Genomics and Proteomics

Cellular processes and external factors generate stress that can damage nuclear DNA. Proteins covalently bound to DNA represent a little-studied but serious type of DNA damage – DNA-protein crosslinks (DPCs). DPCs block transcription and DNA replication and therefore need to be repaired. We have developed a highly efficient genetic screen for the identification of genes involved in DPC repair. Using the candidates from this genetic screen, we aim to reconstruct molecular pathways protecting the plant genome against DPCs. This will help to understand an important mechanism ensuring plant fitness and fertility.

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.

Téma zahrnuje dva studované okruhy:
A. Testování molekulárně biologických změn genomové DNA pocházející z děložní sliznice (normální, prekancerózy, nádoru) a z nebuněčné frakce periferní krve s cílem nalezení prognostického markeru.
Provedeme retrospektivní analýzu panelu molekulárně-genetických změn na základě analýzy vybraných mutací, změn počtu somatických kopií, mikrosatelitové nestability a metylace DNA u karcinomů a prekanceróz endometria
Následně ověříme prognostický význam vybraných molekulárně-biologických změn na klinickém souboru, tvořeném genomovou DNA z buněk získaných při výplachu dělohy a ctDNA z nebuněčné frakce periferní krve

B. Využití elektrodového biočipu v detekci lidského papilomaviru u prekanceróz děložního čípku s cílem vyvinout jednodušší a levnější technologii jako alternativu komerčních HPV testů
Projekt bude rozdělen do následujících okruhů:
1. výběr souboru, histologická analýza a validace komerčními HPV testy
2. příprava vhodných sond, výběr a optimalizace amplifikačních technik
3. zjednodušení a zrychlení testu a aplikace na klinický materiál.

Práce bude probíhat v moderně vybavených laboratořích RECAMO Masarykova onkologického ústavu. Napojení na grantové projekty zajištěno, možnost úvazku po domluvě se školitelem.

Školitel

MUDr. Milan Anton, CSc.

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) or electrochemiluminescence (ECL) 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 or ECL 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. 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 upregulated non-coding RNAs, especially microRNAs and long non-coding RNAs, which play a major role in the carcinogenesis process, (c) Analysis of DNA methylation as an important epigenetic modification, (d) Application of novel amplification techniques for detection of ultralow levels of nucleic acids, (e) Determination of circulating nucleic acids in body fluids for non-invasive diagnostics, or (f) other similar topics depending on the laboratory needs. 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.

Glycosylation as one of the major posttranslational modification (PTM) of proteins is involved in a wide range of fundamental molecular processes. Variations in oligosaccharide (glycan) structures have been also shown in association with different pathological events. Glycans are extraordinarily complex molecules and unlike other oligomers, they are synthesized through interaction with a complex biochemical environment comprising hundreds of glycosyltransferases. Consequently, glycans possess significant structural heterogeneity. In addition, proteins may carry several different glycans, displaying a wide range of site occupancy, which could dynamically change. These facts make investigation of oligosaccharides rather demanding and usually require the sequential employment of several approaches. On the other hand, the above-mentioned characteristics make glycans particularly attractive candidates in medical studies.
Although a number of methods have been developed for identification of glycans, the investigation of glycoconjugate structures and understanding their roles in living systems represents tremendous challenges in the field of proteomics. Mass spectrometry (MS) is one the most sensitive and fast technique for the analysis of biomolecules. The information gained by MS allows to assign putative monosaccharide structures present in detected glycans since the mass of a monosaccharide is measured with a high degree of accuracy. Moreover, tandem MS experiments enable more detailed information and in conjunction with oligosaccharide dissection using exoglycosidase enzyme arrays can provide structural analysis and confirm the types of linkages. Therefore, one of the crucial tasks of the thesis will be the investigation of glycosylation in association with pathological events employing MS based proteomic methodology. Experimental work will be performed in laboratories of RG and CF Proteomics, CEITEC, building E26.

Lattová E., Skřičková J., Hausnerová J., Frola L., Křen L., Zdráhal Z., Bryant J., Popovic M. Ihnátová I.:
N-Glycan profiling of lung adenocarcinoma in patients at different stages of disease
Mod. Pathol., 33 (6), 1146-1156 (2020)

Poznámky

It is necessary to contact Dr. Lattova (or prof. Zdrahal) for informal introduction of the topic before a formal application.

Školitel

RNDr. Erika Lattová, PhD.

Interestingly, we have recently observed a widespread link between homologous recombination (HR) and gene silencing. Though we now know that mutations of HR genes lead to upregulation of transcription of various genes in the S. pombe model organism, the underlying mechanisms remain largely unclear. In this research direction, we plan to investigate the relationship between HR and transcription in detail using molecular biology, bioinformatic, and biochemical approaches. We aim to determine where, when, and how the HR-dependent effect on transcription occurs. To reach this goal, we will use genome-wide NGS approaches, RT-qPCR, site-specific yeast assays, and map the involved interactions at the molecular level. Although this research aims to gain insight into the relationship between HR and gene silencing in fission yeast, the strong similarities between the key molecular mechanisms of S. pombe and humans make it highly likely that the identified processes are shared by both species and may be utilized in human therapy in the future.

Školitel

Mgr. Peter Kolesár, Ph.D.

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.

The CRISPR/Cas system is one of the most promising methods for genome editing in various organisms. In our laboratory, we developed a method for CRISPR-based genome editing in oilseed rape (Brassica napus) and Arabidopsis thaliana using hairy root cultures to study specific genes and their regulatory sequences. The PhD candidate will use molecular biology approaches to assess the functionality and efficiency of various CRISPR editing constructs, transformation methods (stable versus transient), and regeneration protocols to develop transgene-free, genome-edited plant lines in various Brassicaceae species.

Školitel

RNDr. Veronika Jedličková, 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.

We will utilize machine learning techniques such as deep neural networks to identify, analyze and interpret functional genomic segments.

The transcription and translation of genes can be crucially influenced by regulatory elements such as enhancers, silencers, insulators and tethering elements. Gene regulatory elements are possible drivers of many diseases, from leucemia to diabetes.

While those regulators are well mapped and annotated for human genome and some frequently used model organisms; the declining cost of DNA sequencing comes with new diverse genomic datasets for animals and plants where such annotations are not known. Unsupervised neural networks like autoencoders and supervised methods like transformers can take advantage of a vast amount of data and discover similarities and new insights without the need of hand-crafted features.

Because of the black-box nature of neural networks, the special care should be devoted to understanding the data and interpretability of the models.

Školitel

Mgr. Petr Šimeček, MSc., Ph.D.

Young seedlings when germinating have at least two key tropic responses to execute, that is reorient the shoot part toward the energy giving light and re-align the root with the gravity vector to be able to grow into the soil that contains moisture and vital minerals. In the case of the root there are more levels of developmental complexity to be taken into consideration as it grows into the mature root system. While the key principles of auxin role in gravitropism have been worked out, the fine-tuning of auxin transport as well as the interlink between auxin and modifications of gravitropic sensing are still not fully understood, and that knowledge gap we want to supplement with this project.
Within this project we plan to address the molecular mechanism(s) underlying the root directional growth as well as how gravitropic sensing is linked and also unlinked with auxin transport enabling main root and lateral roots gravitropism modifications. We will perform gravity sensing-based forward genetic screen to uncover novel molecular regulators involved in gravity perception and execution. Next we will map obtained mutants and characterize physiological and cellular phenotype of mutants and overexpression lines.

Školitel

Tomasz Nodzynski, B.A., M.Sc., 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.

Posttranslační modifikace (PTM) významně ovlivňují regulaci buněčných procesů. V současné době je známo více než 400 druhů. Analýza PTM je poměrně složitý proces, jelikož neexistuje jedna univerzální metoda, která by byla schopná detekovat všechny druhy PTM současně, a zpravidla je nutno použít pro každý druh modifikace individuální postup přípravy vzorku, resp. metodu analýzy. Navíc modifikovaných forem proteinů je v rámci proteomu kvantitativně řádově méně než odpovídajících nemodifikovaných proteinů, což také znesnadňuje jejich detekci.

Cílem disertační práce bude vývoj a optimalizace souboru metod pro kvalitativní a kvantitativní charakterizaci vybraných typů posttranslačních modifikací hmotnostní spektrometrií a aplikace těchto metod v rámci řešení probíhajících projektů.

Experimentální část bude probíhat v laboratořích VS/CL Proteomika, CEITEC-MU (budova E26, UKB Bohunice), vybavených špičkovou instrumentací.

Poznámky

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

Školitel

prof. RNDr. Zbyněk Zdráhal, Dr.

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.

The project will focus on studying the Adar mutant mice that lack the dsRNA RNA editing enzyme, Adar1. Adar null mutant mice die as embryos and embryonic lethality is rescued to live birth in Adar, Mavs double mutants that also lack a key innate immune sensor protein that is activated by unedited dsRNA. However, these double mutant mice die within a few weeks with massive intestinal cell death. To improve this rescue, we have crossed in mutations removing other innate immune sensors.
Adar, Mavs, Eif2ak2 triple mutant mice that also lacking the dsRNA-activated activated PKR sensor protein further improve the rescue, sixty percent of these triple mutant mice live beyond the first month and have apparently normal lifespans. The project is to cross in various other mutants to reduce cell death, such as Trp53 and Caspase11, to see if these extend survival of Adar, Mavs double mutants. We may cross in further mutations affecting sensors, such as the Z-RNA sensor protein ZBP, to see if there is further improvement in this rescue.
We also have another set of mouse strains starting from AdarE912A which expresses a deaminase-inactive mutant and shows mutant phenotypes similar to Adar null mutant but less severe. AdarE912A, Ifih1 double mutants lacking the Mda5 dsRNA sensor protein activating the Mavs signaling pathway are fully viable, with normal lifespans. However, we have discovered that small size and early death in of pups is merely delayed to the next generation in this strain; possibly the mothers have some inflammation that is harmful to their offspring. The student will examine these AdarE912A, Ifih1 second generation mutants to see if they have the same defects as first-generation Adar, Mavs double mutants.
Finally, another part of the project is to analyze the Adar mutant phenotypes in brain. In humans, ADAR mutants cause an encephalopathy called Aicardi Goutières Syndrome, which involves aberrant interferon expression and gives symptoms that mimic symptoms of congenital virus infection.

Školitel

prof. Mary Anne O'Connell, PhD.

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.

Jak jsou chromozomy organizovány a uspořádány v buněčném jádru? Něco málo víme, ale víc toho nevím, ani po více než 100 letech výzkumu v této oblasti. Disertační práce je zaměřena na analýzu konfigurace interfáznich chromozomů, jejich domén (např. centromery, telomery) a tzv. chromosome territories v jádrech rostlin se sekvenovým genomem z různých fylogenetických skupin. Cílem projektu je pochopení evolučních trendů a zákonitostí organizace chromatinu a chromozomů v interfázních jádrech rostlinných druhů. K zodpovězení těchto otázek budou využity metody molekulární cytogenomiky a imunocytologie (např. FISH, malování chromozomů oligo- malovacími sondami, protilátky proti kinetochorovým a CENH3 proteinům), a srovnávácí genomiky založené na celogenomovém sekvenování (např. kontaktní Hi-C a Pore-C interaktomy). Metodicky práce zahrnuje tři základní okruhy: (1) identifikace unverzálních a chromosomově-specifických DNA a proteinových sond s použitím sekvenovaných genomů, (2) lokalizace těchto sond na chromozomech a v interfázních jádrech (3D imuno/FISH), a (3) analýza a interpretace dostupných 3D genomických dat (sekvenované genomy) a jejich interpretační srovnání s cytogenomickými daty. Vzhledem k výzkumnému zaměření VS M. Lysáka lze předpokládat, že výše uvedené metodické přístupy budou preferenčně aplikovány u druhů čeledi Brassicaceae (brukovovité). Konzultant: Dr. S. Grob (IBMP Strasbourg).

Školitel

prof. Mgr. Martin Lysák, Ph.D., DSc.

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.

Genomy eukaryot nejsou neměnnými genetickými entitami. Zejména v poslední době se stále silněji ukazuje, že se jedná o velmi dynamické systémy, generátory vlastních přestaveb, schopné citlivě reagovat na změny prostředí. Většina eukaryotních genomů je z velké části tvořena opakujícími se úseky DNA, tzv. repeticemi. Mezi repetice patří i klíčoví hráči dynamiky genomů - transponovatelné elementy, tzv. transpozony, populárně označované jako „skákající geny“. Transpozony jsou rozptýleny po celém genomu. Přestože transpozony představují významnou část rostlinných genomů, jejich evoluční dynamika a vliv na fungování buňky začínají být teprve chápány.

V rámci navrhované dizertace budeme pomocí bioinformatických nástrojů i experimentů studovat různé aspekty života transpozonů v rostlinných genomech - jejich věk, strukturní rysy, vlny amplifikací, rozsah genové konverze a ektopické rekombinace stejně jako vliv těchto procesů na velikost genomů a účast při tvorbě centromer a formování 3D organizace interfázního jádra. Naše výsledky přispějí k pochopení struktury, funkce a evoluce transpozonů. Doktorská práce předpokládá zvládnutí širokého spektra metod molekulární biologie a genomiky a také řady bioinformatických nástrojů a rovněž práci s odbornou literaturou. Pro bioinformatické analýzy budou využita jak data z dostupných databází, tak i naše vlastní data pocházející ze sekvenování druhé generace (NGS). Student bude používat nejrůznější bioinformatické nástroje dostupné na internetu i vlastnoručně vytvořené. Výsledky analýz budou publikovány v kvalitních impaktovaných časopisech. Pro studenta nabízíme možnost pracovního úvazku. Projekt je financován Grantovou agenturou ČR.

Školitel

doc. RNDr. Eduard Kejnovský, CSc.

Školitel

doc. RNDr. Miroslav Fojta, CSc.

In brief, intracellular life of telomerase is linked to processes of telomerase biogenesis, action at telomeres and degradation. During these processes telomerase interacts with many protein partners that might be essential for particular steps. Highly dynamic nature of telomerase interactome causes difficulty in uncovering functions of telomerase partners that are important for telomerase and those unrelated to telomerase. Using classical experimental methods as well as genomics and proteomics approaches accompained with in silico analyses, we study structure-functional relationship of telomeres and telomerases.

Školitel

Mgr. Eva Sýkorová, CSc.

Diabetické onemocnění ledvin (DKD) je závažnou komplikací diabetes mellitus, s výrazným zaměřením výzkumu na buňky proximálního tubulu (PTEC), jejichž dysfunkce je klíčová v patogenezi DKD. Tyto buňky jsou zvláště citlivé na mitochondriální dysfunkci kvůli vysoké energetické potřebě. V léčbě DKD se významně prosazují nové terapeutické přístupy, především metformin a SGLT2 inhibitory jako empagliflozin, jež mají výrazný renoprotektivní efekt. Hlavním cílem této práce je zkoumání vlivu metforminu a empagliflozinu na proteinovou a genovou expresi enzymů energetického metabolismu v buňkách HK-2, reprezentujících PTEC, v normo a hyperglikemickém prostředí, pro hlubší porozumění jejich působení v kontextu DKD.

Školitel

Mgr. Katarína Chalásová, 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.

Školitel

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

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.

Heat stress is a worldwide environmental constraint for plants, impairing their growth and fertility and representing a compelling issue in agriculture. While short-term fluctuations of temperature may be tolerated, the long-term cultivation of plants at suboptimal conditions causes the systemic reaction with severe consequences on plant cellular physiology. Our research focuses on examining the DNA damage response in the model plant Arabidopsis thaliana, along with other alternative plant models, specifically assessing the immediate effects of heat stress on DNA damage factors. A key aspect of our study is observing the liquid-liquid phase separation that facilitates the assembly of DNA repair mechanisms during heat exposure. In addition to these reparative processes, we aim to explore changes induced by heat stress in the nuclear structure, chromatin remodeling, and the nuclear proteome. Our methodologies include traditional genetic, biochemical, and microscopy techniques, such as laser-microirradiation and live-cell imaging, which are crucial for in vivo observation of these reparative processes.

Školitel

Mgr. Martina Dvořáčková, Ph.D.