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Institutional positions

Regular recruitment (10 openings; deadline 8th June 2021)

Go to the How to apply page to learn how to apply to the Doctoral Programme and get to the project.

Molecular Mechanisms of Disease lab

Dr. Neli Kachamakova-Trojanowska
1) Project title: Molecular background of microvascular complications in HNF1A-MODY patients: induced pluripotent stem cells as disease modeling tool
Project description: Patients with maturity onset diabetes of the young (MODY), a disease caused by a mutation in HNF1A gene, often develop vascular complications. To model the disease-specific mechanisms which are responsible for the impairment of the vascular function, patient-derived induced pluripotent stem cells (iPSCs) differentiated toward endothelium, could be a valuable tool. In the current project, the molecular basis of increased permeability of endothelial cells, derived from iPSCs, with mutations in the HNF1A gene will be better understood. We will try to elucidate the role of reactive oxygen species, calcium signalling, mitochondrial function and cell junction proteins in HNF1A-MODY vascular pathology.

Max Planck Laboratory

Dr. Sebastian Glatt / Dr. Przemysław Grudnik
1) Project title: Regulation of hypusination in health and disease 
Project description: Protein translation is a highly orchestrated process involving large macromolecular assemblies such as ribosomes and a vast number of auxiliary regulatory factors. During translation, some amino-acid sequences cause stalling of the whole process and such jams may be resolved with the help of translation factor eIF5A. eIF5A activity relies on the hypusination – a unique modification of single lysine residue which is achieved in a two-step mechanism employing two enzymes, namely DHS and DOHH. Our project aims to understand the process of regulation of hypusination by characterizing  DHS/DOHH/eIF5A interactome. In our research, we will employ such techniques as cryo-EM, macromolecular crystallography and mass spectrometry with a plethora of supporting biophysical and biochemical methods.

Laboratory of Photobiology

Dr. Justyna Łabuz
1) Project title: The role of phot2 dark activity in eliciting chloroplast responses 
Project description: The aim is to understand phot2 activity and its cellular trafficking in darkness, in particular to identify phot2 properties and leaf anatomical features important for the dark positioning of chloroplasts. Chloroplast responses to fluctuating light conditions will also be examined, to elucidate the role of subsequent photoreceptor activation occurring before its dark reversal.

Bioinformatics

Dr hab. Pawel Labaj / dr Tomasz Kosciółek
1) Project title: Metagenomic and machine learning analyses of exposome-gut microbiome interactions within the Polish population
Project description: Through the Polish Microbiome Project (PMP) we are accumulating microbiome and demographic data within Poland. The Project is a part of the global Microsetta Initiative infrastructure, so for the first time it will be possible to draw robust conclusions about microbiome composition and function within Poland. The objectives of the PhD are going to be: (1) to further develop the existing PMP bioinformatics infrastructure, (2) establish and analyze clinical populations to determine the microbial signatures of disease; (3) in collaboration with Dr. Paweł Łabaj, work on machine learning methods for clinical data analysis and health-disease status predictions.

Developmental Biology Laboratory

Prof. Grażyna Ptak
1) Project title:  Characterization of the developmental potential of embryos and embryo-derived cell lines from blastocysts at various growth stages.
Project description: The project will concentrate on characterization of conceptuses and embryonic stem cells derived from blastocysts at various growth stages. We are seeking for a motivated Ph.D. candidate that is interested in developmental and cell biology. The student will perform wide range of developmental and cell biology techniques, embryo manipulations and culture, embryonic stem cells derivation, cell lines characterization, RNA and protein analysis, mouse surgeries, etc. The project is carried out in collaboration with University of Würzburg (Germany). International secondments will likely be available during the course of the project.

Bionanoscience and Biochemistry Laboratory

Dr hab. Jonathan Heddle
1) Project title: Harnessing Molecular Motors
Project description: The PhD student will design and purify proteinaceous molecular motors with the aim of understanding how they convert chemical energy to structural changes in their substrates. This is envisaged to have wider ranging applications in  naonstructure design and drug delivery systems.

Protein Crystallography Research Group

Prof. Grzegorz Dubin / Dr. Anna Czarna
1) Project title: Structural biology of diabetic kinases
Project description: The project aims to discover new inhibitors for Dyrk kinase family kinases relevant in diabetes and to associate interaction partners involved in the beta cell proliferation and function. The project involves  protein biochemistry, biophysics, enzymology, X-ray crystallography, characterization of protein-protein interactions within the kinome and phospho-kinome and cell localization studies. The research is carried out in an international and national collaborations. We expect to better understand the mechanism of the proliferation and function of the beta cells and develop new set of inhibitors that would modulate their function for future pharmacological intervention.

Prof. Grzegorz Dubin 
1) Project title: Understanding the structural biology of coronaviruses
Project description: Coronaviruses are lurking in mammals for decades. Prior outbreaks have been largely ignored, but the current pandemics demonstrates the devastating potential of this family of viruses. The project aims at understanding the structural and functional proteins within coronaviruses with the ultimate goal of developing effective inhibitors of viral proliferation. The project is carried out in collaboration with the largest coronavirus laboratory in Poland which provides functional assays at BSL3 level and in international collaborations. The successful candidate will get a chance to support the studies primary in the fields of structural biology and inhibitor screening.

Plant Molecular Biology Laboratory

Dr. Kenji Yamada
1) Project title: Gene Regulatory Mechanism for the Mustard Oil Bomb Defence System of ER Bodies in Brassicaceae
Project description: Plants have developed sophisticated defence systems to adapt to changes in the environment. Brassicaceae (cabbage) family plants produce unique subcellular structure, namely endoplasmic reticulum (ER) bodies, for chemical defence against animal herbivores. The successful candidate will join a project that aims to understand detailed molecular mechanisms for ER body-based defence system. The project includes analysis of transcriptional regulation for ER body formation, plant defence level with insect-plant or fungi-plant interaction assays, identification of new regulatory genes in the defence system, cell biological and physiological analysis of the defence system.

Virogenetics – BSL3 Laboratory of Virology

Prof. Krzysztof Pyrć
1) Project title: Body on chip in virus research.
Project description: For years, research on viral infections has been carried out using in vitro models based on immortalized cell lines. Unfortunately, as viral replication is tightly bound to the cellular microenvironment, such an approach resulted in a number of erroneous results and improper conclusions. To overcome these limitations, efforts were made to reconstitute the studied tissues ex vivo and to examine the infection process in a natural microenvironment. For this reason, we employ the organoids and 3D tissue cultures based on primary cells. This research is carried out in Krakow but is also linked with a number of international collaborative networks, including Organovir (Horizon2020) and CARE (IMI2) projects. Here, we plan to go a step beyond and use state-of-the-art body-on-chip technologies to study the infection in the context of multiple tissues, including the immune system component. For that, collaborative research with the Technical Universities in Denmark and Warsaw has been initiated and the successful candidate will take part in this exciting research.