Master thesis project - updated May 13th, 2024
Single gene mutations represent the leading cause of intellectual disability (ID) and autism spectrum disorder (ASD). Missense variants that result in a change of one amino acid (AA) in the protein sequence, contribute to disease risk to a similar or even greater degree than likely gene-disruptive mutations but their effect on protein structure and function is not known.

In this project, the student will investigate de novo missense variants in gene PTPN11 that encodes a protein tyrosine phosphatase SHP2. These variants were found in individuals with ID/ASD and not in the unaffected siblings and they are predicted as pathogenic. The student will prepare recombinant SHP2 protein with and without the corresponding single AA changes and test the effect of these changes on protein phosphorylation. This will answer whether the variants affect SHP2 function and if yes, whether they increase or decrease its phosphatase activity. The project will complement the characterization of these mutations for cognitive dysfunction in our pre-clinical Drosophila model.

Supervisor: Mgr. Michaela Fencková, Phd
Co-supervisor: RNDr. Petra Havlíčková

contact:https://www.jcu.cz/cz/univerzita/lide/clovek?identita=FENCKOVA_Michaela_13934

Our group is investigating the enigmatic role of phosphonates (molecules with carbon-phosphorus bonds) in eukaryotic cells. The eukaryotic ciliate Tetrahymena thermophila, with a high content of phosphonates on its cell surface, is one of the best models to answer our questions. Our goal is to determine the function of these enzymes in this metabolic pathway by generating knock-out strains and characterising them by molecular and biochemical methods.
In this project, you will learn general molecular biology techniques (CRISPR-cas9 gene KO, DNA cloning, western blot analysis, immunoprecipitation, etc.), culturing, and microscopy. We hope that you will be able to work with us at Centre Algatech in Trebon (https://www.alga.cz/en/c-874-jan-janouskovec-s-group.html) in a friendly and international scientific environment.

Contact: Eva Horáková (This email address is being protected from spambots. You need JavaScript enabled to view it.)
Co-supervisor/Advisor: Ayca Fulya Üstüntanir Dede, Ph.D. (https://www.alga.cz/en/c-923-ustuntanir-dede-ayca-fulya.html )

Bachelor or Master thesis project - UPDATE: project assigned
Intellectual disability (ID) and autism spectrum disorder (ASD) are frequent and often co-occurring neurodevelopmental disorders, characterized by cognitive and behavior deficits. We have learned that these disorders are mostly caused by monogenic (ie. single gene) mutations. They represent a window into the underlying molecular mechanisms and treatment targets. The goal of this project is to investigate established and novel genetic causes of ID/ASD and neuronal and non-neuronal mechanisms, by which they contribute to cognitive dysfunction. The student will use Drosophila, an established model for ID/ASD, and habituation, a fundamental form of learning that is affected in both ID/ASD individuals and Drosophila models and is therefore of high translational value. A specific focus will be given to novel ID/ASD candidate genes identified by our clinical collaborators from 2nd Faculty of Medicine at Charles University. The student will use state-of-the-art approaches to manipulate with gene expression (RNA interference, targeted expression) in tissue (Gal4-UAS) and time (TARGET) specific manner, and to introduce patient-specific mutations (CRISPR/Cas9-based editing, T2A-Gal4) in Drosophila orthologs of ID/ASD genes. These will be complemented with classical genetics, behavior testing and statistical and molecular analysis.

contact:https://www.jcu.cz/cz/univerzita/lide/clovek?identita=FENCKOVA_Michaela_13934

Bachelor or Master thesis project - UPDATE: project assigned
Single gene mutations represent the leading cause of intellectual disability (ID) and autism spectrum disorder (ASD). Missense variants that result in change of one amino acid (AA) in the protein sequence, contribute to disease risk to a similar or even greater degree than likely gene-disruptive mutations but their effect on protein structure and function is not known. In this project, the student will use PyMOL molecular visualization and modeling system to introduce ~ 50 recurrent ID/ASD missense variants into high-resolution crystal structures of 10 proteins from RCSB Protein Data Bank and determine whether they affect folding and stability of the protein, its interaction with other proteins and molecules or alter the protein function. The results will lay down the basis for functional characterization of the underlying molecular and cognitive mechanisms in vitro and in our pre-clinical Drosophila model. If the student is motivated, he/she may be involved in initiation of these studies.

(Co-supervisor/consultant: Prof. Ivana-Kutá Smatanová)

contact:https://www.jcu.cz/cz/univerzita/lide/clovek?identita=FENCKOVA_Michaela_13934

Bachelor or Master thesis project
Honey bees are threatened by the parasitic mite Varroa and the viruses it transmits. The student will test the effect of several natural compounds that could have antiviral properties in honey bees. In vitro and in vivo experiments, virus quantifications by real time q-RT-PCR.

contact:https://web.prf.jcu.cz/en/kmb/people/faculty-and-stuff/rndr.-alena-krejci-ph.d..html

Bachelor or Master thesis project
The honey bee development is a complex process that involves tissue growth and remodelling during the pupation. Using the state of the art micro-CT machine the student will compose an anatomical atlas of larval and pupal development of the honey bee, with the focus on seasonal and stress induced adaptations of the developmental process.

contact:https://web.prf.jcu.cz/en/kmb/people/faculty-and-stuff/rndr.-alena-krejci-ph.d..html

Bachelor or Master thesis project
The currently used pesticides negatively affect the life of the honey bees. A completely new, modern type of pesticides was developed in the laboratory of prof. Jindra that should kill only certain insect species but leave other unharmed, making these compounds much more environment-friendly. The student will test the effect of these chemical compounds on the development of honey bees under in vitro, ex vitro and in vivo conditions.

contact:https://web.prf.jcu.cz/en/kmb/people/faculty-and-stuff/rndr.-alena-krejci-ph.d..html

Bachelor or Master thesis project - UPDATE: project assigned
Diplonemids belong to the most abundant heterotrophic planktonic microeukaryotes in the world ocean and, thus, are likely to play an essential role in marine ecosystems. The primary focus of this research project is to understand the ecological role of diplonemids. The student is expected to perform feeding experiments and analyze the cell morphology and behavior patterns of diplonemids around a variety of prey.

contact: https://www.paru.cas.cz/en/staff/profile/22084/

Bachelor or Master thesis project
Although universal, the standard genetic code present deviations from its canonical coding. In the laboratory we have identified several transfer RNAs (tRNAs) with naturally occurring mutations that induce translational readthrough in trypanosomatids with codon reassignment. These mutations can also recapitulate the phenomenon in yeast and other trypanosomatids without codon reassignment, providing evidence of a conserved mechanism. We aim to expand the analysis to bacteria, for which we will generate and optimize a dual luciferase system in prokaryotic cells.
The student will generate the constructs needed for the expression of this system in bacteria and test it performing luciferase activity measurements in the presence of several co-expressed t-RNAs.

contact: https://www.paru.cas.cz/en/staff/profile/22084/

Bachelor or Master thesis project - UPDATE: project assigned
Naked mole-rat is an African rodent with multiple extraordinary characteristics, including extremely long lifespan, resistance to diseases uncluding cancer and eusocial system with only one reproducing male and female in the colony. Epigenetic changes (changes in histone modifications and DNA methylation landscape) are one of hallmarks of aging, and epigenomic landscape is also reprogrammed during development. In orded to study the epigenome stability and reprogramming in aging and development in naked mole-rat, we need to optimise and establish chromatin immunoprecipitation protocol in this species. The aim of this project is to test the protocol, test different antibodies for various histone modifications, establish the workflow of one of the most important techniques in epigenetics.
Depending on the motivation and time availability of the student, we can proceed to profile specific histone modifications at the loci of interest using ChIP-qPCR, or at the genome-wide level, or apply the technique to the low input material (oocytes).

contact:https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gahurova_Lenka_71061

Bachelor or Master thesis project - UPDATE: project assigned
We offer various projects studying retrotransposon variability across mammals, the genome defence mechanisms for their suppression, as well as their domestication by host genomes. The specific project will be discussed with the student based on their interests and bioinformatics skills.

contact:https://www.jcu.cz/cz/univerzita/lide/clovek?identita=Gahurova_Lenka_71061

Bachelor project
Polycomb repressive complex 2 (PRC2) is an evolutionarily conserved histone methyltransferase present in animals and plants. CRISPR/Cas9 is a state-of-art gene editing strategy, that allows targeted gene modification. We have targeted different domains of PRC2 catalytic subunits by CRISPR/Cas9 and aim to analyse impacts of these mutations.
In this project, you will learn a wide spectrum of general molecular biology techniques, including DNA extraction, primer design, PCR, gel electrophoresis, cloning and Sanger sequencing, RNA extraction, RT-qPCR and related data analyses.

contact: https://mozgovalab.umbr.cas.cz/

Bachelor or Master thesis project
SET-domain proteins are histone methyltransferases that catalyse lysine mono-/di-/or trimethylation. This is a major histone post-translational modification that fundamentally influences chromatin structure and marks gene repression or transcriptional activity. This project will use extensive genomic, transcriptomic and proteomic database search for SET-domain proteins in the genomes protists and phylogeny reconstruction approaches to analyse the evolution of the SET-domain proteins.
If taken up as a longer-term project (or super-efficient:-)), this will be followed by wet-lab experiments to confirm and extend the results. The expected techniques are protein extraction, Western Blotting, DNA/RNA extraction, PCR/qPCR, chromatin immunoprecipitation.
(co-supervised by Mgr. Iva Mozgová, Ph.D.)

contact: https://mozgovalab.umbr.cas.cz/

Bachelor or Master thesis project
Histone H3 is a major histone type subject to regulatory epigenetic post-translational modifications (PTM). It is highly conserved in eukaryotes and present in several variants that differ by only several amino acids. In spite of this, the variants can be subjected to different PTMs by chromatin-modifying enzymes, which has a profound effect on chromatin structure and gene transcription. This project will use extensive genomic, transcriptomic and proteomic database search for the histone H3 variants present in the genomes of early eukaryotes and reconstruct phylogeny to shed light on the evolution of histone H3.
If taken up as a longer-term project (or super-efficient:-)), this will be followed by wet-lab experiments to confirma and extend the results. The expected techniques are protein extraction, Western Blotting, DNA/RNA extraction, PCR/qPCR, chromatin immunoprecipitation.
(co-supervised by Mgr. Iva Mozgová, Ph.D.)

contact: https://mozgovalab.umbr.cas.cz/

Bachelor or Master thesis project
Polycomb repressive complex 2 (PRC2) is involved in the regulation of key developmental mechanisms. We aim to see the level of functional evolutionary conservation of PRC2 catalytic subunit in green lineage by inter-species complementation. We will exchange moss (Physcomitrium patens) catalytic subunit with the algal subunits. We will evaluate the impact on phenotype, gene expression and H3K27me3 distribution.
Here, you can learn sterile cell culture work, moss transformation, genotyping (DNA extraction, PCR), microscopic analysis, RT-qPCR (RNA extraction, cDNA synthesis, quantitative PCR) and, chromatin imunoprecipitation of wild type and transgenic cultures.
(co-supervised by Mgr. Iva Mozgová, Ph.D.)

contact: https://mozgovalab.umbr.cas.cz/

Bachelor project

contact: https://www.entu.cas.cz/pracovnici/profil/284/

Bachelor project

contact: https://www.entu.cas.cz/pracovnici/profil/284/

Bachelor project

contact: https://www.entu.cas.cz/pracovnici/profil/284/

Bachelor or Master thesis project 
for details click here

Bachelor or Master thesis project
for details click here

Bachelor or Master thesis project
for details click here