Mgr. Irena Doubková
Consultant
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Life Sciences
Doctoral degree in full-time or combined form. The language of instruction is Czech.
The programme can be studied only as a single subject.
What will you learn?
The aim of the study is to educate students in the field of life sciences and to prepare them as highly qualified specialists for scientific activities. The introductory part of the study concentrates on deepening theoretical and practical knowledge. At the same time, separate literary research on the assigned topic of the doctoral dissertation is being prepared. The core of students’ activities lies in their own scientific work. Students are guided by the supervisor to be able to independently implement all phases of a scientific project. They are also encouraged to the processing of the obtained experimental data methodologically relevant, as well as to their interpretation and subsequent presentation in various forms. The programme is highly multidisciplinary and, compared to the traditional study of biology, is more methodologically and analytically focused. Thanks to access to state-of-the-art infrastructure, students can better combine various biochemical, bioanalytical and visualization instrumental techniques with solving biological problems, which increases the impact of their scientific activities and their flexibility in the labor market, including positions in academia, e.g. within existing biotechnology companies or in newly emerging spin-offs.
The concept of the programme reflects the current level of scientific knowledge, the needs of the labor market, and overall trends in the field. At the same time, it benefits from the support system within the so-called CEITEC PhD School, which presents the concept of care for doctoral students involved in research teams at CEITEC and at the same time emphasizes expanding the competencies of the future graduates in socio-managerial, technological and soft skills. That will enable them to conduct their follow-up research in an efficient and modern way and provide them with a very good overview of the ethical aspects of research necessary for life sciences research and research and development in general.Life for Science. Science for Life.
The programme aims at the international employment of graduates. It is prepared in Czech and English versions, most subjects are taught, all seminars and, to a large extent, research is conducted in English. The environment at CEITEC MU is significantly international, so students are exposed to communication in English not only during official teaching but practically everywhere within CEITEC.
Practical training
An important contribution to the acquisition of practical skills of DSP students of Life Sciences is their natural involvement in research teams at CEITEC MU. In this way, students can immediately acquire the necessary practical skills for team management and research projects, acquire networking skills and directly engage in research projects and grants (including H2020 projects and ERC grants) to understand the issues of research funding. Students can also routinely use eleven uniquely equipped shared laboratories and gain significant practical experience in this form within the so-called internal internship, or in another institution in the Czech Republic as part of an external internship (recommended volume is 10 working days (80 working hours).
A compulsory part of the study obligations in the doctoral study program is completing part of the study at a foreign institution for at least one month, or participating in an international creative project with results published or presented abroad or another form of student direct participation in international cooperation.
The program supports Collaborative PhD, i.e. completing a doctoral project in cooperation with a commercial entity. That allows students to expose themselves to a more non-academic environment. Also, within the TAC system, students cooperate more often with experts from practice.
Further information
The Office for Doctoral Studies, Quality, Academic Affairs and Internationalization takes care of doctoral students SCI MU
https://www.sci.muni.cz/en/students/phd
On the department's website, you can find the following information:
- Forms (application forms for state examinations and defences, various applications, etc. )
- Legislation (links to: MU Study and Examination Regulations, Scholarship Regulations of MU, Terms of Scholarship Programmes of the Faculty of Science)
- Dissertations (Guidelines for dissertations, templates)
- Manuals (guidelines for Individual Study Plans, study and research obligations in DSP, etc.)
- Doctoral study programmes (recommended study plans, examination committees, overview of accredited programmes)
- Deadlines for the doctoral state examinations and defences
- Enrolment (information needed for the enrolment to the next semester)
- Graduation
but also office hours, contacts, news, information on skills development and scholarships.
Detailed information on stays abroad can be found on this website:
https://www.sci.muni.cz/en/students/phd/develop-your-skills/stay-abroad
Career opportunities
In the doctoral programme, great emphasis is placed on internationalization, there are also conditions for interdisciplinary solutions to the assigned topics of the dissertation, and the emphasis is placed on strengthening socio-managerial and soft-skills. This increases the real chances of graduates to apply in top scientific and technological, academic and commercial teams around the world, such as in:
- research organizations and academic institutions (research institutes, universities) focusing on biological and biomedical research and education, in the first years as the postdoctoral trainees and subsequently as the leaders of a research team or programme, the heads of shared laboratories (so-called facilities), etc., or at lecturer positions;
- cutting-edge laboratories of applied research focused on the development of new biotechnological biomedical methods, in the scientific specialists and developers’ positions;
- the commercial sphere in the field of consulting and marketing of biomedical or biotechnological products;
- thanks to acquired knowledge in the field of intellectual property and technology transfer specifically in their areas of interest, graduates of the field will be well equipped for activities in establishing start-ups and spin-off companies.
Admission requirements
Data from the previous admission procedure (1 Dec 2023 – 28 Feb 2024)
Requirements are specified in detail here. The admission procedure is carried out in two rounds. The first round is based on the application and background information - only complete applications with all mandatory parts will be accepted and reviewed. The applicants selected for the next round will be invited for the admission interview with the committee. Please check your e-mails, including spam folders.
Study options
Single-subject studies
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Full-time studies in czech
What will you learn? -
Combined studies in czech
What will you learn?
Dissertation topics
Single-subject studies
Co-translational quality control and its role in neural tissue
Supervisor: RNDr. Petr Těšina, Ph.D.
Ribosome-associated quality control (RQC) is crucial for degrading truncated nascent proteins produced on aberrant mRNAs. Mutations in RQC components cause neurodegeneration both in animal models and human patients. Moreover, RQC insufficiency and subsequent protein aggregation critically contribute to proteostasis impairment and systemic decline during ageing. The successful candidate will utilize a multidisciplinary approach to provide detailed mechanistic understanding of the critical human RQC system in combination with an in vivo study to reveal processes leading to RQC-driven pathological changes in neural tissue. He/she will utilize human cell cultures, protein expression and purification techniques and biochemistry methods to produce samples for cryogenic electron microscopy (cryo-EM). Comprehensive training in cryo-EM will be available to the successful candidate. The candidate will also have a unique opportunity to acquire expertise in the use of C. elegans as a model organism during a research stay at a collaborating laboratory in Bolzano (Italy).
Requirements on candidates:The ideal candidate should have background in either molecular biology, biochemistry or structural biology. Experience with human cell culture work or protein biochemistry is a plus.
PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).
MORE INFORMATION:
https://www.ceitec.eu/petr-tesina-research-group/rg396/tab?tabId=180
Notes
Recommended literature:
Tesina, P., et al., Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control. Mol Cell, 2023. 83(4): p. 607-621 e4.
Lu, B., Translational regulation by ribosome-associated quality control in neurodegenerative disease, cancer, and viral infection. Front Cell Dev Biol, 2022. 10: p. 970654.
Filbeck, S., et al., Ribosome-associated quality-control mechanisms from bacteria to humans. Mol Cell, 2022. 82(8): p. 1451-1466.
Udagawa, T., et al., Failure to Degrade CAT-Tailed Proteins Disrupts Neuronal Morphogenesis and Cell Survival. Cell Rep, 2021. 34(1): p. 108599.
Aviner, R., et al., Ribotoxic collisions on CAG expansions disrupt proteostasis and stress responses in Huntington’s Disease. bioRxiv, 2022: p. 2022.05.04.490528.
Supervisor
Functions of cyclin-dependent kinase 11 (CDK11) in regulation of gene expression and tumorigenesis
Supervisor: Mgr. Dalibor Blažek, Ph.D.
CDK11 is ubiquitously expressed in all tissues and the CDK11 null mouse is lethal at an early stage of development indicating an important role for Cdk11 in the adult as well as during development. CDK11 is believed to play a role in RNAPII-directed transcription and co-transcriptional mRNA-processing, particularly alternative splicing and 3end processing. However, its genome-wide function in regulating the human transcriptome is unknown. Notably, several recent studies identified CDK11 as a candidate essential gene for growth of several cancers therefore, understanding the molecular mechanism(s) of CDK11-dependent gene expression would be also of significant clinical interest. In this research we will use various techniques of molecular biology and biochemistry to characterize genome-wide role of CDK11 in regulation of gene expression and tumorigenesis.
Requirements on candidates:Background in molecular biology, biochemistry or life sciences. Interest in bioinformatics and data analyses is desirable.
PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).
MORE INFORMATION:
https://www.ceitec.eu/inherited-diseases-transcriptional-regulation/rg38
Notes
Recommended literature:
Gajduskova, P., Ruiz de Los Mozos I, Rajecky M., Hluchy M., Ule J., Blazek D*: CDK11 is required for transcription of replication dependent histone genes. Nature Structural & Molecular Biology 27 (5):500-510 (2020).
Supervisor
Characterization of cyclin-dependent kinase 12 (CDK12) substrates and their roles in regulation of transcription and tumorigenesis
Supervisor: Mgr. Dalibor Blažek, Ph.D.
Cdk12 is transcriptional cyclin-dependent kinase (Cdk) found mutated in various cancers. In previous studies we found that Cdk12 maintains genome stability via optimal transcription of key homologous recombination repair pathway genes including BRCA1. Apart from the C-terminal domain of RNA Polymerase II other cellular substrates for both kinases are not known. In this research we propose using a screen in cells carrying an analog sensitive mutant of CDK12 to discover its novel cellular substrates. The substrates and their roles in normal and cancerous cells will be characterized by various techniques of molecular biology and biochemistry.
Requirements on candidates:Background in molecular biology, biochemistry or life sciences. Interest in bioinformatics and data analyses is desirable.
PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).
MORE INFORMATION:
https://www.ceitec.cz/dedicne-poruchy-transkripcni-regulace/rg38
Notes
Recommended literature:
Pilarova K, Herudek J, Blazek D.*: CDK12: Cellular functions and therapeutic potential of versatile player in cancer: Nucleic Acids Research Cancer (Oxford University Press) k2 (1): zcaa003 (2020).
Chirackal Manavalan A.P., Pilarova K., Kluge M., Bartholomeeusen K., Oppelt J., Khirsariya P., Paruch K., Krejci L., Friedel C.C., Blazek D* : CDK12 controls G1/S progression via regulating RNAPII processivity at core DNA replication genes. EMBO reports 20(9):47592 (2019).
Ekumi KM, Paculova H, Lenasi T, Pospichalova V, Bösken CA, Rybarikova J, Bryja V, Geyer M, Blazek D*, Barboric M*. Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex. Nucleic Acids Research 43(5):2575-89 (2015).
Bösken CA, Farnung L, Hintermair C, Merzel Schachter M, Vogel-Bachmayr K, Blazek D, Anand K, Fisher RP, Eick D, Geyer M. The structure and substrate specificity of human Cdk12/Cyclin K. Nature Communications 5 (2014).
Blazek D*., Kohoutek J., Bartholomeeusen K., Johansen E., Hulinkova P., Luo Z., Cimermancic P.,Ule J., Peterlin B.M.: The CycK/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes. Genes and Development 25 (20): 2158-2172 (2011).
Supervisor
Microenvironment models and their use to study agressivness and targeted therapy in B cell malignancies
Supervisor: prof. MUDr. Mgr. Marek Mráz, Ph.D.
Chronic lymphocytic leukemia (CLL) cells and indolent lymphomas are known to be dependent on diverse microenvironmental stimuli providing them signals for survival, development, proliferation, and therapy resistance. It is known that CLL cells undergo apoptosis after cultivation in vitro, and therefore it is necessary to use models of CLL microenvironment to culture CLL cells long-term and/or to study their proliferation. Several in vitro and in vivo models meet some of the characteristics of the natural microenvironment based on the coculture of malignant cells with T-lymphocytes or stromal cell lines as supportive cell, but they also have specific limitations.
The aim of this research is to develop and use models mimicking lymphoid microenvironment to study mechanisms leading to aggressiveness in B cell malignancies and/or novel therapeutic options, e.g. drugs targeting CLL proliferation, development of resistance in long-term culture or combinatory approaches, which cannot be analyzed in experiments based on the conventional culture of CLL/lymphoma primary cells. This project will utilize models developed in the laboratory and will further optimize and modify them. The biology of CLL and responses to targeted treatment will be interrogated using the developed models. The student will utilize various functional assays, Cripr editing, RNA sequencing, genome editing, drug screening etc., with the use of primary patient’s samples and cell lines. The research might bring new insights into the microenvironmental dependencies and development of resistance to targeted therapy
Requirements on candidates:PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).
MORE INFORMATION:
https://www.ceitec.eu/microenvironment-of-immune-cells/rg115
Notes
Recommended literature:
Hoferkova E, Kadakova S, Mraz M. In Vitro and In Vivo Models of CLL-T Cell Interactions: Implications for Drug tetsing.Cancers (Basel). 2022 Jun 23;14(13):3087.
Sharma et al. …Mraz. miR-29 Modulates CD40 Signaling in Chronic Lymphocytic Leukemia by Targeting TRAF4: an Axis Affected by BCR inhibitors. Blood 2021. https://pubmed.ncbi.nlm.nih.gov/33171493/
Seda V. et al….Mraz. FoxO1-GAB1 Axis Regulates Homing Capacity and Tonic AKT Activity in Chronic Lymphocytic Leukemia. Blood, 2021, https://doi.org/10.1182/blood.2020008101.
Kipps et al. Chronic lymphocytic leukaemia. Nat Rev 2017 https://pubmed.ncbi.nlm.nih.gov/28102226/.
Seda V, Mraz M. B-cell receptor signalling and its crosstalk with other pathways in normal and malignant cells. Eur J Haematol. 2015 Mar;94(3):193-205. doi: 10.1111/ejh.12427. Epub 2014 Sep 13. PMID: 25080849 Review.
Supervisor
Peptide Sequence Motifs for Selective Targeting of Pathogens
Supervisor: prof. RNDr. Robert Vácha, PhD.
Antimicrobial peptides (AMPs) possess the ability to disrupt the membrane barrier function, effectively eliminating bacteria, viruses, and even cancer cells. Consequently, AMPs have emerged as promising candidates for the development of a new class of therapeutics. However, the majority of known AMPs exhibit toxic properties due to their origin from human-unfriendly sources, such as venoms. Our understanding of peptide targeting mechanisms towards specific pathogens and their membranes remains limited, hindering further peptide development. This ERC funded project aims to identify peptide sequence motifs that are responsible for selective targeting pathogens with respect to human cells. Apart from the differences in lipid composition of membranes, we will investigate the impact of membrane local curvature. The main tool for the study will be Molecular dynamics simulations with free energy calculations using Gromacs program package. These simulations will be complemented by in-house experiments providing crucial verification and feedback on peptide-membrane affinity. The acquired knowledge will guide the design of de novo peptides with enhanced pathogen-targeting specificity.
Requirements on candidates:Outstanding candidates with experience in computer simulations and with an MSc/PhD degree in the fields of biophysics, soft matter physics, physical chemistry, computational chemistry, statistical mechanics, or related fields. Experience with molecular dynamics simulations (with GROMACS, CHARMM, NAMD, AMBER, LAMMPS, etc.) or other simulation techniques (Monte Carlo, DPD, etc.) at the atomistic or coarse-grained level would be an advantage.
PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).
MORE INFORMATION:
Notes
Recommended literature:
J Cell Biol. 2018; 217(9): 3109–3126, doi: 10.1083/jcb.201802027
Colloids Surf B Biointerfaces 2017; 153:152-159, doi: 10.1016/j.colsurfb.2017.02.003
Supervisor
Regulation of protein liquid droplets during transcription
Supervisor: prof. RNDr. Robert Vácha, PhD.
Cells employ protein liquid droplets to form dynamic clusters, which function as nanoreactors or storages with the increased local concentration of specific protein components. These membrane-less organelles self-assemble based on weak protein-protein interactions of intrinsically disordered domains. However, the role of specific sequences remains elusive and the mixing between different protein droplets unexplored. This project is focused on the droplets involved in genome transcription, where posttranslational modifications control the droplet composition and regulate the transcription. Expected findings are not only important for the general knowledge but could also be useful in the design of new treatments because translocation malfunction is involved in numerous diseases including cancer. The research is strongly coupled to collaborations with excellent experimental teams and will be more closely discussed during the interview. The employed tools will contain multi-scale simulations using a wide range of advanced sampling techniques and development of protein parametrization.
Requirements on candidates:Outstanding candidates with experience in computer simulations and with an MSc/PhD degree in the fields of biophysics, soft matter physics, physical chemistry, computational chemistry, statistical mechanics, or related fields. Experience with molecular dynamics simulations (with GROMACS, CHARMM, NAMD, AMBER, LAMMPS, etc.) or other simulation techniques (Monte Carlo, DPD, etc.) at the atomistic or coarse-grained level would be an advantage.
PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).
MORE INFORMATION:
https://ls-phd.ceitec.cz/how-to-aplly/
Notes
Recommended literature:
Biochemistry 2022, 61, 2456–2460, doi: 10.1021/acs.biochem.2c00220
Nucleus 2023, 14:1, 2213551, doi: 10.1080/19491034.2023.2213551
PLoS Comput Biol 2023, 19(7): e1011321. doi: 10.1371/journal.pcbi.1011321
Science 2018, 361, 6, 6400, doi: 10.1126/science.aar2555
Supervisor
Translation in the context of human host-pathogen interaction
Supervisor: RNDr. Petr Těšina, Ph.D.
Proteins are produced by ribosome-catalyzed translation of mRNAs in all domains of life. Translation is also critical in the context of human host-pathogen interaction where the ribosome, as the central molecular machine for genetic information expression, is the subject to numerous regulatory and quality control events and pathological interventions. The strategies adopted by viruses to reprogram translation and co-translational quality control machinery to promote infection are poorly understood. Thus, there is an urgent need for further research in this area to develop effective strategies for combating viral infections. The successful candidate will study how viruses affect human translation and co-translational quality control with the aim of providing high-resolution structures of large macromolecular assemblies. He/she will utilize human cell cultures, protein expression and purification techniques and biochemistry methods to produce samples for cryogenic electron microscopy (cryo-EM). Comprehensive training in cryo-EM will be available to the successful candidate.
Requirements on candidates:The ideal candidate should have background in either molecular biology, biochemistry or structural biology. Experience with human cell culture work or protein biochemistry is a plus.
PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).
MORE INFORMATION:
https://www.ceitec.eu/petr-tesina-research-group/rg396/tab?tabId=180
Notes
Recommended literature:
Xu, Z., et al., SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation. Proc Natl Acad Sci U S A, 2022. 119(32): p. e2204539119.
Hsu, J.C., et al., Viperin triggers ribosome collision-dependent translation inhibition to restrict viral replication. Mol Cell, 2022. 82(9): p. 1631-1642 e6.
Thoms, M., et al., Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 2020. 369(6508): p. 1249-1255.
Lu, B., Translational regulation by ribosome-associated quality control in neurodegenerative disease, cancer, and viral infection. Front Cell Dev Biol, 2022. 10: p. 970654.
Supervisor
Study information
| Provided by | Faculty of Science | |
|---|---|---|
| Type of studies | Doctoral | |
| Mode | full-time | Yes |
| combined | Yes | |
| distance | No | |
| 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 | Czech | |
| Doctoral board and doctoral committees | ||