Ústav molekulární genetiky AV ČR, v. v. i.
We mainly focus on cytoskeletal linker proteins, in particular plectin, and we study the functional consequences of cytoskeletal organization in cell/tissue mechanics and mechanotransduction, i.e., conversion of physical cues into intracellular mechanosignalling pathways….
Supervisor
Martin Gregor
Project description
Plectin is a key cytoskeletal crosslinker required for mechanical stability and signaling in skeletal muscle and heart. Mutations in the plectin isoform P1f cause limb-girdle muscular dystrophy accompanied by progressive cardiomyopathy. Due to the large size of full-length plectin, classical gene-replacement strategies are not feasible, necessitating alternative therapeutic approaches.
This PhD project focuses on the development and functional characterization of mini-plectins engineered plectin variants retaining essential functional domains while being compatible with AAV-mediated gene delivery. The main objective is to evaluate their capacity to restore cytoskeletal organization and function in muscle and cardiac cells.
In the in vitro part, the student will analyze expression, localization, and functional integration of miniplectins in cultured cardiomyocytes. Using advanced fluorescence microscopy and biochemical approaches, the project will assess the ability of mini-plectins to reconstitute cytoskeletal networks, cell–cell junctions, and mechanosensitive signaling pathways impaired by P1f deficiency.
In the in vivo part, the therapeutic potential of mini-plectins will be tested in a newly established P1f knockout mouse model that recapitulates key features of human disease. AAV-mediated delivery will be evaluated for its ability to rescue pathological alterations in skeletal muscle and heart using histological, immunofluorescence, and functional readouts. The project will be conducted in close collaboration with international experts in gene therapy and muscle pathology.
This project combines mechanistic cell biology with translational gene-therapy approaches and aims to provide proof-of-concept data for mini-plectin–based therapies for plectin-related muscle and cardiac disease.
Candidate profile
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Supervisor
Martin Gregor
Project description
Hepatocellular carcinoma (HCC) is an aggressive liver malignancy with limited therapeutic options. Tumor progression critically depends on cytoskeletal organization and mechanotransduction, processes in which the cytolinker protein plectin plays a central role. Plectin integrates intermediate filaments, actin filaments, and microtubules and has emerged as a promising therapeutic target in HCC.
This PhD project aims to elucidate the molecular and cellular mechanisms of plectin inhibition using plecstatin, a first-in-class high-affinity plectin inhibitor. The project combines structural characterization with functional analyses in clinically relevant human tumor models.
In the first part, the student will define the plecstatin binding site on the plectin molecule. This will involve in vitro expression and purification of selected plectin domains and engineered variants, followed by biophysical and structural analyses. Hydrogen-deuterium exchange mass spectrometry will be used to identify plecstatin-induced conformational changes and interaction interfaces. Selected plectin–plecstatin complexes will be further analyzed by cryo-electron microscopy to resolve the structural basis of inhibitor binding and its impact on plectin function.
In the second part, the student will investigate plecstatin’s mode of action in patient-derived HCC explants maintained ex vivo to preserve native tumor architecture. Using advanced microscopy approaches, the project will assess plecstatin-induced changes in cytoskeletal organization, cell mechanics, and tumor cell behavior. These analyses will be complemented by quantitative proteomics to identify plecstatin-dependent remodeling of cytoskeletal and signaling networks in human tumor tissue.
By integrating structural biology with functional analyses in patient-derived HCC models, this project will provide mechanistic insight into cytoskeletal targeting strategies in cancer and support the development of plectin-directed therapies.
Candidate profile
Prior experience with protein expression and purification, mass spectrometry, advanced microscopy, or work with primary human tissues will be considered an advantage but is not required. The candidate is expected to actively contribute to data analysis, manuscript preparation, and international collaborations.
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Supervisor
Martin Gregor
Project description
Faithful chromosome segregation during mitosis relies on the assembly and mechanical robustness of the mitotic spindle, a microtubule-based structure that integrates molecular self-organization with force generation across multiple spatial scales. The spindle must dynamically adapt its geometry, material properties, and force balance to ensure accurate chromosome alignment and segregation despite intrinsic noise and external mechanical perturbations. Failures in spindle robustness lead to chromosome missegregation and aneuploidy, a common feature of cancer, developmental defects, and pregnancy loss.
This PhD project aims to elucidate the mechanobiological principles that govern spindle architecture, force integration, and robustness in dividing human cells. The project will combine targeted genetic perturbations of key spindle regulators with advanced mechanical and optical manipulation techniques. Using CRISPR/Cas9-based gene editing, candidate motor proteins, microtubule crosslinkers, and plus-end tracking proteins involved in spindle force transmission will be systematically perturbed. Spindle mechanics will be probed using a combination of optogenetic control of microtubule-associated proteins, magnetic tweezer-based force application, and three-dimensional laser ablation of defined spindle substructures.
Quantitative live-cell imaging will be used to measure spindle geometry, pole positioning, microtubule reorganization, and relaxation dynamics in response to acute perturbations. Experimental data will be integrated with biophysical modeling to define how molecular interactions give rise to emergent spindle properties such as stiffness, resilience, and self-repair. By linking molecular composition to mechanical function, this project will provide a mechanistic framework for understanding spindle robustness and its failure in disease-associated chromosomal instability.
Candidate profile
Prior experience with CRISPR/Cas9-based genome editing, quantitative imaging, optogenetics, laser ablation, or biophysical modeling will be considered an advantage but is not required.
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Tissues in the adult organism contain a population of tissue-specific stem cells that provide the cellular basis for homeostatic maintenance of adult tissues. Our goal is to elucidate the molecular mechanisms influencing the fate of normal and transformed adult stem cells in the intestine and haematopoietic system…
Supervisor
Lucie Láníková
Project description
Hematopoiesis is a highly organized and dynamic process of blood cell production, progressing hierarchically from hematopoietic stem cells (HSCs) through multipotent progenitors to fully differentiated cells of the myeloid and lymphoid lineages. This system is controlled by a complex network of cytokines and growth factors, with signal transduction predominantly mediated by the JAK-STAT pathway, which regulates proliferation, differentiation, survival, and the stability and trafficking of cytokine receptors.
Long-term HSC function critically depends on the maintenance of genomic integrity, safeguarded by DNA damage response (DDR) mechanisms. DDR orchestrates the detection and repair of DNA lesions, activation of cell-cycle checkpoints, and the repair of both double-strand (DSBs) and single-strand DNA breaks. Additionally, DDR protects stem cells from apoptosis, senescence, and premature functional decline. Impairment or failure of DDR—driven by congenital or acquired genetic variation or chronic cellular stress—leads to the accumulation of DNA damage, HSC exhaustion, disrupted differentiation programs, and activation of stress-induced and inflammatory signaling pathways. These alterations promote the clonal expansion of selectively advantaged hematopoietic cells, support clonal evolution, and may contribute to malignant transformation.
The dissertation focuses on understanding the molecular and genetic mechanisms that disrupt normal blood cell formation. Special attention is given to how inherited predisposition, acquired somatic mutations, and defects in DNA damage response influence stem cell behavior and clonal development. To study these processes, advanced experimental models will be used, including genetically modified animals, iPSC-derived hematopoietic cells, 3D organoids, and in vitro HSC culture systems. The aim of the project is to build a general model that explains how increased signaling activity together with impaired DNA repair control can change blood cell differentiation, clonal dynamics, and support the onset of the malignant myeloid transformation.
Candidate profile
The candidate holds a Master’s degree (or similar) in molecular biology, cell biology or a related life-science field and has a strong interest in hematopoiesis, genome integrity, and molecular mechanisms of disease. Practical experience with standard molecular biology and cell biology techniques is expected. Experience with Western blot analysis is considered an advantage. Bioinformatics skills, including basic data processing, statistical analysis, or work with high-throughput or sequencing data, are highly welcome and will be beneficial for the project. The candidate should be willing to work with murine models. The candidate should be able to work independently as well as part of a research team, demonstrate critical thinking, and show willingness to learn new experimental and computational approaches. Good communication skills in English, reliability, and a proactive attitude toward research are essential.
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We investigate embryonic development using an integrative approach combining molecular biology, cell biology, developmental biology, genetics, biochemistry, and bioinformatics in order to get insight into the molecular mechanisms underlying the process of animal development and its tinkering during the course of evolution…
Supervisor
Iryna Kozmiková
Co-supervisor
Jan Pačes
Project description
The project will use bioinformatic analysis together with comparative approaches to individual cells, and machine learning to investigate how the vertebrate head evolved and what mechanisms control cell fate specification. The project will focus primarily on the analysis and comparison of single-cell RNA-seq datasets from different animal groups, including multi-omics and spatial transcriptomics, and will be closely linked to experimental validation in the wet lab environment. In addition, the student will have the opportunity to develop or apply machine learning approaches to link molecular changes to phenotype, including analysis of genetic mutants and exploratory behavioral phenotyping. Our group places great emphasis on biological interpretation: the student will therefore gain practical insight into developmental and evolutionary biology, supported by extensive experimental knowledge in the laboratory. This position offers an excellent environment for growth as an interdisciplinary scientist combining computational and experimental approaches.
Candidate profile
The evo-devo team of laboratory of Transcriptional regulation is searching for a highly motivated, enthusiastic and hard-working Ph.D. student. The candidate must have a basic knowledge of programming fundamentals in R and Python and should hold a master degree in genetics, molecular biology, cell biology, or in a related field. The candidate should be able to work independently as well as part of a research team and demonstrate critical thinking.
We offer a friendly and supporting environment in a state-of-the-art institution.
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