Bio-omika

Pojďme odhalovat genetický kód.

Podat přihlášku

Co se naučíte

Popis oboru

Obor Bio-omika je významným nástrojem systémové biologie, zahrnuje znalosti o metodách používaných pro separaci, analýzu a speciaci komponent biologických systémů z hlediska fungování těchto systémů. Součástí oboru je metodika zpracování a vyhodnocení naměřených dat prostřednictví bioinformatiky.

Obor je určen absolventům magisterského studia se znalostmi v oborech Biologie, Biochemie, Molekulární biologie, Biofyzika a příbuzných oborech. Tento obor umožňuje studentům rozvíjet výzkumné dovednosti i sociálně-manažerské kompetence prostřednictví kompozice studia a výběru přednášek, volených podle zaměření studenta. Ve srovnání s tradičním studiem biologie je studium zaměřeno metodicky a bioanalyticky především na oblasti bioanalytické instrumentace, cytogenomiky, funkční genomiky, proteomiky, metabolomiky, vývojové a produkční biologie (tzv. omické přístupy). Cílem studia je příprava vysoce kvalifikovaných pracovníků pro vědeckou práci.

Úvodní část studia je vyhrazena prohloubení teoretických a praktických znalostí. Paralelně probíhá zpracování samostatné literární rešerše k zadanému tématu doktorské disertace. Samotné těžiště činnosti studentů spočívá v jejich vlastní vědecké práci. Studenti jsou školitelem vedeni, aby byli schopni samostatně realizovat všechny fáze vědeckého projektu. Jsou též vedeni ke zpracování získaných experimentálních dat metodologicky relevantně, stejně tak k jejich interpretaci a následnou prezentaci v různých formách (vystoupení před vědeckou veřejností na odborných fórech, příprava plakátového sdělení i vědeckého článku).

Úspěšný absolvent je schopen

  • disponovat hlubokými teoretickými znalostmi z oblasti funkční a vývojové biologie a je si vědom všech aspektů i aktuálních trendů v dané oblasti;
  • zvládat celou škálu laboratorních metod, stejně jako technik instrumentální analýzy biologických vzorků;
  • navrhovat a standardně používat pokročilé výzkumné postupy s využitím metod používaných pro separaci, analýzu a speciaci komponent biologických systémů;
  • metodologicky relevantně zpracovat naměřená data a hodnotit získané výsledky a vyvozovat argumentačně podložené závěry;
  • využívat moderních informačních technologií k získávání a zpracování vědeckých informací ze světových elektronických databází, ke sběru a zpracování dat v on-line zapojení přístrojů, k testování validity modelů;
  • zapojit se do mezinárodních výzkumných týmů v oblasti Life Sciences;
  • poznatky úspěšně prezentovat a diskutovat v anglickém jazyce.

Další informace

Detailní informace ke studiu na MU i detailní informace k tomuto oboru jsou k dispozici zde

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

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

Uplatnění absolventů

Absolventi oboru Bio-omika mají možnost uplatnění v laboratořích zaměřených na analýzy biologických vzorků, ve firmách zaměřených na funkční a vývojovou biologii, v případě základního výzkumu také v akademických institucích. Inovativní přístup k výuce společně s vysoce kvalifikovaným a současným kurikulem studijního oboru vytváří také skvělé předpoklady pro bezproblémové zapojení absolventů do významných mezinárodních výzkumných týmů.

Přijímací zkouška

Požadavky jsou podrobně uvedeny na http://ls-phd.ceitec.cz/information-for-applicants/ Přijímací řízení probíhá dvoukolově. První kolo je založeno na posouzení dodaných materiálů - pouze kompletní přihlášky včetně všech povinných příloh jsou akceptovány a přezkoumány. Uchazeči, kteří postoupí do druhého kola, jsou pozváni k přijímacímu pohovoru se členy komise.

Kritéria hodnocení

Znalosti v oblasti věd o živé přírodě, komunikace v angličtině, dodané materiály a celkový dojem.

Výzkumná zaměření dizertačních prací

Complexes Maintaining Chromatin Structure

Školitel: 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

Školitel: 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 the regulation of the RNA modifying enzyme ADAR1 and how it regulates other biological pathways and diseases

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

The ADAR enzymes convert adenosine into inosine in dsRNA. Inosine is one of the most abundant and best studied modifications found in different classes of RNA. Hundreds of millions of positions have been identified within the human transcriptome where inosine can occur. The fact that levels of inosine have been found to increase in the RNAs of many cancers has sparked huge interest in this field. The levels of inosine in RNA have also been shown to profoundly affect activation of innate immunity in cancer, infection, and autoimmune diseases.

The goal of this PhD project is to understand how ADAR1 is regulated and it in turn regulates different cellular processes. The methods used will include basis molecular biology techniques such as immune-blotting, RNA isolation, qPCR, cell culture etc.

The candidate will have to be proficient in English, both spoken and written, be experienced in molecular biology or immunology.

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/era-chair-rna-and-immunity-mary-oconnell

Microenvironmental Interactions in the Biology of B Cell Leukemias and Lymphomas

Školitel: 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

Školitel: 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

Školitel: 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

Školitel: 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

Školitel: 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

Školitel: 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

Informace o studiu

Zajišťuje Přírodovědecká fakulta
Typ studia Doktorský
Forma prezenční ano
kombinovaná ano
Doba studia 4 roky
Vyučovací jazyk Čeština

Podat přihlášku

Používáte starou verzi internetového prohlížeče. Doporučujeme aktualizovat Váš prohlížeč na nejnovější verzi.