Genomika a proteomika

Cellular processes and external factors generate stress that can damage nuclear DNA. This includes various types of lesions that need to be recognized by the cell. Their presence must be signaled to activate a cascade of responses, including stopping the cell cycle, initiating DNA damage repair, and, as a last possibility, cell death. Our team uses a mix of cutting-edge methods, including forward genetics, genomics, bioinformatics, proteomics, modeling, and cytology, to study the process of plant DNA damage responses. Our primary models are dicot Arabidopsis thaliana and monocot Hordeum vulgare.

Poznámky

This work will be realized at the Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics in Olomouc.

Školitel

doc. Mgr. Aleš Pečinka, Ph.D.

Detection of tumor biomarkers is essential for early diagnostics of cancer, since it helps to decrease mortality and high cost associated with late treatment, and is also highly beneficial when monitoring response to therapy or possibility of relapse. In recent years, various analytical methods based on electrochemical (EC) detection have been reported. These methods have a great potential to replace standard methods which are often expensive, time-consuming, and complicated; hence, there is an urgent need to develop an affordable, simple and rapid EC  bioassays/biosensors for analysis of tumor biomarkers. The aim of this doctoral thesis is to develop and optimize bioassays for the detection of such biomarkers, mostly based on nucleic acids, i.e. DNA and RNA. The EC readout will be coupled to isothermal amplification techniques, such as LAMP, RPA or RCA, which rapidly amplify nucleic acids at constant temperatures to improve sensitivity and specificity of detection. Here is the list of selected topics anticipated to be studied in this doctoral thesis: (a) Analysis of DNA mutations in important oncogenes or tumor suppressor genes, implicated in cancer, (b) Analysis of epigenetic modifications, e.g. DNA methylation or upregulated non-coding RNAs, especially microRNAs and long non-coding RNAs, which play a major role in the carcinogenesis process, (c) Application of novel amplification techniques for detection of ultralow levels of nucleic acids, (d) Determination of circulating nucleic acids in body fluids for non-invasive diagnostics, or (e) other similar topics depending on the laboratory needs. These may include but are not limited to development of similar bioassays utilizing electrochemiluminescent (ECL) readout on electrode chips as another promising alternative, or application of third-generation Nanopore sequencing technology. The developed bioassays will be applied to biological and clinical samples and validated with standard methods. The work will be carried out in the Laboratory of Bioelectrochemistry at RECAMO, which is a part of the Masaryk Memorial Cancer Institute.

Školitel

Mgr. Martin Bartošík, Ph.D.

This research direction includes the structure, evolution and maintenance of telomeres and their roles in chromosome stability, DNA repair and plant speciation. A special attention is given to characterisation of telomerase components and interactors.
Further, we investigate epigenetic mechanisms in the regulation of gene expression, chromatin assembly, genome stability and telomere homeostasis. Biochemical, bioinformatic and molecular biology approaches are applied in this research. As model systems, we primarily use plants and plant cell cultures.
For more details, see our web pages: https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51

Školitel

prof. RNDr. Jiří Fajkus, CSc.

Plants employ a broad spectrum of reproductive strategies, ranging from asexual species to hermaphroditism and the presence of distinct sexes. This variety significantly impacts genome architecture. Our objective is to examine plant species with varying reproductive strategies and investigate their responses to e.g. environmental changes, encompassing both biotic and abiotic stresses. Furthermore, we aim to explore the relationship between reproductive modes and genome size, genome dynamics, and ploidy levels. Our research will utilize a wide array of cutting-edge techniques in both forward and reverse genomics, including advanced microscopy and bioinformatics analyses.

Školitel

RNDr. Roman Hobza, Ph.D.

Navrhovaný výzkum bude reagovat na potřeby současného pokroku v proteomice, glykomice a biomedicíně, který vyžaduje zavedení nových metod, které mohou přinést nové poznatky o proteinech a jejich komplexních systémech. Ve výzkumu chceme využít výhod vlastností elektrochemických přístupů k studiu proteinů a jejich komplexů na nabitých mezifázích. Plán výzkumu vychází ze současných výsledků práce v laboratoři Biofyzikální chemie a molekulární onkologie Biofyzikálního ústavu AV ČR. Budou navrženy a rozvíjeny nové elektrochemické přístupy studia biomedicínsky důležitých proteinů v komplexech s ligandy i peptidy a proteiny s cílem přispět ke stávajícím znalostem o dynamice proteinových komplexů na nabitých mezifázích. Z proteinů, budou zkoumány i glykoproteiny s cílem získání nových informací o proteinové a glykanové části intaktních a chemicky modifikovaných glykoproteinů.

Školitel

RNDr. Veronika Ostatná, Ph.D.

Recent advances in plant genetic engineering allow precise modifications in desirable genomic region. These methodical approaches are currently employed by both basic researchers and applied biotechnologist to understand complex molecular mechanisms as well as to improve the traits of crop plants. While tools for genetic engineering, such as CRISPR/Cas9, are available for model organisms and most important economically important crops, there are still numerous plant species where precise genetic applications remain complicated or even unfeasible.

This research project will address the identification and overcoming the barriers for successful and high-throughput application of genetic engineering tools in non-model species (including Humulus lupulus, Lotus corniculatus, selected cereal crops etc).

Školitel

Ing. Vojtěch Hudzieczek, Ph.D.

Genome sequencing brings a huge amount of information regarding the genetic basis of life. While this information provides a foundation for our understanding of biology, it has become clear that the DNA code alone does not hold all the answers. Epigenetic modifications and higher order DNA structures beyond the double helix contribute to basic biological processes and maintaining cellular stability. Local alternative DNA structures are known to exist in all organisms. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, triplex and quadruplex structures etc. The formation of cruciforms requires perfect or imperfect inverted repeats of 6 or more nucleotides in the DNA sequence. Inverted repeats are distributed nonrandomly in the vicinity of breakpoint junctions, promoter regions, and at sites of replication initiation. Cruciform structures could for example affect the degree of DNA supercoiling, the positioning of nucleosomes in vivo, and the formation of other secondary structures of DNA. The three-dimensional molecular structure of DNA, specifically the shape of the backbone and grooves of genomic DNA, can be dramatically affected by nucleotide changes, which can cause differences in protein-binding affinity and phenotype. The recognition of cruciform DNA seems to be critical not only for the stability of the genome, but also for numerous, basic biological processes. As such, it is not surprising that many proteins have been shown to exhibit cruciform structure-specific binding properties [1] or G-quadruplex binding properties [2]. Contemporary we have developed easy accessible web tools for analyses of inverted repeats [3] and G-quadruplexes[4] and we have analyzed the presence of inverted repeats and G-quadruplexes in various genomic datasets, such as all sequences mitochondrial genomes [5], all bacterial genomes [6], in S.cerevisiae (in review), in human genome etc. A deeper understanding of the processes related to the formation and function of alternative DNA structures will be an important component to consider in the post-genomic era.

Školitel

prof. Mgr. Václav Brázda, Ph.D.

Our lab is interested in the chromatin structure and dynamics. The chromatin structure must be not only maintained through the cell cycle, but also dynamically modulated during processes like mitosis and replication. Amongst the chromatin-associated complexes, the SMC (Structural Maintenance of Chromosomes) complexes play the central role. Two of them, Cohesin and Condensin, facilitate chromosome segregation and condensation, respectively. Third, the most enigmatic SMC5/6 complex is involved in the DNA damage repair and replication restart, however its essential chromatin-modulating function is still unclear. Our laboratory focuses on the SMC5/6 architecture and functions using state-of-the-art structural biology approaches and various molecular biology tools. For further details please refer to our website (http://www.ncbr.muni.cz/SPEC/) and our publications (https://orcid.org/0000-0002-6223-5169).

Školitel

doc. Mgr. Jan Paleček, Dr. rer. nat.

Our workgroup is interested in molecular basis of severe dyslipidemias in human. The most common of dyslipidemias is familial hypercholesterolemia (FH). The frequency of FH in most populations is about 1/200, and so it is possible to predict that about 50,000 people could be affected in the Czech Republic. The clinical phenotype of FH is caused predominantly by mutations in the LDLR gene. LDLR mutations have been reported along the whole length of the gene. Our workgroup focuses on functional assays of LDLR mutations. For further details please refer to our publications (PMIDs: 27175606, 20663204, 28379029, …).

Školitel

Mgr. Lukáš Tichý, Ph.D.

Proteomická analýza je jedním z klíčových faktorů umožňujících zásadní pokrok našeho poznání nejen v oblasti molekulární biologie a biochemie. Proteomická analýza je souborem jednotlivých kroků zahrnujících přípravu vzorku, jeho vlastní analýzu, převážně s využitím hmotnostní spektrometrie (MS), zpracování naměřených dat, jejich statistické hodnocení a bioinformatickou analýzu, přičemž každý z kroků má zásadní vliv na kvalitu získaných výstupů. Cílem disertačních prací v rámci tohoto výzkumného zaměření bude vývoj nových postupů, zejména v oblasti přípravy různých typů vzorků před MS analýzou, resp. vývoj postupů pro zpracování MS dat umožňujících podrobnější charakterizaci analyzovaného vzorku. Studenti budou mít přístup k nejmodernější MS instrumentaci a možnost zapojení do projektů VS Proteomika (CEITEC MU) i spolupracovat s výzkumnými týmy v rámci MU i mimo ni.

Poznámky

Před podáním přihlášky je nutno se neformálně seznámit s tématem, kontaktujte prof. Zbyňka Zdráhala.

Školitel

prof. RNDr. Zbyněk Zdráhal, Dr.

Poznámky

Před podáním přihlášky je vhodné se seznámit s konkrétními tématy pro daný kalendářní rok. Kontakt: doc. Hrstka, MOÚ, Brno.

Školitel

doc. Mgr. Roman Hrstka, 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 motifs (telo-boxes) within the genome is not random, and proteins associated with these telomeric repeats 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.

Poznámky

Poznámky: Práce může být vypracována ve slovenštině či angličtině.

Školitel

doc. Mgr. Petra Procházková Schrumpfová, Ph.D.

Histone sequence variants and their post-translational modifications (PTMs) are epigenetic marks that significantly influence a number of processes, including the cell cycle and protein interactions. The diversity of histones and the complexity of their modifications in amino acid sequences make histone characterization challenging. The aim of this research is to develop and refine methodologies for the characterization of histone variants and PTMs for mass spectrometry analysis, which will subsequently be used in projects focused on epigenetic regulation in plants, mammals and humans. Epigenetic changes in histones will be investigated in the context of proteome of related cellular signaling pathways.

Školitel

Mgr. Gabriela Lochmanová, Ph.D.

Školitel

doc. RNDr. Miroslav Fojta, CSc.

Glykoproteomika je nově vznikající obor, který odhaluje souvislosti glykoforem proteinů s rozvojem onemocnění. V organismu je až 80% všech proteinů posttranslačně modifkovaných glykosylací ovlivňující mnoho biologických procesů. Struktura glykanů a místa glykosylace na proteinu mohou být různá, čímž vznikají proteoformy s různými funkcemi, které mohou aktivovat nebo inhibovat různé buněčné procesy. Oblast glykoproteomiky tedy odhaluje tyto složité vztahy, jejich souvislosti se zdravím a nemocemi a je tedy využívána pro identifikaci dalších biomarkerů v oblasti diagnostiky nejen onkologických onemocnění.
Cílem této práce bude využití klinického materiálu (sér pacientů s definovaným onkologickým onemocněních a zdravých dárců) pro identifikaci a label-free kvantifikaci změněných glykoforem vázaných na proteinech. K tomu budou využívané proteomické analýzy založené na měření hmotnostním spektrometrem Fusion Orbitrap (Thermo Fisher Scientific). Data budou hodnocena proteomickými programy (Byonic, Peaks, Proteome Discoverer) a pomocí pokročilých statistických nástrojů v programovacím jazyku R budou definované peptidy se specifickými glykany, které jsou významné pro danou skupinu pacientů. Následně bude pomocí strojového učení hodnoceno, zda dané glykoformy peptidů pomohou zlepšit diagnostiku nebo postup v léčby onemocnění.
Doporučená literatura: (1) Fang, K., Long, Q., Liao, Z. et al. Glycoproteomics revealed novel N-glycosylation biomarkers for early diagnosis of lung adenocarcinoma cancers. Clin Proteom 19, 43 (2022). https://doi.org/10.1186/s12014-022-09376-8, (2) Kim EH, Misek DE. Glycoproteomics-based identification of cancer biomarkers. Int J Proteomics. 2011; 2011:601937. https://doi.org/10.1155/2011/601937, (3) Pan, J., Hu, Y., Sun, S. et al. Glycoproteomics-based signatures for tumor subtyping and clinical outcome prediction of high-grade serous ovarian cancer. Nat Commun 11, 6139 (2020).
https://doi.org/10.1038/s41467-020-19976-3

Školitel

prof. Ing. Lenka Hernychová, Ph.D.