Biochemistry

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.

Supervisor

prof. RNDr. Jaroslav Turánek, DSc.

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.

Notes

Ad hoc školitelé podléhají schválení Vědeckou radou PřF MU.

Supervisor

Mgr. Vojtěch Pavlík, 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.

Supervisor

doc. Mgr. Jan Lochman, 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.

Supervisor

prof. RNDr. Igor Kučera, DrSc.

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.

Supervisor

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.

Notes

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

Supervisor

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.

Supervisor

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.

Supervisor

doc. Mgr. Roman Hrstka, 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.

Supervisor

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.

Supervisor

doc. Mgr. Pavel Bouchal, 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.

Supervisor

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.

Supervisor

prof. RNDr. Michaela Wimmerová, 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.

Supervisor

doc. Ing. Martin Mandl, CSc.

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.

Supervisor

prof. Mgr. Tomáš Kašparovský, Ph.D.

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.

Notes

Ad hoc školitelé podléhají schválení Vědeckou radou PřF MU.

Supervisor

Mgr. Kristina Nešporová, Ph.D.

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.

Supervisor

Mgr. Jan Víteček, Ph.D.