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.

Kinetic study of the native and perturbed denitrification pathway
BACKGROUND: Denitrification is a type of anaerobic respiration in which nitrate is progressively reduced to nitrogen in four successive enzymatic reactions. This process causes a loss of 25-90% of nitrogen from soils, greatly reducing the availability of fertilizer nitrogen to plants. In addition, it can release nitrous oxide, which is a greenhouse gas and a disruptor of the stratospheric ozone layer. Despite these negative effects, denitrification has positive applications in the biological treatment of wastewater.
FOCUS: Factors influencing the dynamics of denitrification at the level of activities of individual denitrifying enzymes and membrane nitrate and nitrite transporters will be investigated. Special attention will be paid to the possibilities of increasing the rate of denitrification by extracellular electron donors or, on the contrary, suppressing it by specific inhibitors.
EXAMPLES: Aerobic denitrification possibilities. Electrochemical and photochemical support of denitrification. Bacteria as scavengers for N2O. Inhibition of denitrification by secondary plant metabolites.
METHODS: Microbial cultivation techniques, spectrophotometry, membrane inlet mass spectrometry, amperometry, liquid chromatography, cassette mutagenesis, PCR methods, etc.
MORE INFORMATION: https://ubch.sci.muni.cz/en/our-research/research-groups/biochemistry-of-denitrification-bacteria
PLEASE NOTE: Before starting the formal application process for doctoral studies, the candidate must contact Prof. Igor Kucera at ikucera@chemi.muni.cz. Školitel

prof. RNDr. Igor Kučera, DrSc.

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.

Cílem této disertační práce je prozkoumat a optimalizovat metabolické a bioenergetické dráhy zelených sirných bakterií (GSB) za účelem maximalizace jejich efektivity v procesu detoxikace sirovodíku a asimilace oxidu uhličitého v prostředí fotobioreaktoru. Práce se zaměří na detailní analýzu molekulárních mechanismů, které řídí anoxygenní fotosyntézu a autotrofní fixaci uhlíku, včetně identifikace klíčových genů a enzymů. Důraz bude kladen na vliv vnějších faktorů, jako jsou světelné podmínky, teplota a chemické složení média, na optimalizaci kultivačních podmínek a zvýšení výnosu cílových bioproduktů, jako jsou elementární síra a organické kyseliny. Výsledky studie mohou přispět k rozvoji inovativních biotechnologií pro environmentální aplikace, jako je čištění odpadních vod nebo udržitelná produkce biomateriálů, a zároveň nabídnout nové přístupy k efektivnímu snižování emisí oxidu uhličitého v průmyslových procesech.

Školitel

doc. Ivan Kushkevych, 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.

BACKGROUND: Extracellular vesicles (EVs) produced by cancer cells function as a unique form of intercellular communication that can promote cell growth and survival, help shape the tumor microenvironment, and increase invasive and metastatic activity.

FOCUS: To identify and validate biomarkers at the molecular level, in particular transcriptome, miRNome, and proteome with special attention paid to the research of alternative resources of nucleic acids and proteins for non-invasive or minimally invasive diagnostics in relevant clinical situations.

EXAMPLE of potential doctoral project - the student will focus on:

• Optimization of EVs isolation from cell cultures and body fluids
• Identification of protein biomarkers and patterns of EVs using mass spectrometry
• RNA sequencing to identify specific transcripts that are associated with the manifestation of the disease
• Functional analysis and validation of newly identified cancer-related biomarkers loaded on EVs.

We expect that the identified potential biomarkers, therapy targets or molecular patterns will contribute to a more efficient treatment of cancer patients. It will be supported by the project SALVAGE (P JAC; reg. no. CZ.02.01.01/00/22_008/0004644) – co-funded by the European Union and by the State Budget of the Czech Republic.

METHODS: Size exclusion chromatography, mass spectrometry, isolation of nucleic acids, RNA sequencing, data analysis, molecular and cellular biology, Western blotting, PCR methods, etc.

MORE INFORMATION: https://www.mou.cz/vyzkumne-centrum-aplikovane-molekularni-onkologie-recamo/t1478

PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact assoc. prof. Roman Hrstka for informal discussion.

Školitel

doc. Mgr. Roman Hrstka, Ph.D.

BACKGROUND:

The soil microbiome and its diversity play a crucial role in the process of plant nutrient uptake and resistance to biotic and abiotic stresses, including plant resistance to the presence of hydrocarbons in the soil. Modification of the soil microbiome by application of different fertilizers or bioactive compounds is therefore of great interest in agricultural practice.

FOCUS:

In the first part of this project, we will apply phosphate fertilizer recovered from sewage sludge and test its effectiveness on model crops. At the same time, the levels of toxic metals in the soil and plants will be analyzed and the microbial diversity in the soil will be identified. In the second part of the project, we will study the complex interactions between plants, arbuscular mycorrhizal fungi (AMF) and mycorrhizal helper bacteria (MHB) in hydrocarbon-contaminated soils and the role of these interactions in plant resistance to soil hydrocarbons.

EXAMPLES:

The role of phosphate fertilizer on plant root system parameters and plant growth. Analysis of microbiome changes after fertilizer application by NGS techniques. Analysis of transcriptomic changes in plants and selected AMF and MHB in hydrocarbon-contaminated soil. Analysis of changes in stress-related enzyme activities due to the presence of hydrocarbons in soil.

METHODS:

Plant cultivation and phenotyping techniques, NGS techniques for analysis of microbiome and transcriptomic changes, RT-qPCR method, LC-MS analysis of phytohormones

MORE INFORMATION:

https://ubch.sci.muni.cz/nas-vyzkum/vyzkumne-skupiny/molekularni-patologie, Supported by INTERREG project ATCZ00043 - PHOS4PLANT.

PLEASE NOTE: Before starting the formal application process for doctoral studies, the candidate must contact assoc. prof. Jan Lochman at jlochman@sci.muni.cz.

Školitel

doc. Mgr. Jan Lochman, Ph.D.

BACKGROUND: Chronic wounds such as ulcers or decubiti burden ageing populations of developed countries. Hyaluronic acid proved to help healing of such wounds. However, it remains elusive, what happens with topically applied hyaluronic acid, and how it contributes to wound healing.

OBJECTIVES: The aim is to characterize the fate of hyaluronic acid applied topically on a wound.

FOCUS: Vojtěch Pavlík investigates wound-promoting properties of combinations of active compounds and hyaluronic acid.

EXAMPLES: The role of hyaluronidases in chronic wound exudate; The effect of bacteria on the degradation of hyaluronic acid; The penetration of hyaluronic acid through dermis; The effect of different molecular weights of hyaluronic acid on wound promotion

METHODS: Molecular and biochemical characterization of chronic wound exudates. Histology, fluorescence and confocal microscopy of ex vivo animal dermis and animal models of wound healing. Analytical quantification of hyaluronic acid and its fragments.

MORE INFORMATION: https://www.hyaluronanhealing.com/10.1111/wrr.12214; 10.12968/jowc.2020.29.12.782

PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Vojtěch Pavlík (e-mail: vojtech.pavlik@contipro.com, phone: 465 519 586) for an informal discussion.

Poznámky

Ad hoc školitelé podléhají schválení Vědeckou radou PřF MU.

Školitel

Mgr. Vojtěch Pavlík, 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.

BACKGROUND: Fusarium mycotoxins are secondary metabolites of fungi of the genus Fusarium and are found in almost all agricultural commodities worldwide. Fusarium mycotoxins often occur in crops and products thereof together with their conjugated forms that originate from free mycotoxins by binding to polar substances during plant detoxification processes. After ingestion they can be hydrolyzed in the digestive tract of animals to cleave off the „parent“ mycotoxin and thus increase the overall exposure.

FOCUS: Factors influencing the metabolism of selected Fusarium mycotoxins and their conjugated forms will be investigated. Special attention will be paid to the impact of these mycotoxins on parameters of rumen milieu and digestibility of nutrients. Overall exposure of animals to mycotoxins will be evaluated. Mycotoxin carry-over into animal derived products will be predicted.

EXAMPLES: The main focus will be on the determination of selected Fusarium mycotoxins and their conjugated forms in different matrices by liquid chromatography. Adjustment of parameters of chromatography depending on the type of matrices and analytes. The determination of volatile fatty acids and ammonia and their quantification. Performing in vitro experiments

METHODS: In vitro cultivation techniques, liguid chromatography, gas chromatography, spectrophotometry, etc.

Školitel

prof. Mgr. Tomáš Kašparovský, Ph.D.

Výzkumné téma se zabývá mikrobiálními proteiny podílejícími se na tvorbě kyseliny sírové, která se používá při bioloužení ekonomicky atraktivních kovů z odpadů. V tomto procesu hrají zásadní roli acidofilní chemolitotrofní mikroorganismy oxidující elementární síru a další anorganické sirné sloučeniny na kyselinu sírovou. Běžným zdrojem elementární síry a dalších anorganických sirných sloučenin v přírodě jsou sulfidové rudy. Tyto rudy obsahují drahé kovy a jsou po celá desetiletí předmětem biotěžebního průmyslu. V poslední době se princip bioloužení používá k získávání drahých kovů z umělých rud, jako je elektronický odpad a zbytky ze spalování komunálního odpadu. Cílem práce je studium proteinů zapojených do tvorby biogenní kyseliny sírové. Pochopení biologické aktivity těchto proteinů odhalí molekulární mechanismy tvorby kyseliny sírové. Téma patří k základnímu výzkumu s dalším potenciálním využitím zejména v environmentální biotechnologii recyklace kovů.

Školitel

doc. Ing. Martin Mandl, CSc.

BACKGROUND: Mesenchymal stem cells (MSC) are a natural source of regenerative and healing potential inside a human body. Their unique properties are sought after in medicine and tissue engineering. On the other hand, the preparation and subsequent application of MSC can be tricky. The key is to enable the longer survival and retention of these living cells in the area of application which can be helped by utilizing biocompatible biomaterials. Alternatively, the bioactive secretome of MSC can be used instead of living cells.

OBJECTIVES: Provide insights into the ability of hyaluronan-based biomaterials to influence the phenotype, cultivation parameters and therapeutic use of MSC or their secretome.

FOCUS: The benefitial effects of natural glycosaminoglycan, hyaluronan, on the survival, applicability and therapeutic potential of MSC.

EXAMPLES of potential student doctoral projects: Hyaluronan hydrogels for MSC cultivation and implantation; Role of hylauronan in MSC niche; Antiinflammatory effects of MSC-loaded biomaterials, Mechanical cues in MSC biology

METHODS: Cell cultures, hydrogel mechanics characterization, HA biomaterial preparation, methods of cellular and molecular biology, fluorescent microscopy, histology

MORE INFORMATION: https://www.scopus.com/authid/detail.uri?authorId=57220308587

PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Kristina Nešporová (e-mail: kristina.nesporova@contipro.com, phone: 465 519 571) for an informal discussion.

Poznámky

Ad hoc školitelé podléhají schválení Vědeckou radou PřF MU.

Školitel

Mgr. Kristina Nešporová, Ph.D.

OBJECTIVES: Small molecules often regulate biological processes. Therefore such molecules with molecular weight up to 900 Da can be utilized as a research tool to study biological function. Some of them can modulate the function of specific proteins (e.g. enzymes), simply refer on protein activity (e.g. genomic variants and respective phenotypes), act as signal molecules in cell signalling pathways, or disrupt interactions protein-protein. Pharmacologically active molecules often behave as effectors changing the activity or function of its target. Thus drug metabolism studies can refer on a relevant enzyme activity which can be individually different. Many therapeutically active molecules have only narrow therapeutic range to be effective and safe as well. To evaluate their action any analytical method, which enables quantification of multiple targeted small molecules promotes research progress in many fields like biochemistry, pharmacology and clinical analysis. Contrary to large proteomic studies, this more traditional field of analysis has still its importance as many new effector molecules being developed.

FOCUS: Target small molecules will cover drugs of different classes, their metabolites or naturally occurring metabolites and clinically important markers in body fluids (blood, saliva, urine).

METHODS: Liquid separation methods (HPLC and capillary electrophoresis) with different detection techniques (UV-VIS, LIF and MS) or alternatively direct MS analysis will be employed. If possible, alternative sampling methods will be examined.

LITERATURE: https://is.muni.cz/auth/osoba/zeisbergerova#publikace

PLEASE NOTE: Before initiating the formal application process to doctoral studies, the candidate is required to contact Assistant Prof. Marta Pelcová for an informal discussion.

Školitel

Mgr. Marta Pelcová, 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, DSc.

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: 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.