Bio-omics

Let's reveal the genetic code.

Programme specification

General information

Bio-omic sciences (i.e. the bio-omics) is one of the major tools of system biology. It covers the knowledge of methods used for the separation, analysis and speciation of components of biological systems in terms of their functioning. It is focused on methods of processing and evaluation of measured data through bioinformatics.

The field is open for graduates of the Master's study programmes with knowledge in the fields of biology, biochemistry, molecular biology, biophysics and other related fields. This study programm enables students to develop their research skills and socio-managerial competence by arranging their studies and selecting lectures according to their specialization. Compared to the traditional study of biology, this type of study is mainly focused methodically and bio analytically on the area of bioanalytical instrumentation, cytogenomics, functional genomics, proteomics, metabolomics, development and production biology (i.e. the omic approaches). The aim of the study is to prepare highly qualified specialists for scientific work.

The introductory part of the study is focused on deepening theoretical and practical knowledge. In parallel, students will review the literature on the topic of their doctoral thesis. The essence of students' activity is focused on their own scientific projects. Students are taught to work independently and encouraged to process experimental data in methodologically relevant manners. An integral part of the study is a comprehensive interpretation of the obtained data and subsequent presentation of novel results by various means (presentation before the scientific community at professional forums, preparation of a poster and a scientific article).

A successful graduate is able to

  • have profound theoretical knowledge in the field of functional and developmental biology and be aware of all aspects and current trends in the area
  • manage a wide variety of laboratory methods as well as techniques of instrumental analysis of biological samples
  • propose and utilise advanced research processes using methods for the separation, analysis and speciation of components of biological systems
  • process the obtained data in methodologically relevant way and derive reasoned conclusions from own findings
  • use modern information technologies to acquire and process scientific information from the world electronic databases, to collect and process data online, to test the validity of models
  • join the international research teams in the field of Life Sciences
  • handle own findings in English language, not only in the form of writing a scientific paper, but also presenting and discussing with scientific experts worldwide

Additional information

Detailed information regarding studies at MU and this particular study programme is available here

http://ls-phd.ceitec.cz/

https://www.sci.muni.cz/student/phd/doporuceny-pruchod-studiem

Graduate destination

Graduates of Bio-omics have a range of opportunities in laboratories focused on the analysis of biological samples, in companies focused on functional and developmental biology, and in case of fundamental research also in academic institutions.

An innovative approach to teaching along with a highly qualified and current curriculum is the best prerequisite for the smooth integration of graduates in major international research teams.

Admission Requirements

Requirements are specified in detail at http://ls-phd.ceitec.cz/information-for-applicants/ 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.

Evaluation criteria

Knowledge in the field of Life Sciences,motivation to do research, communication in English, supplied materials and general impression.

Dissertation topics

Complexes Maintaining Chromatin Structure

Supervisor: doc. Mgr. Jan Paleček, Dr. rer. nat.

The SMC (Structure Maintenance of Chromosome) complexes are the key components of higher-order chromatin fibers and play important roles in genome stability. Three SMC complexes are present in most eukaryotic cells: cohesin (SMC1/3), condensin (SMC2/4) and SMC5/6 complex. Cohesin can make internal loops or embrace two sister chromatids (feature essential for proper chromosome segregation); condensin interconnects loops to condense chromatin during mitosis. The SMC5/6 complex is involved in the homologous recombination-based DNA repair, in replication fork stability and processing, and in cohesin regulation.

In our lab, we study assembly and functions of SMC5/6 complexes (http://www.ncbr.muni.cz/SPEC/). New student will use combination of genetic (fission yeast model), biochemical (mostly yeast two-hybrid system and other binding assays) and bioinformatics methods to get deep insights into SMC5/6 features.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz

https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus

Characterization of cyclin-dependent kinases 12 and 11 (CDK12 and CDK11) in gene expression 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.

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 3 end 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.

EXAMPLES OF POTENTIAL PHD TOPICS:

  • Characterization of cyclin-dependent kinase 12 (CDK12) substrates and their roles in regulation of transcription and tumorigenesis
  • Functions of cyclin-dependent kinase 11 (CDK11) in regulation of gene expression

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz

https://www.ceitec.eu/inherited-diseases-transtricptional-regulation-dalibor-blazek

Investigating epitranscriptomics in a mouse model, with particular focus on the ADAR enzymes

Supervisor: prof. Mary Anne O'Connell, PhD.

The ADAR enzymes deaminate adenosine bases in dsRNA in pre-mRNAs to inosine, which can be read as guanosine by the translational machinery, recoding individual codons in some ADAR-edited transcripts. In vertebrates, one of the most critical recoding events maintains the calcium impermeability of GluA2 subunit-containing AMPA receptors and this is catalyzed by Adar2. Adenosine to inosine conversion in endogenous dsRNA also helps the cell distinguish self from foreign/viral/pathogenic dsRNA. This is essential as without it, unedited endogenous dsRNA binds to cellular dsRNA sensors and activates innate immune responses (doi: 10.1016/j.celrep.2014.10.041) and Adar1 required for this. A PhD student will investigate these roles of Adar1 and Adar2 further using mouse mutants and cell cultures which are available within the group.

We are looking for applicants who are motivated and creative. Experience in research with mice is desired but not essential. The applicant must have good English language skills – both spoken and written. The PhD candidate must have a Masters degree. For additional information on our research please go to https://www.ceitec.eu/era-chair-rna-and-immunity-mary-oconnell/rg112.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz

Microenvironmental Interactions in the Biology of B Cell Leukemias and Lymphomas

Supervisor: doc. MUDr. Mgr. Marek Mráz, Ph.D.

The laboratory is focused on the basic and translational biology of microenvironmental interactions and B-cell Receptor (BCR) signaling in B cell leukemias and lymphomas. Targeting microenvironmental interactions is a promising therapeutic strategy in B cell neoplasms, and we mainly use chronic lymphocytic leukemia (CLL) and follicular lymphoma/DLBCL as model diseases. Our overall goal is to understand the microenvironmental interactions in B cell malignancies.

We are looking for a motivated PhD student that would like to work on the following project funded by the ERC (European Research Council) Starting grant.

EXAMPLES OF POTENTIAL PHD TOPICS:

1. LONG NON-CODING RNAs (lncRNAs) IN LEUKEMIAS

2. REGULATION OF CELL MIGRATION IN B CELL LEUKEMIAS AND LYMPHOMAS

3. ROLE OF TRANSCRIPTION FACTORS IN ONSET AND PROGRESSION OF B-CELL MALIGNANCIES

4. REGULATION OF BCR SIGNALLING BY DNA DAMAGE RESPONSE AND P53 PROTEIN

WHAT DO WE OFFER:

- modern laboratories, project funded by the prestigious ERC grant - high risk and high gain, state-of-the-art instrument, stable funding, competitive scholarship

- You will work in a team of young investigators that challenge some long-standing problems in the field of hematology. We do basic science, but with the objective to help patients in the future (we have access to primary samples with hem. malignancies).

WHAT WILL YOU LEARN/DO:

- How to think and work independently as a scientist

- Writing of abstracts and papers (and course in grant writing and presentation of data)

- How to present data and will attend conferences to present your research

- You will spend 1-2 months visit(s) in collaborating labs in Europe or US

- Collaboration with experts in wet lab research and bioinformatics

- Novel methods such as Next Generation Sequencing (Illumina) and genome editing (Crispr).

- How to critically analyze scientific data (regular journal clubs)

- Classical methods of molecular biology (e.g. immunoblotting, flow cytometry, qRT-PCR, cell cultures, cloning), and you will use our in vitro models for microenvironmental interactions, and artificial activation/inhibition signalling pathways to decipher the gene regulatory loops

- You can supervise bachelor and diploma students if interested

WHO ARE WE LOOKING FOR:

- Motivated smart people that have the “drive” to work independently, but also willing to learn from other people in the lab and collaborate.

- Candidates should have a master’s degree in Molecular biology, Biochemistry, or similar field and have deep interest in molecular biology and cancer cell biology.

PLEASE NOTE: To apply please submit a CV by email to: marek.mraz@email.cz (Subject: PhD School) and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz OR ceitec.cz/mrazlab

Plant telomeres and telomerases

Supervisor: prof. RNDr. Jiří Fajkus, CSc.

The origin of linear chromosomes associated with divergence of eukaryotes led to the evolution of mechanisms counteracting the incomplete replication of hromosome ends––the telomeres. The most common mechanism to overcome the end-replication problem involves a ribonucleoprotein complex enzyme––telomerase. Telomerase elongates the 3_-end of telomeric DNA using the catalytic activity of its core protein subunit––telomerase reverse transcriptase (TERT) - which can repeatedly add a short DNA stretch to telomeric DNA. The sequence added by telomerase is directed by a template region in telomerase RNA (TR), the other core telomerase subunit. In addition to these two core subunits, the complex of telomerase involves several other associated proteins which affect various steps of telomerase function in vivo, as, e.g. telomerase assembly, trafficking, localisation, processivity, or its recruitment to telomeres. Importantly, TR functions not only as the telomerase templating subunit but also as a scaffold to assemble the entire functional telomerase complex. Recently we identified genuine TRs across land plants (Fajkus et al., 2019). This opened a possibility to investigate plant telomere and telomerase structure, function and evolution and elucidate the principle of its reversible regulation in plants, contrary to its permanent developmental silencing is humans.

Ph.D. candidates should have MSc. or an equivalent degree in biochemistry, molecular biology, genomics or a related life science field. Basic proficiency in bioinformatic tools and molecular biology techniques is expected.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz

https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus

Proteins involved in the regulation of telomeric repeats

Supervisor: Mgr. Petra Procházková Schrumpfová, Ph.D.

Telomeres are the physical ends of linear chromosomes that protect these ends against erroneous recognition as unrepaired chromosomal breaks and regulate the access to telomerase, a reverse transcriptase that solves the problem terminal DNA loss in each cell cycle. Telomeric structures are known to be composed of short repetitive DNA sequences (telomeric repeats), histone octamers, and number of proteins that bind telomeric DNA, either directly or indirectly, and together, form the protein telomere cap.

Interestingly, telomeric repeats are not exclusively located at the chromosome ends, but they belong among cis-regulatory elements present in promoters of several genes. The distribution of short telomeric repeats (telo-boxes) within the genome is not random, and proteins associated with these telomeric motifs may serve as the epigenetic regulatory mechanisms facilitating metastable changes in gene activity.

The telomeric cap proteins of diverse organisms are less conserved than one might expect. In plants, knowledge of telomere-associated proteins associated with telomeres and regulation of access to telomerase complex is incomplete. The research aims to elucidate the roles of candidate proteins involved in telomerase biogenesis in plants. The outcomes contribute to the characterization of new telomere- or telomerase-associated proteins, complete our knowledge of telomerase assembly or telomere maintenance in plants. In addition, we would like to examine the regulatory factors associated with the telo-boxes present in promoters of the genes active during plant development.

Candidates should be experienced in basic proteomic and genomic techniques: cloning, transformation/transfection, work with DNA and proteins. The knowledge of techniques used to study protein-protein interactions, RNA-proteins interactions, Chromatin-immunoprecipitation (ChIP) is considered as a plus.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz

https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus

Subcellular trafficking in plant survival

Supervisor: Tomasz Nodzynski, B.A., M.Sc., Ph.D.

Endosomal trafficking is vital in plant development both in optimal and stress conditions. This regulated vesicle trafficking is necessary for membrane integrity preservation and therefore plant resistance to acute osmotic stress. We identified proteins differentially localized along the secretory pathway in response to stress indicating their role in cellular stress response. Characterization of those proteins will provide insights into the role of subcellular machinery in plant response to stress and might have potential applications to engineer stress resistant plants that might be curial regarding incoming climate changes. The PhD student will perform the physiological and cellular phenotype analysis of mutants and overexpression lines. The admitted candidate will perform genetic and molecular biology studies, including in situ protein localization and life confocal imaging techniques. In parallel the student will continue with the characterization of isolated candidate genes interactors.

The candidate should have a basic knowledge of molecular bilology methods and quite strong background in microsopy.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz

https://www.ceitec.eu/developmental-and-cell-biology-of-plants-tomasz-nodzynski

The role of protein-protein interactions in the dynamics of m6A RNA modification

Supervisor: doc. Mgr. Štěpánka Vaňáčová, Ph.D.

The internal mRNA modifications play crucial roles in a number of essential processes of eukaryotic organisms. They regulate the production of germ cells, cellular differentiation, response to stress, and defects in this pathway have been linked to a number of human diseases. The aim of this project is to study the protein-protein interactions of factors involved in the regulation of adenosine methylation (m6A) in coding and noncoding RNAs. The student will master number of diverse methodical approaches, such as human cell culture manipulations (cultivation, RNAi, CRISPR/Cas9, etc.), recombinant DNA preparation, protein expression and purification, high-throughput analyses and enzymatic assays.

She/he will have the opportunity to present the results at prestigious international conferences. Moreover, this project will involve collaboration with other leading researches in European institutes.

Prospective student should ideally have done masters in molecular biology/biochemistry and have laboratory experience in nucleic acids and/or protein purification and analysis. The most highly valued feature will, however, be excitement for science and a strong drive in tackling important biological questions.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz

https://www.ceitec.eu/rna-quality-control-stepanka-vanacov

The use of CRISPR/Cas9 technology to develop innovative strategies for cellular therapy of hematological malignancies

Supervisor: Mgr. Michal Šmída, Dr. rer. nat.

T lymphocytes are a terrific weapon of our immune system able to kill non-self, infected or transformed cells. They can be genetically engineered to carry artificial chimeric antigen receptor (CAR), thereby being reprogrammed to recognize and kill tumor cells in a very specific and effective manner. CAR-T cells achieved remarkable responses in the cellular therapy of hematological B-cell malignancies, yet, CAR-T cell cancer therapy still encounters numerous problems and requires extensive development. No biomarkers predicting the response to CAR-T cells are available, failure of CAR-T cell product and treatment resistances are the major hurdle of this therapy. CRISPR/Cas9 functional screening represents a unique way of identifying genetic factors that affect the efficiency of CAR-T cell treatment.

Using genome-wide CRISPR/Cas9 knockout screening, the student will systematically interrogate cellular factors that are able to modulate and further improve the efficacy of CAR-T cells upon malignant B cells. Factors affecting the response strength of malignant B cells as well as factors influencing CAR-T cell activity or persistence will be identified. These modulating factors (genes) will be thoroughly validated and underlying molecular mechanisms elucidated. This project will propose novel specific cellular targets that can be utilized to improve the performance of CAR-T cell therapy.

Candidates should have M.Sc. in molecular biology, biochemistry or related fields. Experience with mammalian cell biology, experience with CRISPR/Cas9 technology welcome but not required.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz

https://www.ceitec.eu/functional-genomics-michal-smida

Using Drosophila as a model to study the epitranscriptome and how it regulates innate immunity

Supervisor: prof. Mary Anne O'Connell, PhD.

The ADAR enzymes deaminate adenosine bases in dsRNA in pre-mRNAs to inosine, which can be read as guanosine by the translational machinery, recoding individual codons in some ADAR-edited transcripts. The conversion of adenosine to inosine in endogenous dsRNA also helps the cell distinguish self from foreign/viral/pathogenic dsRNA. This is essential as without it, unedited endogenous dsRNA binds to cellular dsRNA sensors and activates innate immune responses (doi: 10.1016/j.celrep.2014.10.041). In Drosophila, many important neuronal transcripts are edited by the single Adar. The Adar mutant is partially viable and suffers ataxia as well as synaptic defects and age-related neurodegeneration (doi: 10.1186/s12915-020-0747-0). Unexpectedly the Drosophila mutant also has aberrant innate immune induction and antiviral response activation (doi: 10.1186/s12915-020-0747-0). The PhD student will study Adar’s role in innate immunity in Drosophila and also in Drosophila S2 cell lines.

We are looking for applicants who are motivated and creative. Experience in research with Drosophila is desired but not essential. The applicant must have good English language skills – both spoken and written. The PhD candidate must have a Masters degree. For additional information on our research please go to https://www.ceitec.eu/era-chair-rna-and-immunity-mary-oconnell/rg112. Before applying all applicants should read the eligibility criteria for the MSCA-ITN PhD program at https://ec.europa.eu/research/mariecurieactions/sites/mariecurie2/files/msca-itn-fellows-note_en_v2.pdf.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION: http://ls-phd.ceitec.cz/http-ls-phd-ceitec-cz

Study field data

Faculty Faculty of Science
Type of study Doctoral
Mode full-time Yes
combined No
Standard length of studies 4 years
Language of instruction Czech

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