Bio-omika

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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, motivace k výzkumu a studiu, komunikace v angličtině, dodané materiály a celkový dojem.

Výzkumná zaměření dizertačních prací

ADAR2 RNA editing in cns

Školitel: Liam Keegan, PhD.

The main part of the work will use Drosophila and we seek a student with some fly experience who would like to study behaviour and brain function using fly asssays. In Drosophila we found that the Adar mutant has dsRNA activated Dicer-2-mediated innate immune induction (Nat. Comms, 2020 accepted). Adar mutant phenotypes are rescued by increased autophagy which clears synaptic defects and, probably also, unedited dsRNA (BMC Biology, 2020 accepted). The Adar mutant defects may be due to loss of RNA editing in specific transcripts such as synaptotagmin, synapsin and cacophony that encode key synaptic proteins. We will try to rescue Adar mutant behavioural defects by expressing edited forms of cDNAs for these specific transcripts. Ideas coming from the fly work can be tested in Adar2 mutant mice which have a circadian defect and model the severe epilepsy caused by ADAR2 mutations in humans (AMHG, under revision); mutant pups develop seizures and die at or before weaning.

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

Development of bioinformatics methods for data integration from various diagnostic types in clinical oncology

Školitel: Mgr. Vojtěch Bystrý, Ph.D.

In the state of the art personalised therapy planning for oncology patients multiple examinations and laboratory tests are performed to get a thorough characterisation of a tumour. These examinations include all the various types of NGS based analysis such as fusion gene detection, mutation profiling, gene expression profiling, methylation profiling or micro RNA profiling, but also other pathological examination such as PET scan. Each of the analysis produces a huge and complex data that requires a specialised non-trivial computer processing to extract useful information. However, the real bioinformatics challenge is to integrate these data into a single model which would be able to make use of mutual information between different data sources and provide a comprehensive assessment of patients risks. The aim of the PhD study will be to develop such bioinformatics methods and machine learning models that will be capable of combining the various data into a single comprehensive result. The developed methods should be able to capture the 'expert knowledge', and close collaboration with clinical genetics and other medical professionals will be necessary. 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/bioinformatics-core-facility

Dynamics of the Structure Maintenance of Chromosome (SMC) complexes

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

Elucidation of novel therapy targets for B-cell malignancies

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

Therapy of B-cell lymphomas and B-cell chronic lymphocytic leukemia is based predominantly on CD20 monoclonal antibodies and/or on three approved targeted drugs. However, their success rate is often hampered by the development of resistance, resulting in therapy failure and disease relapses. It is therefore essential to identify novel vulnerabilities of malignant B cells that might be exploited as novel targets of therapy. This goal will be the aim of this PhD thesis.

Successful candidate will learn diverse modern techniques of molecular and cell biology like cell culture, lentiviral transduction, molecular cloning, CRISPR/Cas9 or next-generation sequencing. The candidate will make use of the CRISPR/Cas9 technology to generate individual knockout cells or to perform a genome-wide knockout screen. He/she will investigate the molecular mechanisms underlying the effect of candidate vulnerability genes. The candidate will use sets of specific small molecule inhibitors and collection of mouse models to elucidate the translational potential of novel prospective targets.

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

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

Mass spectrometric imaging of biological tissues

Školitel: prof. Mgr. Jan Preisler, Ph.D.

Mass spectrometry imaging (MSI) exploits the ability of mass spectrometry to identify molecules according to their specific mass and image their distribution across the sample. The method allows direct visualization of endogenous compounds (lipids, proteins, small molecules) as well as exogenous drugs and their metabolites. The aim of the research will be development of a suitable matrix-assisted laser desorption/ionization (MALDI) MSI method for the study of distribution and the effect of chosen drug selected tissues and cell lines. Special attention will be devoted to sample preparation and matrix deposition (spray, sublimation, piezoelectric dispenser) and data processing. The samples will be supplied by cooperating institutions (e.g. the Department of Experimental Biology, the Department of Pharmacology or the Regional Centre for Applied Molecular Oncology). The analyzed compounds include selected drugs or endogenous compounds (e.g. lipids, glycans).

Hands-on experience with MALDI MS and software skills (MATLAB, R) are welcomed.

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/synthesis-and-analysis-of-nanostructures-jiri-pinkas

Microenvironmental interactions and non-coding RNAs in the biology of B cell leukemia

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 deciphering novel mechanisms of BCR signalling regulation mediated by microenvironmental signals, CD20, p53, and the signals from T cells (Pavlasova et al. Blood, 2016; Pavlasova et al. Leukemia, 2018). We showed for the first time that non-coding RNAs, namely microRNAs (miRNAs), regulate the BCR signaling which opens an interesting field of research (Musilova et al. Blood, 2018; Mraz et al. Blood, 2014; Cerna et al. Leukemia, 2018).
We have identified candidate miRNAs, lncRNAs and protein-coding genes that might act as novel regulators of the crosstalk of BCR signalling/T-cell interactions/adhesion in B cell malignancies. This will be further investigated by the PhD student using technics such as NGS miRNA/RNA sequencing, genome editing (Crispr/Cas9), functional studies with various in vitro models and co-culture systems. The research is also relevant for pre-clinical development of novel clinical trials, and studies of the resistance mechanisms to BCR inhibitors. We have opened 4 PhD topics: for details see: http://ls-phd.ceitec.cz/dissertation-topics-current-call/
Long non-coding RNAs (lncRNAs) in the pathogenesis of B cell lymphomas
Migration of malignant B cells and their adaptive response to BCR inhibitor therapy
Non-coding RNAs (microRNAS/lncRNAS) and microenvironmental interactions of malignant B-cells
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, and we suggest novel clinical trials).

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.

RNA Quality Control

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

The internal and external RNA 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 PhD projects is to study in details on how specific terminal RNA modifications regulate cellular differentiation and to study the protein-protein interactions of factors involved in the regulation of adenosine methylation (m6A) in coding and noncoding RNAs.

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.

EXAMPLES OF POTENTIAL PHD TOPICS:

  • The role of posttranscriptional RNA modifications in cell differentiation
  • The role of protein-protein interactions in the dynamics of m6A RNA modification

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

Role of phosphorylated 14-3-3 proteins

Školitel: RNDr. Mgr. Jozef Hritz, Ph.D.

14-3-3 proteins play key role in the neurobiochemistry of brain and are also associated with neurodegenerative amyloid diseases such as Alzheimer and Parkinson disease. 14-3-3 proteins bind more than 850 diverse target phosphoproteins, thereby forcing conformational changes or/and stabilizing active conformations in their target proteins. The main aim of this PhD project is to quantify extent of the phosphorylation of different isoforms of 14-3-3 protein family in different cell types. Subsequently, the potency of homo and heterodimerization involving the phosphorylated 14-3-3 proteins will be quantified by fluorescence, ITC and NMR biophysical assays. Finally, the impact on the binding of phosphorylated client proteins will be analyzed.

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/protein-structure-and-dynamics-lukas-zidek

Structure, function and evolution of plant telomere components

Školitel: prof. RNDr. Jiří Fajkus, CSc.

Telomeres are terminal, but nevertheless integral parts of chromosomes, and as such they are also formed and function as supramolecular nucleoprotein (chromatin) structures. Their DNA component is usually formed by repetitive DNA whose incomplete end-replication by the conventional replication machinery can be compensated by elongation via a specific ribonucleoprotein complex with RNA-dependent DNA polymerase activity – the telomerase. Besides preventing the replicative shortening, telomeres also protect chromosome ends from being mistaken for unrepaired chromosome breaks. For the latter function, protein components of telomeres are responsible. Our group has described evolutionary changes in plant telomere DNA repeats and some protein components of plant telomeres. Recently we have described the bona fide RNA component of telomerase in Arabidopsis and the other land plants, including plants with unusual telomeres and important crop plants. It will be important to follow-up these studies with description of further protein components of telomeres together with testing their functional importance for telomere maintenance and chromosome stability. In addition, the impact of the evolutionary change in telomere DNA sequence on its protein interactors will be examined. Background in molecular biology, biochemistry and bioinformatics will be an asset for selection of a suitable candidate.

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

Informace o studiu

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

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