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Institute of Physiology of the CAS, v. v. i.

List of available PhD theses

3D superresolution microscopy for accessing mitochondrial ultramorphology

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: RNDr. Petr Ježek, CSc.

Annotation

3D nanoscopy has not yet assessed mitochondrial cristae morphology, nor the internal structure of mitochondrial DNA (mtDNA) & protein complexes, termed nucleoids. Hence, we’ll survey 3D-redistribution of cristae and their shaping proteins or nucleois employing our prototype Vutara 3D superresolution microscope for stochastic techniques such a PALM and dSTORM. We will conduct studies under physiological situations vs. pathology (type-2 diabetes, cancer) using dSTORM with nanobodies or FRET excited PALM/dSTORM. Thus nm changes will be reflected by novel 3D nanoscopy methods. Also mtDNA nucleoids will be studied at increased and diminished mitochondrial biogenesis, while applying own mitoFISH nanoscopy for D-loop counting. Artificial manipulations of nucleoid size and mtDNA content will be studied as well as nucleoid division. Results will be translated into specific protocols for 3D nanoscopy, specifically developing novel relevant 3D image analyses based upon the Ripley’s K-function and Delaunay algorithm. Molecular cell biology will thus be combined with up-to-date 3D nanoscopy. Note, the molecular biology techniques will be conducted and be ready for the applicants by the coworkers of the Department No.75.

Characterization of early postnatal development using a biobank of tissues of human newborns

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: MUDr. Jan Kopecký, DrSc.

Annotation

Early postnatal period is critical with respect to development of the key physiological functions and homeostatic mechanism of the newborn, as well as for imprinting the metabolic features that could be manifested during the adolescence and adulthood. A unique biobank of the autopsy samples of various is available that had been collected from human newborns, mostly very premature newbors. Characterization of the transcriptome of the tissues using RNA sequencing analysis is ongoing.
The project will focus on tah data analysis in order to reveal various aspects of early human development and its control, also with regards to various pathologies. Model experiments on mice will reperesent the main experimental part of the project. It will proceed in close collaboration between the Department of Adipose Tissue Biology and the Department of Metabolomics of the Institute of Physiology of the Czech Academy of Sciences (http://www.fgu.cas.cz/en/departments/adipose-tissue-biology), and the Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University (http://udmp.If1.cuni.cz/en/genomics-and-bioinformatics-laboratory) in Prague. This multidisciplinary environment will be key for the appropriate tarining of the student and successful work on the projekt. The basic PhD scholarship will be supported by the employement at the Department.

Complex characterization of transcriptome and proteome in tissues of human newborns

Department: Department of Informatics and Chemistry, Faculty of Chemical Technology
Study programme: Bioinformatika
Theses supervisor: Mgr. Michal Kolář, Ph.D.

Annotation

Early postnatal period is critical with respect to development of the key physiological functions and homeostatic mechanism of the newborn, as well as for imprinting the metabolic features that could be manifested during the adolescence and adulthood. A unique biobank of the autopsy samples of various is available that had been collected from human newborns, mostly very premature newbors. Characterization of the transcriptome (RNAseq) and proteome of the tissues is ongoing. The project will focus on the data analysis in order to reveal various aspects of early human development and its control. It will proceed in close collaboration between the Laboratorty of Adipose Tissue Biology of the Institute of Physiology of the Czech Academy of Sciences (CAS) (http://www.fgu.cas.cz/en/departments/adipose-tissue-biology), the Institute for Inherited Metabolic Disorders, First Faculty of Medicine, Charles University (http://udmp.If1.cuni.cz/en/genomics-and-bioinformatics-laboratory) in Prague and the Laboratory of Genomics and Bioinformatics of the Institute of Molecular Genetics CAS (https://www.img.cas.cz/research/michal-kolar/ ).

Light upconversion nanoparticles for infra red photodynamic therapy of tumors

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: RNDr. Petr Ježek, CSc.

Annotation

For numerous tumor types resistance to long-term monotherapies usually develops. In order to overcome it, we shall develop and photophysically test nanoparticle-based systems for infra red photodynamic therapy. Threrefore, we will study detailes photophysics of nanoparticles, namely luminescence kinetics for upcovversion nanoparticles NaY(Gd)F4:Yb3+(Nd3+)/Er3+(Tm3+), which convert either 980? 650/540 nm or 808?650 nm. All these studies will be conducted in the absence and in the presence of a photosenzitizer in the nanoparticle shell, which creates singlet oxygen upon the desired excitation. The second imaging mode will be enabled for cracking these nanoparticles by NMR or PET. Particle surface engineering will include coating with polymers to achieve the highest energy transfer, immobilization a photosenzitizer to induce optimal singlet oxygen formation, and attachment of addressing peptides to facilitate cell internalization. Chelator for 64Cu or 125I attachment will be also introduced to integrate upconversion luminescence with PET imaging. Singlet oxygen production and pharmacokinetics of the particles on nude mice with xenotransplanted tumors will be also determined. The molecular biology techniques will be conducted by the coworkers of the Department No.75., Inst. Physiology.

Liquid chromatography–mass spectrometry for metabolomics and lipidomics studies

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: doc. Ing. Tomáš Čajka, Ph.D.

Annotation

Over the last decade, mass spectrometry-based metabolomics and lipidomics have become key disciplines for the comprehensive profiling of polar metabolites and complex lipids in biological systems. Liquid chromatography–mass spectrometry (LC–MS) is the preferred technique in metabolomics and lipidomics permitting effective compound separations and detection. However, there is still a lack of sufficient data on the metabolome and lipidome characterizing biofluids (i.e., plasma, serum, urine) and tissues, which can be easily accessible and reused at any time for future studies. The PhD project aims to focus on (i) merging targeted and untargeted metabolomics and lipidomics methods, (ii) standardization of methods, and (iii) extending the breadth and scope of methods for metabolomics and lipidomics studies (e.g., type 2 diabetes, circadian rhythms). The work will be conducted at the Institute of Physiology CAS and financially supported by various grants (GACR, MSMT, AZV).

Mass spectrometry-based metabolomics of biological systems

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Theses supervisor: doc. Ing. Tomáš Čajka, Ph.D.

Annotation

Untargeted metabolomics methods focus on the analysis of all the detectable metabolites in a sample, including chemical unknowns. Liquid chromatography coupled to mass spectrometry (LC-MS) is the preferred technique in metabolomics permitting effective compound separations and detection. However, up to 80% of all detected signals from untargeted profiling represent unknown metabolites. Such a big obstacle in biomedical and biological research hinders meaningful biochemical and pathway interpretations. The PhD project aims to focus on (i) increasing the coverage of spectral libraries used for metabolite annotation, (ii) applying programs for the prediction of ‘unknown’ metabolites, and (iii) using bioinformatics tools for visualization and interpretation of the data obtained within metabolomics studies (e.g., type 2 diabetes, circadian rhythms). The work will be conducted at the Institute of Physiology CAS and financially supported by various grants (GACR, MSMT, AZV).


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