Biochemistry

This doctoral study programme is organized by the Faculty of Science in English and the studies are subject to tuition. There is an alternative option for the international applicants to be accepted in the free programme administered in Czech with the possibility of receiving a scholarship. The study language of the programme is still English (Czech is the administrative language). Before officially applying, please contact us at admission@sci.muni.cz to find all the necessary information related to the scholarship and see our FAQ’s.

Podat přihlášku

International applicants for doctoral study (Czech and Slovak Republics applicants NOT included)
Termín podání přihlášky do půlnoci 15. 12. 2024.

Co se naučíte

The goal of studies is to prepare highly-qualified specialists for further working in the field of biochemistry. The student will get necessary theoretical background and skills to realize his/her own research project in a research group under the guidance of a supervisor. Modern instrumentation and experienced personnel at the Department of Biochemistry create unique opportunities for student to be involved in numerous research activities concerning metabolic and regulatory processes in bacteria, fungi and higher plants as well as various biochemical aspects of human pathogenesis. The research covers a wide spectrum of biological levels from whole organisms to tissues, cells and individual proteins. The palette of possibilities is broadened through long-term cooperation with several research institutions at home and abroad. Biochemistry is marked by its open and interdisciplinary character, the classical biochemical approaches being frequently combined with methodology from other disciplines such as microbiology, molecular biology, informatics, and biophysics. This increases graduates’ adaptability and their ability to apply acquired skills in working life.

„Life as chemical reactions“

Chcete vědět víc?

O doktorské studenty PřF MU se stará Oddělení pro doktorské studium, kvalitu, akademické záležitosti a internacionalizaci:

https://www.sci.muni.cz/student/phd

Na webové stránce oddělení najdete informace ke studiu:

  • formuláře (přihlášky k SDZ a ODP, různé žádosti aj.)
  • legislativa (odkazy na: SZŘ, Stip. řád MU, OD ke stipendijním programům PřF)
  • disertační práce (OD Pokyny k vypracování disertačních prací, šablony)
  • manuály a metodiky (návod pro ISP, studijní a výzkumné povinnosti v DSP apod.)
  • doktorské studijní programy (Doporučený průchod studiem, zkušební komise, přehled akreditovaných programů)
  • termíny SDZ a ODP
  • zápisy (potřebné informace pro zápis do dalšího semestru)
  • promoce

ale také úřední hodiny, kontakty, aktuality, informace k rozvoji dovedností a ke stipendiím.

Podrobné informace k zahraničním stážím najdete na této webové stránce:

https://www.sci.muni.cz/student/phd/rozvoj-dovednosti/stay-abroad

Uplatnění absolventů

Graduates a doctoral degree program may continue their academic career at universities and research institutions both in the Czech Republic and abroad. They will be qualified for team member and leadership positions in scientific research and development at private firms and biochemical laboratories at a broad range of institutions specializing in human or veterinary medicine, pharmaceuticals, agriculture, and biotechnology. The professional specialization of the graduates is also compatible with further work in the field of environmental protection and with environmental movements and initiatives.

Podmínky přijetí

Admission procedure
Graduates of a master's degree in the same or a related field of study are admitted to the doctoral programme in biochemistry. Previous work experience is not a prerequisite for admission. Applicants should demonstrate the prerequisites for creative work in the field based on their thesis or their own publications. In addition, he/she should have an active knowledge of general biochemistry (structure and metabolism of carbohydrates, lipids, proteins and nucleic acids) and preparative and analytical biochemistry (procedures for the isolation of proteins, enzymes, nucleic acids and low molecular weight substances, basic principles and applications of optical, chromatographic, electromigration, electrochemical and immunochemical methods). The ability to communicate in English at the level of understanding a popular science article, writing a short English summary and general discussion on topics related primarily to one's CV, university and research activities is required. The admission procedure includes the proposal of a supervisor (from a list of experts pre-approved by the Faculty of Science and appointed by the Dean) and a framework study plan. The selection of candidates is carried out by a committee appointed by the Dean of the Faculty.

More information about admission process for international applicants in general can be found in the section Admission Process.

Date of the entrance exam
The applicants will receive information about the entrance exam by e-mail usually at least 10 days before the exam.
Please, always check your e-mails, including spam folders.

Conditions of admission
Candidates are scored according to their knowledge of biochemistry (maximum 100 points) and English (maximum 100 points). To be accepted, they have to earn at least 50 points in each category.
Successful applicants are informed of their acceptance by e-mail and subsequently receive an invitation to the enrolment.

Programme capacity
The capacity of a given programme is not fixed; students are admitted based on a decision by the Doctoral Board after assessing their aptitude for study and motivation.

Termíny

2. 1. – 15. 12. 2024

Termín pro podání přihlášek

Podat přihlášku

Výzkumná zaměření dizertačních prací

Jednooborové studium

Biokompatibilní nanomateriály pro cílení léčiv, konstrukci vakcín a teranostik
Školitel: prof. RNDr. Jaroslav Turánek, DSc.

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

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

EXAMPLES of potential doctoral projects:

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

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

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

Školitel

prof. RNDr. Jaroslav Turánek, DSc.

Cévní modely pro studium fyziologie a patologie kardiovaskulárního systému
Školitel: Mgr. Jan Víteček, 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.
Školitel

Mgr. Jan Víteček, Ph.D.

Klasifikace solidních nádorů ve vztahu k prognóze a terapeutické odpovědi na základě proteotypů
Školitel: 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.
Školitel

doc. Mgr. Pavel Bouchal, Ph.D.

Metabolické markery obanyschopnosti zemědělských plodin
Školitel: Mgr. Kateřina Dadáková, 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.

Molekulární mechanismy patogeneze Alzheimerovy choroby
Školitel: prof. RNDr. Omar Šerý, Ph.D.

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

Školitel

prof. RNDr. Omar Šerý, Ph.D.

Osud a působení kyseliny hyaluronové aplikované na ránu
Školitel: Mgr. Vojtěch Pavlík, 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.

Patogeneze COVID-19 a SARS-CoV-2 infekce
Školitel: prof. RNDr. Omar Šerý, 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.

Proteogenomová klasifikace trojitě negativních nádorů prsu ve vztahu k prognóze a cílené terapii
Školitel: doc. Mgr. Pavel Bouchal, 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.

Strukturně-funkční studium proteinů zapojených do rozpoznávání hostitelských buněk
Školitel: prof. RNDr. Michaela Wimmerová, 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.

Studium proteinů zapojených do mikrobiální produkce kyseliny sírové
Školitel: doc. Ing. Martin Mandl, CSc.

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.

Využití hyaluronanu v biotechnologické přípravě kmenových buněk a jejich biologicky aktivního sekretomu
Školitel: Mgr. Kristina Nešporová, 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.

Poznámky

Ad hoc školitelé podléhají schválení Vědeckou radou PřF MU.

Školitel

Mgr. Kristina Nešporová, Ph.D.

Informace o studiu

Zajišťuje Přírodovědecká fakulta
Typ studia doktorský
Forma prezenční ano
kombinovaná ano
distanční ne
Možnosti studia jednooborově ano
jednooborově se specializací ne
v kombinaci s jiným programem ne
Doba studia 4 roky
Vyučovací jazyk angličtina
Spolupracující instituce
  • Akademie věd ČR
  • Biofyzikální ústav AV ČR
Oborová rada a oborové komise
Poplatky za studium
Studium v cizích jazycích je zpoplatněné, platba je za akademický rok
3 000 EUR
Více informací

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