8.2. 2018, Biomathematics

PhD project 1: 

Alteration of plasma membrane protein and lipid composition by oxidative stress; studies of rat brain and model cell lines                                     

Most cell functions occur in or around membranes. Membranes represent a meeting point for lipids and proteins. The reactive intermediates, produced by oxidative stress, can alter the membrane and cause the lipid peroxidation of polyunsaturated fatty acids. Highly reactive products of lipid peroxidation are able to modify the structure and function of membrane leading to changes in the permeability and fluidity of the lipid bilayer. Oxidation of membrane lipids may also influence the environment and functional efficiency of membrane proteins.

Oxidative stress is believed to cause a number of diseases. Present discussions also consider that induction of oxidative stress participates in cognitive, emotional and many other physiological functions of organism. The delineation of the border between reversible and irreversible changes proceeding in plasma membrane of the given cell type is in the focus of present research. In our research group, we are for example testing the validity of two and mutually related hypotheses of lithium action in pharmacotherapy of bipolar disorder which are based on modulation of Na+/K+-ATPase activity and oxidative stress. We also determine the effect of lipoperoxidative damage of plasma membrane on G protein-coupled receptors initiated signalling cascades in connection with opioid addiction.

 

Candidate’s profile (requirements): MSc, MD or equivalent degree in physiology, cellular biology, chemistry, molecular biology, pharmacology or physics. Basic practice in laboratory of biochemistry, cell biology, pharmacology, molecular biology or biophysics.

Relevant publications:

U. Banerjee, A. Dasgupta, J. K. Rout, O. P. Singh, Effects of lithium therapy on Na+–K+-ATPase activity and lipid peroxidation in bipolar disorder, Prog. Neuropsychopharmacol. Biol. Psychiatry. 37 (2012) 56-61.

Z. Qiusheng, M. Jun, Reactive Oxygen Species and Morphine Addiction. In S.I. Ahmad (editor) Reactive Oxygen Species in Biology and Human Health, CRC Press (2016): pp 501-512.

M. Vosahlíková, P. Jurkiewicz, L. Roubalova, M. Hof, P. Svoboda, High- and low-affinity sites for sodium in δ-OR-Gi1α(Cys351-Ile351) fusion protein stably expressed in HEK293 cells; functional significance and correlation with biophysical state of plasma membrane, Naunyn-Schmiedebergs Arch. Pharmacol. 387 (2014) 487-502.

M. Vosahlikova, P. Svoboda, Lithium - therapeutic tool endowed with multiple beneficiary effects caused by multiple mechanism, Acta Neurobiol. Exp. 76 (2016) 1-19.

M. Vosahlikova, H. Ujcikova, O. Chernyavskiy, J. Brejchova, L. Roubalova, P. Svoboda, Effect of therapeutic concentration of lithium on live HEK293 cells; increase of Na+/K+-ATPase, change of overall protein composition and alteration of surface layer of plasma membrane, Biochim. Biophys. Acta-Gen. Subj. 1861 (2017) 1099-1112.

 

Supervisor: Ing. Miroslava Vosahlikova, PhD

 

PhD project 2: 

Studies of spatiotemporal distribution of plasma membrane proteins by advanced techniques of confocal fluorescence microscopy                                                               

Plasma membrane is a complex cell surface structure composed from many different types of lipids and proteins. Distribution of individual protein and lipid molecules in this structure is not homogeneous. Moreover, plasma membrane exhibits high level of spatiotemporal variability. Proteins residing in plasma membrane are important players in the cellular communication. Transduction of extracellular signals into the cell requires the coupling of cell surface receptors with intracellular signaling proteins. Signaling partners have to encounter each other in the right place and at the right time in order to induce the proper cellular response. Their spatiotemporal distribution therefore needs to be dynamically adjusted according to changes in the surrounding environment/incoming stimuli. Organization of proteins within the plane of plasma membrane bilayer is regulated by the interplay of many factors, e.g., protein-lipid and protein-protein interactions, association with the underlying cytoskeleton meshwork, or inhomogeneities of lipid phase of membrane bilayer. Despite the significant efforts put into the elucidation of the underlying principles, they are still far from being understood.

 

Candidate’s profile (requirements): MSc, MD or equivalent degree in cellular and molecular biology, biochemistry, physiology, pharmacology or physics. Basic laboratory practice in biochemistry, cell biology, pharmacology or biophysics.

Relevant publications:

A. Baker, A. Sauliere, F. Dumas, C. Millot, S. Mazeres, A. Lopez, L. Salome, Functional membrane diffusion of G-protein coupled receptors, Eur. Biophys. J. 36 (2007) 849-860.

A. Kusumi, K.G. Suzuki, R.S. Kasai, K. Ritchie, T.K. Fujiwara, Hierarchical mesoscale domain organization of the plasma membrane, Trends Biochem. Sci. 36 (2011) 604-615.

F.J. Alenghat, D.E. Golan, Membrane protein dynamics and functional implications in mammalian cells, Curr. Top. Membr. 72 (2013) 89-120.

J. Brejchova, J. Sykora, K. Dlouha, L. Roubalova, P. Ostasov, M. Vosahlikova, M. Hof, P. Svoboda, Fluorescence spectroscopy studies of HEK293 cells expressing DOR- Gi1α fusion protein; the effect of cholesterol depletion, Biochim. Biophys. Acta 1808 (2011) 2819-2829.

J. Brejchova, J. Sykora, P. Ostasov, L. Merta, L. Roubalova, J. Janacek, M. Hof, P. Svoboda, TRH-receptor mobility and function in intact and cholesterol-depleted plasma membrane of HEK293 cells stably expressing TRH-R-eGFP, Biochim. Biophys. Acta 1848 (2015) 781-796.

J. Brejchova, M. Vosahlikova, L. Roubalova, M. Parenti, M. Mauri, O. Chernyavskiy, P. Svoboda, Plasma membrane cholesterol level and agonist-induced internalization of δ-opioid receptors; colocalization study with intracellular membrane markers of Rab family, J. Bioenerg. Biomembr. 48 (2016) 375-396.

Supervisor: Mgr. Jana Brejchová, PhD

 

 

PhD project 3:  

Protein composition of rat brain exposed to morphine-, methadone- or peptide ligands with mixed µ/δ-opioid receptor activity                   

Opioid addiction is recognized as a chronic relapsing brain disease resulting from repeated exposure to opioid drugs. Spontaneous tendency of any drug addict is to increase the doses of the drug with the aim to achieve the desired effect. This tendency is primarily based on the general physiological phenomenon – desensitization of response, which is manifested after repeated or long-term stimulation of the target cell, tissue or the whole organism by a given drug. Cellular and molecular mechanisms underlying the ability of organism return back to the physiological norm after cessation of drug supply are not understood.

Proteomic analysis of forebrain cortex of rats exposed to morphine for 10 days and subsequently nurtured for 20 days without this drug indicated a dramatic decrease in the number of morphine-altered proteins when compared with animals exposed to morphine for 10 days. The aim of PhD project is to compare the effect of morphine with those of methadone- and peptide ligands with mixed µ/δ-opioid receptor activity in animals exposed to these drugs for the period of time sufficient to induce the addicted state. Such animals will be compared with those in the state of drug withdrawal after cessation of morphine or methadone drug supply. We shall work with forebrain cortex, hippocampus and other parts of rat CNS. We shall also follow the effect of these opioid receptor agonists on cell lines expressing a given type of OR.

 

Candidate’s profile (requirements): MSc, MD or equivalent degree in physiology, cellular biology, biochemistry, molecular biology or pharmacology. Practice in laboratory of biochemistry, cell biology, pharmacology or molecular biology.

 Relevant publications:

A.I. Leshner, Addiction is a brain disease, and it matters, Science 278 (1997) 45-47.

L. Bourova, M. Vosahlikova, D. Kagan, K. Dlouha, J. Novotny, P. Svoboda, Long-term adaptation to high doses of morphine causes desensitization of µ-OR- and δ-OR-stimulated G-protein response in forebrain cortex but does not decrease  the amount of G-protein alpha subunit, Med. Sci. Monit. 16 (2010) 260-270.

H. Ujcikova, K. Dlouha, L. Roubalova, M. Vosahlikova, D. Kagan, P. Svoboda, Up-regulation of adenylylcyclases I and II induced by long-term adaptation of rats to morphine fades away 20 days after morphine withdrawal, Biochim. Biophys. Acta 1810 (2011) 1220-1229.

H. Ujcikova, J. Brejchova, M. Vosahlikova, D. Kagan, K. Dlouha, J. Sykora, L. Merta, Z. Drastichova, J. Novotny, P. Ostasov, L. Roubalova, M. Parenti, M. Hof,  P. Svoboda, Opioid-receptor (OR) signaling cascades in rat cerebral cortex and model cell lines: the role of plasma membrane structure, Physiol. Res. 63 (2014) S165-S176.

H. Ujcikova, A. Eckhardt, D. Kagan, L. Roubalova, P. Svoboda, Proteomic analysis of post-nuclear supernatant and percoll-purified membranes prepared from brain cortex of rats exposed to increasing doses of morphine, Proteome Sci. 12 (2014) 11.

H. Ujcikova, M. Vosahlikova, L. Roubalova, P. Svoboda, Proteomic analysis of protein composition of rat forebrain cortex exposed to morphine for 10 days; comparison with animals exposed to morphine and subsequently nurtured for 20 days in the absence of this drug, J. Proteomics 145 (2016) 11-23.

H. Ujcikova, M. Hlouskova, K. Cechova, K. Stolarova, L. Roubalova, P. Svoboda, Determination of μ-, δ- and κ-opioid receptors in forebrain cortex of rats exposed to morphine for 10 days; comparison with animals after 20 days of morphine withdrawal, PLoS ONE 12 (10) (2017) e0186797.

 

Supervisor: RNDr. Hana Ujčíková, PhD

 

PhD project 4:

PhD project: Image analysis and stereology of cytoskeleton and other cell components based on 3D images acquired by confocal and superresolution microscopy.

Microtubules (MT) are cylindrical cytoskeletal polymers indispensable for many vital cellular activities such as maintenance of cell shape, division, migration and ordered vesicle transport powered by motor proteins. The PhD project will be focussed on development, implementation and application of advanced methods of image analysis, stereology and spatial statistics for measurement of morphological parameters of MT, mitochondria and endoplasmic reticulum, especially in combination with virtual reality (VR) exploiting custom-made VR image analysis software, currently being developed at the Department of Biomathematics (Institute of Physiology CAS).

The PhD project will be performed in cooperation with the Laboratory of Biology of Cytoskeleton (Institute of Molecular Genetics CAS) and Bioelectrodynamics Research Team (Institute of Photonics and Electronics CAS) in the framework of ongoing common project.

 Candidate’s profile (requirements):

• Master degree in biomedical engineering, mathematics, informatics, biology
• IT skills
• Interest in microscopy and microscopic structures
• Openness to interdisciplinary cooperation and new scientific approaches
• Creativity

 

Relevant Publications:

1. Marek J, Demjénová E, Tomori Z, Janáček J, Zolotová I, Valle F, Favre M, Dietler G: Interactive measurement and characterization of DNA molecules by analysis of AFM images. Cytometry 63A: 87-93, 2005.

2. Janáček J, Čapek M, Michálek J, Karen P, Kubínová L: 3D microscopic imaging and evaluation of tubular tissue architecture. Physiol. Res. 63 Suppl.1: S49-S55, 2014.

3. Kubínová L, Janáček J: Confocal stereology: an efficient tool for measurement of microscopic structures. Cell Tiss. Res. 360: 13-28, 2015.

4. Chiu et al., Stochastic Geometry and Its Applications, Wiley Series in Probability and Statistics        3rd ed., John Wiley & Sons, 2013.

  

Supervisor: RNDr. Lucie Kubínová, CSc. (PhD Programme „Imaging Methods in medicine“ or „Developmental and Cell Biology“, Charles University in Prague)