part of the roots will be taken into account. The methodology involves analysis of the cell/tissue/organ specific expression (RealTime PCR technique; expression of promoter:reporter protein constructs),  silencing the NtZIP1 and determining the molecular and physiological consequences.

The research will be carried out within the grant NCN: OPUS.

Requirements: Strongly motivated candidates. Preferred experience in a plant study and a background in molecular biology, computer skills, fluent in English.

Candidates are ask to contact the scientific advisor personally, by email or by phone or with dr Anna Barabasz
( This e-mail address is being protected from spambots. You need JavaScript enabled to view it ), phone number the same as for D.M.Antosiewicz.

Interrelations between chloroplast stroma and thylakoids proteoms in spatial organization of thylakoid membranes system

Supervisor:
Prof. dr hab. Maciej Garstka
Dept. Metabolic Regulation
Inst. Biochemistry
phone: (48 22) 55 43 213
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Scope: The thylakoid system in plants is organized into two distinct domains: grana arranged in stacks of appressed membranes and non-appressed membranes consisting of stroma thylakoids and margins of granal stacks. The research project will be focused on the clarification of the interrelations between chloroplast stroma and thylakoid membrane proteins and the role of chlorophyll-proteins supercomplexes and microdomains in the spatial organization of the thylakoid membranes system. The qualitative and quantitative analysis of stroma and thylakoid proteins and recognizing protein arrangement within supramolecular complexes allow point out the key proteins/complexes that play role in maintaining three-dimensional (3D) thylakoid structure. The Arabidopsis thaliana mutants with distorted membranes organization, plants affected by abiotic stress and plastids under the primary stages of biogenesis will be used in experiments. The TEM and CLSM microscopy will be used in visualization of chloroplast structure, whereas the in vivo photosynthetic activity will be measured with modulated fluorescence. A formation of supercomplexes and microdomains will be investigated with biophysical and crystallography methods.

Requirements: The good background in cell and molecular biology, biochemistry and biophysics. Practical and theoretical approach to spectrometry, proteomics, and molecular biology as well as microscopic technics. Skillful at analytical device and computer programs. The good command of the English language.

Purine salvage pathway enzymes as a target for therapy against Helicobacter pylori.

Supervisor:
Prof. dr hab. Elżbieta Katarzyna Jagusztyn-Krynicka
Dept. Bacterial Genetics
Inst. Microbiology
phone: (4822) 5541 216
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Prof. Dr hab. Maria Agnieszka Bzowska
Dept. Biophysics
Inst. Experimental Physics
Faculty of Pysics UW
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Scope:  The main goal of the proposed project is to identify new drug targets for eradication of pathogenic organisms, such as Helicobacter pylori, that are not able to synthesise de novo purine and purine nucleosides. Such organisms are dependent on metabolic pathway known as salvage pathway to obtain purines, the indispensable building blocks for DNA and RNA synthesis. Therefore, blocking of the salvage pathway should stop Helicobacter pylori growth and replication. Recent reports describing details of Helicobacter pylorisalvage pathway, and our preliminary experiments on inhibition of one enzyme of this pathway, suggest that it will be possible to completely stop Helicobacter pylorigrowth and replication when two key enzymes of salvage pathway, purine nucleoside phosphorylase (PNP) and adenylosuccinate synthetase (AdSS), will be the targets of inhibition, and specific inhibitors - designed on the basis of molecular mechanisms of both enzymes - will be used. Therefore we plan to isolate recombinant enzymes form Helicobacter pylori, purine nucleoside phosphorylase and adenylosuccinate synthetase, determine their properties in solution, crystallize them and determine their three-dimensional structure with atomic resolution by X-ray crystallography, and characterize inhibition of these enzymes by known inhibitors of similar enzymes, formycin and hadacidin. Using molecular modelling methods, results of biophysical studies and Helicobacter pylori enzyme PNP and AdSS X-ray structures determined, we plan to design new inhibitors, specific for Helicobacter pylori enzymes, synthesise them and check their influence on Helicobacter pylori grow in vitro, in order to check if these two enzymes are potential drug targets for Helicobacter pylori eradication. The proposed studies may, if continued on the more applicable level, result in developing new therapy against gastrointestinal diseases caused by the presence of Helicobacter pylori.

Requirements: Status of M.Sc. Student in the field of biotechnology/ microbiology/molecular biology. Good knowledge of microbiology, biochemistry and molecular biology. Basic knowledge of molecular biophysics, in particular general properties of enzymes and methods of enzyme kinetics (determination of kinetic parameters characterizing substrates and inhibitors). Strong interest in science.Strong motivation to learn new experimental techniques of molecular biophysics necessary for testing the scientific hypothesis of the PhD project(for example spectroscopic and calorimetric methods to characterize enzyme-ligand interactions, methods to crystallize proteins and determine their three-dimensional structure using diffraction methods).

Investigating the regulatory relationships between RNA metabolism and biotic stress defense in Arabidopsis thaliana

Supervisor:
Prof. dr hab. Joanna Kufel
Inst. Genetics & Biotechnology
phone: (4822) 59 22 245
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Scope: The proposed research involves the systematic and comprehensive analysis of Arabidopsis thaliana mutants in specific RNA metabolism pathways, including mRNA splicing and degradation, to identify defects that lead to changes in the response to biotic stress induced by the infection of Pseudomonas syringae pv. tomato DC3000. The proper cellular signaling in each organism depends on the optimal control of gene expression, not only under normal conditions but also under stress. Recent studies have shown that a number of mutants in major RNA quality control pathways, such as NMD, show defects in pathogen response, but the exact mechanism of this correlation is not clear. Also a comprehensive scheme of links between regulation of gene expression and activation of the immune response is lacking. Two important players in these pathways are the cascade of phosphorylation signaling via MAP kinases, and small RNAs (siRNA and miRNA) through silencing of gene expression (RNAi) on the transcriptional or posttranscriptional level. Furthermore, recently a number of long noncoding RNAs (lncRNAs) have been identified in plants and several of these may play an important role in antibacterial immunity. Therefore, we propose to identify a network of interdependencies and connections between RNA factors and key regulators of pathogenesis, such as MAP kinases or ncRNAs. For this purpose, in selected mutants we determine the level and stability of MAPK mRNAs (northern blot, qRT-PCR) and their kinase activity (in gel kinase assay, western blot), as well as changes in phosphorylation status of known and potential MAPK substrates in RNA metabolism factors. As ncRNA play an increasingly recognized part in many cellular processes, we plant to assess their role in plant pathogen defense by carrying out high-throughput sequencing (RNA-Seq) of total and small RNA libraries following the treatment with P. syringae for selected Arabidopsis mutants with the most significant changes in sensitivity to pathogen infection.

Requirements: M.Sc. in biology, biotechnology or related fields. Prior experience in RNA and plant molecular biology techniques is a bonus.

Structural role of lipid membrane components in early stages of chloroplast biogenesis

Supervisor:
Prof. dr hab. Agnieszka Mostowska
Dept. Plant Anatomy and Cytology
Inst. Experimental Plant Biology
phone: (4822) 55 41 103
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Scope: This research project will be focused on the clarification of the role of carotenoids essential for the formation of internal membrane systems within developing chloroplasts during early biogenesis. Therefore we will analyze crucial developmental stages of chloroplast biogenesis in leaves of Arabidopsis thaliana mutants with distorted carotenoid biosynthesis pathways important for the formation and maintaining of plastid membranes and compare them with the corresponding structures at the same stages of chloroplast development in wild plants. Reconstructed spatial structure (3D) allows visualization and understanding of real membrane connections and their interconnections during the key stages of chloroplast biogenesis and makes visible places of disturbance in internal membranes. and thus points the role of a particular carotenoid in transformation of tubular structure of prolamellar body to linear one of the thylakoids and grana.. Structural results will be correlated with the membrane protein and lipid composition and with their functionality. We also expect that the results of this project will contribute to the development of methods of spatial reconstruction of various structures and organelles in biological systems.

Requirements: MSc degree in biology or related area. Knowledge of general cell biology and bioenergetics, of plant physiology, plant biochemistry and molecular biology of plants. Knowledge of light microscopy (especially fluorescence and confocal laser scanning microscopy) and electron microscopy. Ability to master and apply dedicated computer software (especially image analysis and spatial modeling). Knowledge of English.

Role of cytochrome b6f complex in regulation of activity of thylakoid complexes.

Supervisor:
Prof. dr hab. Elżbieta Romanowska
Dept. Molecular Plant Physiology
Inst. Botany
phone: (4822) 55 43 916
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Scope: Photosynthetic electron transport is performed by a chain of redox components electrochemically connected. Its efficiency depends on the activity of photosystem with interaction with dark reaction of photosynthesis. Plants developed different acclimation mechanisms that maintain photosynthesis under stress conditions. Recent studies indicate that redox signal from photosynthetic electron transport and reactive oxygen species play a central role in the regulation of acclimation and responses to stress. The imbalance between reduced and oxidized forms can change the photosystem stoichiometry. Cytochrome b6f complex, kinases and phosphatases activities and expression of photosynthesis gens are regulated by the redox state of PQ pool and energetic status of chloroplasts. We want to show that cytochrome b6f complex play a key role in perception and transduction of redox signal when light intensity and quality induce imbalance in electron transport system (ratio ATP/NADPH) and causes differences in antenna complexes. Changes in illumination, dark- light shift and inhibitors will be used to induce different responses in organization of chloroplasts of plants represented different metabolic  types (C3, C4 and red alga) to identify role of cytochrome b6f complex in mechanisms responsible for chloroplast acclimation.