Biochemie

Školitel: RNDr. Lubomír Janda, Ph.D.

OBJECTIVES: The aim of the research is to study postbiotics, which are responsible for the positive effect of probiotic bacteria. They are functional bioactive compounds produced in and around the cellular environment during fermentation. The outcome contribute to know if the metabolite, enzyme, peptide, lipopolysaccharide or sugar component of the probiotic bacterium may be responsible for the health effect.

FOCUS: The doctoral research project is focused on the study of enzymes capable of cleaving gluten. Students who will participate in this project will have a unique opportunity to combine basic research with applied research.

EXAMPLES of potential student doctoral projects:

• How diet and colon affect the expression of probiotic enzymes, which utilize gluten
• Mapping of epitopes of immunotoxic gluten peptides
• Study of digestion of gluten in the human body Use in vitro cell model for study of intestinal barrier
• Analysis of the effects of microbiome on celiac disease

MORE INFORMATION: https://www.vri.cz/cz/o_nas/oddeleni/oddeleni-imunologie

Školitel: doc. RNDr. Jaroslav Turánek, DSc.

OBJECTIVES: The research aims the field of nanomedicine, especially to immunopharmacotherapy of cancer, infection diseases (vaccines) and diagnostics. Outcomes (publications and eventually patent applications) will contribute to development of modern immunotherapeutics like vaccines and adjuvants, targeted anticancer/antiviral drugs and theranostics for in vivo imaging and monitoring the progress of treatment.

FOCUS: Doctoral research projects focus on preparation and complex characterisation of biocompatible functionalised nanoparticles applicable for development of modern therapeutics and theranostics. Student will benefit from world class infrastructure at VRI, including laboratory of physical-chemical methods (microfluidic system, MALS, MADLS, NTA, TRPS, UV VIS/CD/FL/FT-IR spectroscopy, Field Flow Fractionation, thermal methods like DSC and ITC, laboratory of microscopic methods (AFM, TEM, SEM and confocal microscopy), laboratory of tissue culture and biotechnology (FPLC/HPLC, various unique bioreactors for production of recombinant proteins, ultracentrifugation, QRT-PCR, multifunctional multiplate reader, flow cytometry and cell sorter), laboratory of surgery and in vivo imaging (microcomputer tomography microCT and optical whole body scanner) and animal house for experiments on small and large animals, laboratory of histology.

EXAMPLES of potential doctoral projects:

• Preparation and formulation of mRNA in liposomes and evaluation of transfection potential in vitro and in vivo, study of immune response in vivo on mice model
• Expression, purification and characterisation of recombinant proteins/antigens (e.g. HIV-1, influenza, Borrelia), construction of experimental vaccines and study of immune response in vivo
• Preparation of nanoparticle based contrast agents (e.g. gold nanoparticles) for in vivo imaging via microCT and MRI: tumour and thrombi as targets
• New antiviral drugs and their formulation, modification for targeting of macrophages, testing in tissue culture and in vivo models
• New molecular adjuvants and immunomodulators: formulation in nanoliposomes, testing in models in vitro and in vivo
• Nano and microstructures for non-invasive vaccination: preparation, characterisation and testing in in vivo models with model antigens, evaluation of immune response (mice, pig)
• Physiologically active compounds from venom, characterisation, purification, preparation of antisera

MORE INFORMATION: www.vri.cz/en//

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Ass. Prof. RNDr. Jaroslav Turánek, Res. Prof. (turanek@vri.cz) for informal interview.

Školitel: prof. RNDr. Viktor Brabec, DrSc.

OBJECTIVES: New helical compounds that act in a similar way to the natural defense proteins made by many invertebrate, plant, and animal species are at present intensely investigated. This research has been motivated by the original results obtained by Nobel laureate Jean-Marie Lehn who first described metallohelices – organic components wrapped around metal atoms in a helical structure – around 20 years ago. The results so far obtained revealed that the resulting metallohelices displayed antibiotic activity akin to antimicrobial peptides yet have clear advantages over peptides as potential drug molecules. Peptides are difficult and expensive to make and also get chewed up by proteases before they can do their job. In contrast, metallohelices are easy to make on a relatively large scale, and should not be susceptible to those enzymes. They are also optically pure, stable and water soluble, which make them ideal candidates for application in pharmacology as peptide mimetics.

FOCUS: Doctoral research projects focus on the molecular and cellular mechanisms of biological effects of the selected metallohelices connected with their interactions with nucleic acids, in particular with their unusual structures. These studies will be performed using modern biochemical methods and methods of molecular and cellular biophysics available at the Department of Molecular Biophysics and Pharmacology of the Institute of Biophysics, Czech Academy of Sciences in Brno.

EXAMPLES of potential student doctoral projects:

• Interactions of supramolecular helicates with unusual conformations of DNA
• Interactions of supramolecular helicates with unusual conformations of RNA
• Mechanistic studies of antiproliferative effects of supramolecular helicates

MORE INFORMATION: https://www.ibp.cz/en/research/departments/molecular-biophysics-and-pharmacology/info-about-the-department

Školitel: doc. Mgr. Tomáš Kašparovský, Ph.D.

OBJECTIVES:
Study of metabolism estrogenic compounds in ruminants under adverse physiological conditions. The impact of product compounds with estrogenic activity in the animal production on the environment.
FOCUS:
Due to the intake of easily fermentable nutrients, the production of volatile fatty acids is increased. The result of these changes is the decrease in pH, which negatively affects the microbial activity. This work will focus on the effect of this change, so called subacute acidosis, on the production of estrogenic substances. Furthermore, the impact of estrogenic production on the environment as a consequence of nutrition-based feeding containing a certain group of isoflavones will be studied.
EXAMPLE of potential doctoral project - the student will focus on:
Identification of secondary metabolites with estrogenic activities by LC/MS-TOF eventual LC/MS-Q-TOF. Adjustment of rumen fluid culture parameters in the Sartorius bioreactor to simulate subacute acidosis. Tracking of the influence of cultivation factors (aeration, type of food) on isoflavone metabolism under conditions simulating subacute acidosis. Quantification of secondary metabolites with estrogenic activity in the feed. Development of a method for isolation and quantification of secondary metabolites with estrogenic activities in the environment.
PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Assoc. Prof. Tomas Kasparovsky for informal discussion.

Školitel: prof. RNDr. Omar Šerý, Ph.D.

Alzheimerova choroba vzniká jako důsledek více faktorů, mezi které patří faktory životního stylu, ale také genetické faktory. Mírná kognitivní porucha (MKP) je heterogenní klinická jednotka, u které se rozeznávají dvě formy, a to amnestická forma mírné kognitivní poruchy, kdy dochází k objektivní poruše paměti a neamnestická forma mírné kognitivní poruchy. Amnestická forma MKP je charakterizována poruchou paměti, případně postižením dalších kognitivních funkcí, které však nedosahují úrovně demence. Udává se, že tato forma přechází do Alzheimerovy choroby ve 12-18% za rok.
V rámci disertační práce budou sledováni a vyšetřováni pacienti s Alzheimerovou chorobou a s amnestickou formou MKP s cílem zjistit, zda některé genetické markery, které souvisejí s Alzheimerovou chorobou, nejsou přítomny u MKP, což by mohlo v budoucnu přispět k časnému záchytu rizikových osob. Doktorand bude v rámci své práce izolovat DNA ze vzorků pacientů. Pro genotypizace minimálně 400 probandů bude použita metoda NGS sekvenování a kapilárního sekvenování. Jedním z cílů disertační práce bude také porovnávání vlastností buněčných kultur získaných z fibroblastů pacientů s Alzheimerovou chorobou. Zkoumány budou např. rozdíly transkriptomu. Výsledná data budou statisticky analyzována a budou začleněna do stávajícího modelu patogeneze Alzheimerovy choroby.

Školitel: prof. RNDr. Omar Šerý, Ph.D.

Alzheimerova choroba vzniká jako důsledek více faktorů, mezi které patří faktory životního stylu, ale také genetické faktory. Mírná kognitivní porucha (MKP) je heterogenní klinická jednotka, u které se rozeznávají dvě formy, a to amnestická forma mírné kognitivní poruchy, kdy dochází k objektivní poruše paměti a neamnestická forma mírné kognitivní poruchy. Amnestická forma MKP je charakterizována poruchou paměti, případně postižením dalších kognitivních funkcí, které však nedosahují úrovně demence. Udává se, že tato forma přechází do Alzheimerovy choroby ve 12-18% za rok.
V rámci disertační práce budou sledováni a vyšetřováni pacienti s Alzheimerovou chorobou a s amnestickou formou MKP s cílem zjistit, zda některé genetické markery, které souvisejí s Alzheimerovou chorobou, nejsou přítomny u MKP, což by mohlo v budoucnu přispět k časnému záchytu rizikových osob. Doktorand bude v rámci své práce izolovat DNA ze vzorků pacientů. Pro genotypizace minimálně 400 probandů bude použita metoda NGS sekvenování a kapilárního sekvenování. Jedním z cílů disertační práce bude také porovnávání vlastností buněčných kultur získaných z fibroblastů pacientů s Alzheimerovou chorobou. Zkoumány budou např. rozdíly transkriptomu. Výsledná data budou statisticky analyzována a budou začleněna do stávajícího modelu patogeneze Alzheimerovy choroby.

Školitel: prof. RNDr. Jana Kašpárková, Ph.D.

OBJECTIVES: With the intention to better understand the effects, which may play an important role in the biological (pharmacological) action of new combinations of anticancer metallodrugs and agents capable of targeting mechanisms connected with resistance of tumor cells to metallodrugs, new, “dual or multi-action” combinations of chemotherapeutics having the genes that confer resistance to anticancer drugs (cancer resistome) as one of the targets of their action will be introduced and tested. New combinations of metallodrugs and molecules targeting cancer resistomes capable of dual targeting of resistance mechanisms and at the same time DNA will be developed; detailed studies of cytotoxicity, selective targeting into tumor cells, inactivation by coordination to sulfur-containing proteins, DNA binding, cell accumulation, efficiency to affect DNA repair, tolerance of the resulting DNA damage, cellular responses and signaling pathways of new combinations will be performed. To achieve these goals, modern methods of biochemistry, molecular biophysics, oncology, and cell pharmacology will be used.

FOCUS: The aim of this research is to address the need for new combinations of chemotherapeutics capable of targeting mechanisms connected with the resistance of tumor cells to anticancer drugs. The identification of such combinations will improve the efficiency of drugs to kill tumor cells. These studies will be performed using modern biochemical methods and methods of molecular and cellular biophysics available at the Department of Molecular Biophysics and Pharmacology of the Institute of Biophysics, Czech Academy of Sciences in Brno.

EXAMPLES of potential student doctoral projects:

• Targeting resistance to chemotherapy of tumor cells to reinstate their susceptibility to novel, existing and unsuccessful anticancer metallodrugs
• Nanocarriers co-encapsulating two or multiple therapeutic agents
• Synergistic effects of polypharmacology involving metallodrugs in combination with other drugs capable of targeting cancer resistome

MORE INFORMATION: https://www.ibp.cz/en/research/departments/molecular-biophysics-and-pharmacology/info-about-the-department

Školitel: doc. Mgr. Pavel Bouchal, Ph.D.

OBJECTIVE: Renal cell carcinoma (RCC) represents a serious oncological disease with the highest incidence in the Czech Republic. The reliable molecular markers related to the critical clinical scenarios are still missing.

FOCUS: We will use a novel mass spectrometry technique in data independent acquisition mode to acquire digital fingerprints or a well-characterized set of RCC tumors collected accross the Czech Republic. We will aim to identify protein markers or patterns relevant for the clinical scenarios in question, characterize these markers functionally, modulate them therapeutically, and validate.

EXAMPLE of potential doctoral project - the student will focus on:
*Protein biomarkers and patterns identifying patients with localized RCC with a high risk of relapse
*Protein biomarkers and patterns identifying patients with metastatic RCC with a high risk of poor response to available therapy
*Functional characterization of identified proteins using CRISPR/Cas9 technique followed by analysis of cell migration, invasiveness and sensitivity to potential inhibitors.
*Development of a targeted mass spectrometry method for a routine quantification of the novel marker proteins.
We expect that the identified potential biomarkers, therapy targets or molecular patterns will contribute to a more efficient treatment of RCC patients. Supported by Ministry of Health of the Czech Republic, project NV19-08-00250.

MORE INFORMATION: http://www1.sci.muni.cz/en/UBCH/Proteomika

PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Doc. Pavel Bouchal for informal discussion.

Školitel: RNDr. Veronika Ostatná, Ph.D.

Adsorbované proteiny se účastní mnoha biologických funkcí. Proces adsorpce ovlivňuje (i) jejich vlastní aktivitu (enzymatická aktivitu, schopnost adsorbované protilátky vázat se na svůj antigen); (ii) schopnost jiných látek, jako jsou buňky nebo protilátky, vázat se na adsorbovaný protein. V současnosti se adsorpce peptidů zkoumá pomocí teoretických simulací a srovnávající experimenty často chybějí. Elektrochemie může přinést nový pohled na vlivy interakcí proteinů i jejich složitějších systémů, díky možnosti studia proteinů v různých prostředích na nabitých rozhraních.

Školitel: doc. Mgr. Jan Lochman, Ph.D.

OBJECTIVE: Extensive infections of crop plants by plant pathogens have repeatedly resulted in catastrophic harvest failures that have caused major economic and social problems worldwide. Successful plant defence against pathogens is based on early recognition and fast activation of inducible defence responses. Compounds that are recognised by plants and elicit any type of plant defence response have been termed elicitors. Generally, the model of complex plant immune system includes two branches when uses surface pattern recognition receptors (PRRs) acting as initial detectors that recognise slowly evolving microbial-associated molecular patterns (MAMPs) to induce a basal resistance response called MAMPs-triggered immunity (MTI). A major part of plant defences against microbes depends on the effective detection of MAMPs by membrane-localised PRRs. Despite the increasing number of PRRs discovered in the past 20 years, for most of them, it has not been determined whether they are indeed true receptors and especially for receptor-like proteins representing parallel with Toll-like receptors in animal cells.

FOCUS: A well described and accessible model of plant-pathogen interaction is represented by interaction between Solanaceae plants with proteinaceous elicitors secreted by oomycetes including many economically significant crop pathogens, like Late blight, caused by Phytophthora infestans or Oomycetes, on the other hand, include the mycoparasite Pythium oligandrum, which is used as a biocontrol agent against pathogenic fungi. Thus understanding the mechanisms taking place in the oomycal infection process could lead to new methods providing a durable resistance. From culture filtrates of Phytophthora and Pythium spp. small proteinaceous elicitors named elicitins were isolated and today, elicitins are among the most well-known oomycetes MAMPs inducing systemic resistance (SR) on several responding plant genotypes across various families.

EXAMPLE of a potential doctoral project - the student will focus on: A position for a double degree PhD student is available in the group of Jan Lochman at Department of Biochemistry and the group of Nathalie Leborgne Castel at Plant Microorganism Interactions Research Cluster of UMR AGROECOLOGY in Dijon. The project aims to increase understanding of mechanisms involved in the perception of MAMPs from oomycetes in different plants models represented by the plants of agriculture importance, tobacco (Nicotiana spp.) and tomato (Solanum lycopersicum spp.). The main goals of the project are the characterisation of structure regions important for the interaction of selected MAMPs with their recently described receptor, a better understanding of processes on plasma membrane related to elicitins perception and detailed characterisation of general signalling events following MAMPs perception by the receptor. To pursues these objectives methods of proteins expression and structural analysis will be adopted together with methods studying changes in membranes parameters (order, fluidity) as well as approaches focused to transcriptomic and proteomic changes and targeted genome editing (CRISPR/Cas9).

PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Assoc. Prof. Jan Lochman for an informal discussion.

Školitel: doc. Mgr. Tomáš Kašparovský, Ph.D.

OBJECTIVES:
An in-vitro study of the metabolism of minor mycotoxins enniatin B, B1, A and A1, beauvericin and fusaproliferin in ruminal fluid.
FOCUS:
Ruminants are generally considered less susceptible to fusarium mycotoxins because their rumen microflora is able to degrade mycotoxins to some extent. The degradative capacity of the rumen microflora can be affected by many factors, including pH and redox potential. The metabolism of minor mycotoxins in the rumen in ruminants has not yet been satisfactorily described, as has their possible effect on the rumen microflora due to their biological effects.
EXAMPLE of potential doctoral project, the student will focus on:
Identification of mycotoxins: enniatin B, B1, A and A1), beauvericin (BEA) and fusaproliferin by LC/MS-TOF eventual LC/MS-Q-TOF. Adjustment of rumen fluid culture parameters in the Sartorius bioreactor to study of mycotoxins metabolism. Tracking of the influence of cultivation factors (aeration, type of food) or non-physiologic level of mycotoxins on mycotoxins metabolism.
PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Assoc. Prof. Tomas Kasparovsky for an informal discussion.

Školitel: Mgr. Jiří Šána, Ph.D.

OBJECTIVES: The human genome contains less than 2% of protein-coding genes, although at least 90% of the genome is transcriptionally active. Thus, the human transcriptome contains not only sequences of protein-coding genes and splice variants but also includes a disproportionately larger number of non-coding RNAs. In addition to the so-called "housekeeping" non-coding RNAs, such as tRNA, rRNA, snRNA, or snoRNA, regulatory non-coding RNAs have also been described. These molecules are involved in gene expression regulation at various levels and thus play essential roles in cell development, physiology, but also pathological conditions. The aim of the dissertation thesis will be the study of these non-coding RNAs in solid tumors.
FOCUS: The dissertation thesis will be focused on the detailed description of molecular mechanisms of action of some non-coding RNAs in selected solid tumors and on the study of these molecules as new diagnostic, prognostic, and predictive biomarkers and potential therapeutic targets useful in clinical practice.
METHODS: Next-generation sequencing, Sanger sequencing, capillary electrophoresis, qRT-PCR, digital PCR, in vitro techniques including cell culturing, non-coding RNA transitional and stable transfection, CRISPR-Cas9 genome editing, pull-down assays, flow-cytometry analysis, immunocytochemistry, western blot analysis.
LITERATURE: https://www.sci.muni.cz/en/about-us/faculty-staff/184506/publications
GRANT PROJECTS: https://www.sci.muni.cz/en/about-us/faculty-staff/184506/projects
PLEASE NOTE: Before initiating the formal application process to doctoral studies, all interested candidates must contact dr. Jiri Sana (jiri.sana@ceitec.muni.cz) for an informal discussion.