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. Jaroslav Turánek, DSc.

BACKGROUND: Cardiovascular diseases currently contribute the biggest burden of the mortality worldwide. The molecular mechanisms behind are frequently underexplored.
Current pre-clinical research of cardiovascular diseases utilizes animal models predominantly. However, they provide low throughput and may fail to recapitulate certain aspects of human pathophysiology. That is why an in vitro model can be a suitable alternative especially if combined with biological material of human origin. OBJECTIVES: Provide insights into selected aspects of a cardiovascular disease using a specifically tailored vasculature model.
FOCUS: The group of Jan Víteček is focused on thrombolysis in connection with ischemic stroke treatment and the role of blood flow in vascular pathophysiology.
EXAMPLES of potential student doctoral projects:
Mechanisms of thrombolysis and recanalization; Biochemical mechanisms of clot thrombolytic resistance; Role of blood flow in development of aneurysms and stenoses; Electrical phenomena in vasculature homeostasis.
METHODS: Vascular model construction, cell cultures, mechanobiological characterisation of blood clots, fluorescence confocal and electron microscopy, basic approaches of biochemistry and molecular biology.
MORE INFORMATION:
https://www.ibp.cz/en/research/departments/biophysics-of-immune-systems/research-profile/group-of-vitecek-jan
https://www.strokebrno.com/members/institute-of-biophysics/
PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Jan Víteček for an informal discussion. Školitel

Mgr. Jan Víteček, Ph.D.

BACKGROUND: Extremely acidophilic and chemolithotrophic microorganisms are well known for their ability to dissolve metals directly via redoxolysis or indirectly via acidolysis and complexolysis. The microbial oxidation of ferrous iron and elemental sulfur generates ferric iron and sulfuric acid, facilitating the dissolution of oxide or sulfide minerals and releasing the incorporated metals. FOCUS: Our research group aims to study the metabolism of extreme acidophiles and their role in recovering valuable metals from natural and waste minerals. EXAMPLES of potential student doctoral projects: Study of metabolic pathways related to the production of important metabolites in extreme acidophiles using a multi-omics approach; characterize proteins essential for their metabolism and adapt to extreme environments using heterologous protein expression. METHODS: Microbial cultivation up to the level of bioreactors; biochemical methods: isolation, separation, purification, and identification of biomolecules (ultrafiltration, ultracentrifugation, gel electrophoresis, FPLC, HPLC); enzyme kinetics (UV/VIS spectrophotometry, ITC, MST); molecular biology and genetic engineering methods: PCR, qPCR, RT-qPCR, immunodetection, sequencing, cloning, transformation, mutagenesis, protein-protein interactions (SPR); omics methods: genomics and transcriptomics (NGS), proteomics and metabolomics (UHPLC-MS/MS); biotechnological methods: heterologous protein expression, bioleaching. MORE INFORMATION: https://www.orion.sci.muni.cz/cs/veda-a-vyzkum/vyzkumna-skupina-environmentalni-biotechnologie.html

Poznámky

Školitelem této práce bude dr. Kučera po schválení Vědeckou radou PřF MU.

Školitel

Mgr. Jiří Kučera, Ph.D.

BACKGROUND: 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 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 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. In the later phase of the study, this concept can be extended to further solid malignancies such as colorectal cancer and breast cancer.

METHODS Liquid chromatography-mass spectrometry, data analysis, molecular and cellular biology, CRISPR/Cas9, analysis of cell migration and invasion
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

doc. Mgr. Pavel Bouchal, Ph.D.

BACKGROUND: Modern methods of crop protection aim to reduce the pesticide application and their presence in food and environment. Precise monitoring of the pathogen pressure and, if possible, the crop resistance is necessary to prevent superfluous pesticide application.
FOCUS: The group is focused on finding metabolic markers of crop defensive power. We will monitor the pathogen presence and crop disease symptoms in the field as well as the levels of potential metabolic markers of defence in the crop plants during the season.
EXAMPLES of potential student doctoral projects: Monitoring of defence-hormones levels; Expression analysis of defence-related genes; Targeted and untargeted metabolomics of healthy and diseased plants; Quantification of specialized metabolites.
METHODS: PCR, LC/MS, basic biochemical methods
MORE INFORMATION: https://www.orion.sci.muni.cz/cs/veda-a-vyzkum/vyzkumna-skupina-sekundarni-metabolity.html
PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Katerina Dadakova for an informal discussion.

Poznámky

Školitelkou této práce bude paní dr. Dadáková po schválení Vědeckou radou PřF MU.

Školitel

Mgr. Kateřina Dadáková, 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.

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

prof. RNDr. Jana Kašpárková, Ph.D.

V průběhu roku 2020 byl svět zachvácen pandemií virem SARS-CoV-2, která pokračuje i v roce 2021. První případy onemocnění COVID-19, způsobených virem SARS-CoV-2 jsou popsány na tržišti s divokými zvířaty ve Wuchanu. Pacienti trpěli závažnými respiračními infekcemi doprovázenými dalšími příznaky, jako jsou horečky, zánět plic, kašel, dušnost, průjmy atd. Analýzou sekvence RNA viru se ukázalo, že se jedná o zatím nepopsaný druh koronaviru, který je příbuzný virům SARS a MERS. Virus rozšířil po celém světě a do konce dubna 2021 způsobil úmrtí více než 3 milionů lidí. Většina osob, které umírají, jsou osoby nad 60 let věku. Nové varianty koronaviru ale způsobují úmrtí i mladších osob a nevyhýbají se bohužel ani těhotným matkám.
Cílem disertační práce bude analyzovat vzorky získané z těl osob, které byly nakaženy koronavirem SARS-CoV-2. Bude zkoumána přítomnost virů v různých tkáních a orgánech metodou RealTime PCR, mikroskopickými a imunologickými technikami. Tkáně budou vyšetřovány mikroskopickými technikami v souvislosti se strukturálními změnami vzniklými onemocněním COVID-19. Bude zkoumána genová exprese vybraných genů v odebraných vzorcích. Výsledná data budou statisticky zpracována, vyhodnocena a začleněna do aktuálních poznatků o patogenezi onemocnění COVID-19.

Školitel

prof. RNDr. Omar Šerý, Ph.D.

BACKGROUND: Triple negative breast cancer (TNBC) appears as a homogenous group within a current breast cancer (BC) classification based on hormonal and Her-2 receptors. It is typically treated using chemotherapy. Based on gene expression classification, however, this is a molecularly heterogeneous subtype that can be classified into several sub-subtypes.
FOCUS: We will (i) classify the well characterized set of ca. 100 TNBC tumors into sub-subtypes based on proteotypes obtained using data independent acquisition mass spectrometry, (ii) differences between transcriptomics (RNA-Seq) and proteomics profiles will be characterized and gene products typical for protein level will be identified, and (iii) impact of somatic mutations on levels of key proteins identified in proteotypes will be analyzed. We will aim to identify proteins, molecular pathways and mutations critical for TNBC proteotype classification that associate with therapy response, patient survival and could serve as targets of stratified TNBC treatment.
EXAMPLE of potential doctoral project - the student will focus on:
*Protein and transcript biomarkers, gene mutations and patterns typical of TNBC subtypes.
*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.
*The student will be involved in a collaboration with local and international research team members to analyze and intepret associations between gene mutations, transcript and protein levels.
METHODS: Liquid chromatography-mass spectrometry, RNA-Seq, exome sequencing, proteomics, data analysis, molecular and cellular biology, CRISPR/Cas9, analysis of cell migration and invasion.
MORE INFORMATION:
Supported by Ministry of Health of the Czech Republic, project NU22-08-00230 (2022-25). https://www.muni.cz/vyzkum/projekty/65540
https://www.orion.sci.muni.cz/cs/veda-a-vyzkum/vyzkumna-skupina-proteomiky.html
PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Doc. Pavel Bouchal for informal discussion. Školitel

doc. Mgr. Pavel Bouchal, Ph.D.

Lectins are ubiquitous carbohydrate-binding proteins, which play a key role in various processes including cell-cell communication and host-pathogen interaction, but also serve as a valuable tool for medicine and life sciences research. Carbohydrate-mediated recognition plays an important role in the ability of pathogenic bacteria to adhere to the surface of the host cell in the first step of their invasion and infectivity. Lectin-carbohydrate interactions are usually characterised by a low affinity for monovalent ligands that is balanced by multivalency resulting in high avidity for complex glycans or cell surfaces.
The main aim of the PhD work will be the structure-functional studies of carbohydrate binding proteins involved in a bacterial pathogenesis and/or their application as the bioanalytical tool to study a specific glycosylation related to cell specific tissues.

Školitel

prof. RNDr. Michaela Wimmerová, Ph.D.

Our research is focused on the development of new experimental methods in bioanalytical chemistry that enable highly sensitive measurements. We employ surface-modified photon-up-converting nanoparticles, which can be detected under near-infrared excitation light without any background interference even at the single nanoparticle level. With our broad repertoire of methods, we detect pathogens, cancer markers and environmental toxins and analyze the function of enzymes.
Objectives: We will use UCNPs as a detection label for single-molecule (digital) immunoassays. While UCNPs enable the detection of analytes without any optical background noise, non-specific binding is still a challenge because it lowers the sensitivity of the immunoassays. Non-specific binding has conventionally been reduced by optimizing the surface architecture of UCNP labels and coating of microtiter plates. In this project, we will investigate an entirely new approach for the reduction of non-specific binding, which is only possible by using single-molecule immunoassays: If we use two labels showing different colors for the detection of one analyte, the presence of the analyte can be verified by two-color detection under the microscope; however, if there is only one color detectable, the signal can be attributed to non-specific binding. In this way, we aim to achieve the highest possible sensitivity for the detection of cancer markers and virus particles such as Covid-19.

Profile: High motivation and joy in working on new experimental approaches in bioanalytical chemistry. Willingness to use English communication in an international team.

We offer: Supportive environment for Interdisciplinary work in an international team. Work on state-of-the-art projects with high societal relevance. Publications in high-impact journals. Building an international network with various European groups.

Školitel

Dr. rer. nat. habil. Hans-Heiner Gorris

OBJECTIVES: Development of instrumentation and methods for comprehensive and/or selective enrichment and analysis of nucleic acids, proteins and metabolites. The work will include electrophoretic and mass spectrometric instrumentation and will be focused on instrumental as well as methodological development of new techniques based on preliminary results obtained with an industrial partner.

FOCUS: Proof of principles of epitachophoresis for biology related samples; design and construction/modification of instrumentation for large volume sample processing. The topic is based on entirely new procedures currently in the state of patent application in the USA.

METHODS: epitachophoresis, MS, capillary electrophoresis and HPLC in combination with different detection techniques

LITERATURE: see WOS.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates should contact Ing. František Foret, CSc., e-mail: foret@iach.cz at CEITEC or Instute of nalytical Chemistry Academy of Science Czech Republic for informal discussion.

Školitel

Ing. František Foret, CSc.

OBJECTIVE: Neurodegenerative foldopathies represent a group of human protein-misfolding disorders that are characterized by a pathological alteration in conformation of a native protein which makes it resistant to degradation and leads to pathological gain and loss of function. These are followed by aggregation of the misfolded proteins into insoluble deposits. One of the most prominent protein-misfolding disorders is AD. The number of patients suffering dementia in the Czech Republic is estimated at 160 thousand. Up to two-thirds of cases are due to Alzheimer's disease, others include, for example, vascular dementia, Parkinson's disease or other degenerative brain disorders.

FOCUS: In neurodegenerative disorders (including Alzheimer's disease, AD) astrocytes/astroglia undergo complex changes that range from atrophy with loss of function to accumulation of reactive cells around disease-specific lesions (senile plaques in the case of AD). The cellular pathology of astrocytes in the context of human AD remains enigmatic; mainly because of severe limitations of animal models, which, although reproducing some pathological features of the disease, do not mimic its progression in full. The human induced pluripotent stem cells (hiPSCs) technology creates a novel and potentially revolutionizing platform for studying fundamental mechanisms of the disease and for screening to identify new therapeutic compounds.

EXAMPLE of a potential doctoral project - the student will focus on: Suitable procedures for studying early pathology of Alzheimer's disease (AD) are currently being sought. The main aim of the project is to create a model of cell cultures suitable for monitoring changes in the biology of nerve cells (neurons and astrocytes) in patients with AD. Using the induced pluripotent cell method (iPSC), the role of nerve cells in the formation of sporadic form of AD will be studied.

The specific aims are following:
• Analysis of DEGs (differently expressed genes) between patients and controls and measured physiological parameters in and between groups.
• Analysis of DEGs (differently expressed genes) between patients and controls and measured physiological parameters in and between groups.
• Verification of selected differences in genes expression by qPCR analysis.
• Verification of very promising candidate genes expression by Western Blot.
• Analysis of selected neurotransmitters by LC-MS/MS.

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. Jan Lochman, Ph.D.

OBJECTIVES: Use metal nanoparticles as labels for sensitive mass spectrometry imaging. The method allows detection of a single molecule on a tissue section.

EXAMPLES of doctoral projects:

- Development of sample preparation protocol for specific detection of selected markers on sections of 3D cell aggregates or other tissues.

- Optimization of specific labelling with nanoparticles. The specificity will be based on antibody-antigen and avidin-biotin interactions, aptamer bindings etc.

- Development of nanoparticle detection schemes using inductively coupled plasma (ICP) and matrix-assisted laser desorption/ionization (MALDI) techniques.

- Study of nanoparticle transport efficiency in ICP MS. Confocal fluorescence or electron microscopy will be used as a reference method.

MORE INFORMATION: bart.chemi.muni.cz Školitel

prof. Mgr. Jan Preisler, Ph.D.

OBJECTIVES: The dissertation projects focus on matrix-assisted laser desorption ionization mass spectrometry imaging (MALDI MSI) for visualization of spatial distribution of biologically important compounds without chemical labelling.

EXAMPLES of doctoral projects:

- Development of sample preparation protocols for MALDI MSI. Samples may include 3D cell aggregates or other biological tissues.

- MALDI MSI of perifosine and other antitumor agents in 3D cell aggregates.

- Optimization of reactions on tissue sections. The aim will be, e.g., determination of double bond position in fatty acid chains in lipids.

MORE INFORMATION: bart.chemi.muni.cz Školitel

prof. Mgr. Jan Preisler, Ph.D.

OBJECTIVES: Immunochemical assays are well-established analytical tools that combine the specificity of antibodies with sensitive readout based on various signal-generating labels. The use of antibodies allows for the detection of a large variety of analytes, from small molecules, through proteins, to pathogens. The aim of this thesis is the development of advanced immunochemical methods based on nanomaterials for highly sensitive bioanalysis.

FOCUS: The research will focus on clinically and environmentally relevant analytes, including biomarkers and pathogens. The highly sensitive detection of low analyte levels is essential for rapid diagnosis in preventing the spreading of infections.

METHODS: The particular detection methods will be chosen with respect to the target analyte and sample matrix to fully exploit the potential for practical applications. Due to their robustness and simplicity, the conventional enzyme-linked immunoassays will be carried out for first tests and optimizations. Afterward, the possibilities of assay performance improvement will be explored. Nanomaterial-based labels will be used for the detection based on their catalytic (e.g., Prussian blue nanoparticles) or luminescence (e.g., photon-upconversion nanoparticles or quantum dots) properties. Furthermore, sample preconcentration will be carried out using magnetic micro- and nanoparticles. The advantages of magnetic particles will also be exploited in the detection based on microfluidics, including multiplexed analysis.

LITERATURE: https://www.muni.cz/en/people/357740-zdenek-farka/publications

PLEASE NOTE: Before initiating the formal application process to doctoral studies, interested candidates should contact Zdeněk Farka (farka@mail.muni.cz) for an informal discussion.

Školitel

doc. Mgr. Zdeněk Farka, Ph.D.

DNA sequencing is a key technology for the life sciences and clinical diagnosis, which enables early individual risk assessment of various diseases (such as cancer) that have a genetic component. We aim to develop a new nanoparticle-based multicolor resonant energy transfer (FRET) system in combination with single DNA polymerase molecules (DNA nanoreaders) to read out DNA sequences continuously, accurately, and in parallel. This interdisciplinary project will involve the development of new instruments, new anti- Stokes luminescent nanomaterials for multicolor FRET that can be detected without autofluorescence and their biofunctionalization to overcome the fundamental limitations of state- of-the-art DNA sequencing techniques.

Poznámky

This project is supported by the Czech grant agency (GAČR) within the binational (Czech-Polish) project: https://gacr.cz/dalsich-sest-cesko-polskych-projektu-se-zacne-resit-pristi-mesic/

Školitel

Dr. rer. nat. habil. Hans-Heiner Gorris

OBJECTIVES: The advanced nanomaterials as quantum dots (QD), photon up-converting nanoparticles (UCNP) and coloid metal nanoparticles (Au, Ag, Cu NP) will be combined with sensing systems as waveguides, optical and Raman microscopic set-ups, surface plasmon resonance transducers and other options in order to develop biosensing devices with enhanced sensitivity. Both static evaluation - analog response and scanning / tracking / discriminating approaches - digital response for single-molecules (object, cell, nanoparticle) detection will be evaluated.

FOCUS: The target analytes will include metabolites and clinical markers in body fluids (serum, saliva), food and drinks (allergens, contaminants, toxins) and infectious microbes (honey bee pathogens, Salmonella, Enterobacteria).

METHODS: Bioconjugation and immobilization of biomolecules, characterization of bioconjugates and biointerfaces, ink-jet based microarrays, scanning probe microscopies, design of biosensing devices, advanced optical techniques, scanning probe microscopy, signal acquisition and processing, chemometrics, software development.

LITERATURE: https://www.muni.cz/en/people/2202-petr-skladal/publications

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates should contact Petr Skladal (skladal@chemi.muni.cz) for informal discussion. Školitel

prof. RNDr. Petr Skládal, CSc.

OBJECTIVES: Immunochemical assays combine the specificity of antibodies with the sensitivity of various kinds of readout methods to allow detecting target molecules. The great flexibility, provided by the possibility to use antibodies specific to desired structure, allows detecting all sorts of analytes, from small molecules, through proteins, to viruses and bacteria. The aim of this thesis is the development of advanced immunochemical approaches for use in clinical diagnostics.

FOCUS: The research will focus on clinically relevant targets, including biomarkers (prostate cancer, breast cancer, acute myocardial infarction) and pathogens (Salmonella, SARS-CoV-2). In all these cases, the highly sensitive detection with low cross-reactivity is essential for rapid diagnosis, allowing early disease treatment.

METHODS: The particular choice of the detection method will be made with respect to the target analyte and sample matrix to maximize the potential for practical applications. The first tests will be carried out using conventional enzyme immunoassays due to their simplicity and robustness. Afterward, various ways to improve the assay performance will be explored. Nanoparticle-based labels will be exploited to allow detection based on their catalytic (e.g., Prussian blue nanoparticles) or luminescence (e.g., photon-upconversion nanoparticles or quantum dots) properties. The sample preconcentration will be carried out using magnetic micro- or nanoparticles. Furthermore, the potential for point-of-care analysis will be demonstrated on lateral flow immunoassays and optical or electrochemical biosensors. The close collaboration with the Faculty of Medicine and industrial partners promises that apart from writing scientific publications, the developed methods can also find commercial applications.

LITERATURE: https://www.muni.cz/en/people/357740-zdenek-farka/publications

PLEASE NOTE: Before initiating the formal application process to doctoral studies, the interested candidates should contact Zdeněk Farka (farka@mail.muni.cz) for an informal discussion.

Školitel

doc. Mgr. Zdeněk Farka, Ph.D.

Bioortogonální aktivace pro-léčiv je nový přístup v terapii nádorových onemocnění. Spočívá v katalytické aktivaci léčiva se zablokovanou funkční skupinou přímo v nádorové tkáni. V naší laboratoři se zabýváme aktivitou organokovových komplexu paladia a ruthenia v biologicky relevantních podmínkách. Pro studium katalytické aktivity jsou často využívány fluorescenční sondy, které lze také využít pro detekci paládiové kontaminace ve farmaceutických přípravcích. Z různých důvodů (buněčná toxicita, buněčný efflux) je mnoho standardních fluorescenčních látek nepoužitelných pro dlouhodobé studium katalytické aktivity organokovových sloučenin. Úkolem studenta bude podílet se na přípravě modifikovaných fluorescenčních sond se sníženou toxicitou a zvýšenou retenci v buňkách. Bude studovat citlivost vyvinutých sond k paladiu a dalším kovovým komplexům. Dále se bude podílet na syntéze a charakterizaci nových organokovových katalytických komplexů a evaluaci jejich katalytické aktivity v buňkách. Práce bude metodologicky obšírná a bude zahrnovat techniky organické syntézy, purifikace látek, biochemické analýzy a techniky tkáňových kultur.

Školitel

Mgr. Vladimír Pekařík, Dr.

Hyaluronan(HA) je lineární polysacharid z disacharidických jednotek kyseliny D-glukuronové a D-N-acetylglukosaminem. HA je štěpen na kratší fragmenty dvěma typy enzymů. Savčí hyaluronidázy hydrolyticky štěpí řetězce za vzniku menších fragmentů z nezměněných monosacharidů. Mikroorganismy produkují hyaluronan lyázy, které rovněž štěpí řetězce hyaluronanu beta–eliminační reakcí, při které na neredukujícím konci fragmentu vzniká kyselina glukuronová s dvojnou vazbu mezi C4 a C5. Houba Talaromyces stipitatus produkuje hyaluronidázu (TsHr), která štěpí hydrolyticky 1,4 glykosidickou vazbu. Ačkoli svojí primární strukturou je savčím hyaluronidázám podobná jen vzdáleně, patří do rodiny hydroláz glykosidických vazeb GH16, konečnými produkty jsou krátké fragmenty ze 4 až 6 monosacharidů. Předběžné výsledky s rekombinantní TsHr ukazují, že dokáže štěpit deriváty HA savčím enzymem neštěpitelné. TsHr je strukturně příbuzný s transglykosylázami, které patří do stejné rodiny. To by mohlo být využitelná v chemoenzymatických syntézách derivátů HA s definovanou polohou substituentů.
Cílem první části studia bude přispět k poznání TsHr po stránce kinetiky i mechanismu enzymatické reakce a porovnat získané výsledky se savčí bovinní testikulární hyaluronidázou. Bude studována inhibice TsHr různě dlouhými a modifikovanými fragmenty hyaluronanu. Poté by mělo být rozhodnuto, zda enzym TsHr spolu s dalšími enzymy bude využitelný při stanovování rozložení substituentů na řetězci derivátů HA. U savčích hydroláz byla prokázána transglykosylační aktivita - spojování kratších fragmentů HA na delší řetězce. Nikdo však neprokázal, že je to možné u fragmentů substituovaných vybranými substituenty v určitých polohách. Pokud se prokáže, že enzym TsHr není tak citlivý na substituci hyaluronanu jako savčí enzymy, bude zkoumána transglykosylační aktivita a případně hledány podmínky pro využití při syntéze derivátů HA.
Enzym štěpí vysokomolekulární hyaluronan na kratší fragmenty, čímž vytváří koktejl kratších fragmentů hyaluronanu v reakční směsi. Tyto nově vzniklé fragmenty jsou rovněž štěpeny hyaluronidázou, avšak pravděpodobně s jinými kinetickými parametry. Ve výsledku by se tento stav mohl jevit jako inhibice substrátem/produktem. V savčích organismech by toto mohla být cesta regulující rychlost degradace hyaluronanu ve tkáních. Toto by mohlo přispět jednak k potvrzení potenciální regulační role fragmentů a k poznání rozdílů mezi houbovým a savčím enzymem. Navíc v literatuře se popisují interakce různých fragmentů HA se savčím enzymem, které se odehrávají mimo aktivní centrum - projevuje se změnou kinetických parametrů.

Literatura:
L. Bobková, D. Smirnou, M. Krčmář, J. Kulhák, M. Hermannová, L. Franke, V. Velebný (2018) Discovery and characteristic of hyaluronidases from filamentous fungi. Current Biotechnology 7: 2.

Školitel

prof. RNDr. Petr Skládal, CSc.

Experimentální část práce bude zahrnovat vývoj nových mikroextrakčních technik, které jsou založeny na selektivních přechodech analytů přes semi-permeabilní fázová rozhraní [1,2]. Při přechodu analytů bude využito difuze [1] nebo bude přechod urychlen účinkem elektrického pole [2]. Výsledné mikroextrakční techniky budou spojeny off-line nebo in-line s vhodnými analytickými metodami (primárně s kapilární elektroforézou) a adekvátnost takového spojení bude demonstrována analýzami biologicky, klinicky a toxikologicky významných analytů v reálných komplexních vzorcích jako je moč, krevní sérum/plasma a plná krev. [1] Kubáň, P., Boček, P., J. Chromatogr. A 1234 (2012) 2-8. [2] Kubáň, P., Šlampová, A., Boček, P., Electrophoresis 31 (2010) 768-785.

Školitel

RNDr. Pavel Kubáň, DSc.

OBJECTIVES: Droplet microfluidics offers significant advantages for performing high-throughput screens and sensitive assays. Droplets allow sample volumes to be significantly reduced, leading to concomitant reductions in cost and increasing of assay sensitivity. It combines these powerful features to enable currently inaccessible high-throughput screening applications, including single-cell and single-molecule assays.

FOCUS: The subjects of the study will be medicinally and pharmacologically important enzymes and the screening of their enzymes.

METHODS: droplet microfluidic system with the LIF detection, MS, UV-VIS, LIF, C4CD. A new sampling technique based on the dry blood spot will be used. Capillary electrophoresis and HPLC in combination with different detection techniques – MS, UV-VIS, LIF, C4CD will be used as supporting methods.

LITERATURE: https://www.sci.muni.cz/en/about-us/faculty-staff/1865-zdenek-glatz/publications

GRANT PROJECTS: https://www.sci.muni.cz/en/about-us/faculty-staff/1865-zdenek-glatz/projects

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates should contact Zdenek Glatz (glatz@chemi.muni.cz) for informal discussion.

Poznámky

Only one of the proposed theme will be finally occupied.

Školitel

prof. RNDr. Zdeněk Glatz, CSc.

OBJECTIVES: Ambient mass spectrometry (MS) offers the versatile group of techniques providing analysis of solid sample surfaces and liquids in an open atmospheric pressure environment. It provides fast, direct analysis of objects without any sample pretreatment with the use of the mass spectrometer. Direct Analysis in Real Time (DART) and Desorption electrospray ionization (DESI) will be used in this project for the important clinical and pharmacological studies. As a comparative methods Direct Injection (DI) and MS combination with the separation methods HPLC a CE will be used.

FOCUS: The target analytes will include drugs and their metabolites and clinical markers in body fluids (blood, serum, saliva).

METHODS: DART-MS and DESI-MS, capillary electrophoresis and HPLC in combination with different detection techniques – MS, UV-VIS, LIF, C4CD. A new sampling technique based on the dry blood spot will be used.

LITERATURE: https://www.sci.muni.cz/en/about-us/faculty-staff/1865-zdenek-glatz/publications

GRANT PROJECTS: https://www.sci.muni.cz/en/about-us/faculty-staff/1865-zdenek-glatz/projects

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates should contact Zdenek Glatz(glatz@chemi.muni.cz) for informal discussion.

Poznámky

Only one of the proposed theme will be finally occupied.

Školitel

prof. RNDr. Zdeněk Glatz, CSc.