Biochemistry

Life as chemical reactions

What will you learn?

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 a 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 here (https://www.sci.muni.cz/en/studies/doctoral-degree-study-programme/admission-process-faq).

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.

Career opportunities

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.

Dissertation topics

Single-subject studies

Biocompatible nanomaterials for targeted drug delivery, construction of vaccines and theranostics
Supervisor: 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.

Supervisor

prof. RNDr. Jaroslav Turánek, DSc.

Molecular mechanisms of the pathogenesis of Alzheimer's disease
Supervisor: 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.

Supervisor

prof. RNDr. Omar Šerý, Ph.D.

Pathogenesis of COVID-19 and SARS-CoV-2 infection
Supervisor: 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.

Supervisor

prof. RNDr. Omar Šerý, Ph.D.

Proteotype-based classification of renal cell carcinoma for prognosis and therapy response
Supervisor: doc. Mgr. Pavel Bouchal, Ph.D.
OBJECTIVE: Renal cell carcinoma (RCC) represents a serious oncological disease with the highest incidence in the Czech Republic. The reliable molecular markers related to the critical clinical scenarios are still missing.

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

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

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

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

doc. Mgr. Pavel Bouchal, Ph.D.

Structure-functional study of proteins involved in host cell recognition
Supervisor: 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.

Supervisor

prof. RNDr. Michaela Wimmerová, Ph.D.

Structure-functional study of proteins involved in host cell recognition
Supervisor: 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.

Supervisor

prof. RNDr. Michaela Wimmerová, Ph.D.

structure-functional study of proteins involved in host cell recognition
Supervisor: 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.

Supervisor

prof. RNDr. Michaela Wimmerová, Ph.D.

Targeting resistance to chemotherapy of tumor cells to reinstate their susceptibility to novel, existing and unsuccessful anticancer metallodrugs
Supervisor: prof. RNDr. Jana Kašpárková, Ph.D.

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

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

EXAMPLES of potential student doctoral projects:

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

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

Supervisor

prof. RNDr. Jana Kašpárková, Ph.D.

Vasculature models for study of physiology and pathology of cardiovascular system
Supervisor: 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.
Supervisor

Mgr. Jan Víteček, Ph.D.

Supervisors

There are no supervisors recorded for this study programme.

Study information

Provided by Faculty of Science
Type of studies Doctoral
Mode full-time Yes
combined Yes
Study options single-subject studies Yes
single-subject studies with specialization No
major/minor studies No
Standard length of studies 4 years
Language of instruction English
Collaborating institutions
  • The Czech Academy of Sciences
  • Biofyzikální ústav AV ČR
Doctoral board and doctoral committees
Tuition fees
The studies are subject to tuition, fees are paid per academic year
€3,000
Find out more

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