Ph.D. studies

This PhD project focuses on advancing the integration of metabolomics and lipidomics to unravel the regulation of complex biochemical networks and metabolic dynamics. The study leverages state-of-the-art data processing techniques, computational tools, and machine learning algorithms to extract actionable insights from large-scale fluxomics datasets. Python-based pipelines will be developed to standardize data preprocessing, feature extraction, and analysis while incorporating machine learning models for network clustering, classification, and predictive modeling of metabolic pathways.

The project emphasizes cross-disciplinary approaches, blending expertise in biochemistry, computational biology, and data science to create robust tools for understanding metabolic systems. Outcomes are expected to contribute to personalized medicine, metabolic engineering, and systems biology, offering novel methodologies and software frameworks for the scientific community.

The work will be conducted at the IPHYS CAS, where the metabolomics and proteomics service laboratory is located. The work is financially secured in terms of material and full time position.

Candidate’s profile (requirements):

The prerequisites for success are knowledge of programming languages for working with data (Python), basic biochemistry (metabolites, pathways, cellular compartments), and an overview of omics disciplines. The candidate should be fluent in English and willing to travel to collaborating laboratories abroad.

Supervisor: Ondrej Kuda (ondrej.kuda@fgu.cas.cz)

References:

Lopes et al. Metabolomics atlas of oral 13C-glucose tolerance test in mice. Cell Rep. 2021 Oct 12;37(2):109833. doi: 10.1016/j.celrep.2021.109833

Vondrackova et al. LORA, Lipid Over-Representation Analysis Based on Structural Information. Anal Chem. 2023 Aug 29;95(34):12600-12604. doi: 10.1021/acs.analchem.3c02039

https://github.com/IPHYS-Bioinformatics

This PhD project investigates the rewiring of lipid metabolic pathways in cancer using an integrative approach combining metabolomics, fluxomics, metabolic engineering, and in silico modeling. The research aims to deconvolute complex lipid metabolic pathways through metabolic flux analysis and stable isotope tracer studies, supported by Python-based data processing pipelines and advanced computational modeling.

The study incorporates experimental work, including cancer cell culture models and in vivo mouse models, to validate findings and quantify metabolic fluxes under physiological and pathological conditions. In silico simulations of lipid metabolism will be used to predict pathway behavior and identify potential intervention points. Machine learning approaches will aid in biomarker discovery and the prediction of metabolic vulnerabilities, offering insights into the mechanisms driving cancer progression and potential therapeutic targets.

This interdisciplinary project bridges computational biology, biochemistry, and experimental cancer research, contributing to our understanding of lipid metabolism and the development of precision strategies for metabolic engineering and cancer therapy.

The work will be conducted at the IPHYS CAS. The work is financially secured in terms of material and full time position.

Candidate’s profile (requirements):

The prerequisites for success are knowledge of programming languages for working with data (Python), basic biochemistry (metabolites, pathways, cellular compartments), and an overview of omics disciplines. Previous experience with cell cultures and mouse experiments is an advantage.

Supervisor: Ondrej Kuda (ondrej.kuda@fgu.cas.cz)

Department: Laboratory of Pancreatic Islet Research

PhD project: Crosstalk of glucose-induced lipid metabolism and redox homeostasis in beta-cell physiology and pathology

Our newly established laboratory investigates the physiology and pathophysiology of pancreatic beta cells. Beta cells are the guardians of glucose homeostasis in the body, and their deficiency and impaired function trigger the development of diabetes. We focus on the role of redox homeostasis and lipid metabolism during glucose stimulation and subsequent signaling in beta cells. Altered redox status and modified glucose-induced lipid metabolism may affect cellular signaling i.e. insulin secretion, while in the long term they may induce cellular stress. The switching point and metabolic targets of signaling are unknown in beta cells.
The aim of this PhD project is to identify redox regulated glucose-induced lipid signaling and lipid metabolism under physiological conditions of insulin secretion on the one hand and the mechanism of its dysregulation to develop diabetes on the other hand. A unique mouse model with altered redox status in beta cells and isolated Langerhans islets/cells will be used for the study, employing novel experimental strategies in combination with omics analyses.

Candidate’s profile (requirements):
We are looking for talented and motivated biological problem solving graduates with a background in biological and biomedical sciences and computational biology. Experience with cell culture, mouse/rat models, molecular biology and biochemistry, omics data analysis and computational biology is a plus. We offer a full-time salary.

Supervisor: Lydie Plecitá (lydie.plecita@fgu.cas.cz)

References:

• Holendová B, Benáková Š, Křivonosková M, Pavluch V, Tauber J, Gabrielová E, Ježek P, Plecitá-Hlavatá L. NADPH oxidase 4 in mouse β cells participates in inflammation on chronic nutrient overload.
• Obesity (Silver Spring). 2023 Dec 12.
• Holendova B, Plecita-Hlavata L. Cysteine residues in signal transduction and its relevance in pancreatic beta cells. Front Endocrinol (Lausanne). 2023 Jun 29;14:1221520. doi: 10.3389/fendo.2023.1221520.
• Benakova S, Holendova B, Plecita-Hlavata L. Redox Homeostasis in Pancreatic beta-Cells: From Development to Failure. Antioxidants (Basel). 2021;10(4).
• Plecita-Hlavata L, Jaburek M, Holendova B, Tauber J, Pavluch V, Berkova Z, et al. Glucose-Stimulated Insulin Secretion Fundamentally Requires H2O2 Signaling by NADPH Oxidase 4. Diabetes. 2020.
• Plecita-Hlavata L, Engstova H, Holendova B, Tauber J, Spacek T, Petraskova L, et al. Mitochondrial Superoxide Production Decreases on Glucose-Stimulated Insulin Secretion in Pancreatic beta Cells Due to Decreasing Mitochondrial Matrix NADH/NAD(+) Ratio. Antioxid Redox Signal. 2020;33(12):789-815.

Department: Laboratory of Neurochemistry

PhD project: Mechanisms of selective modulation of individual subtypes of muscarinic receptors

The disruption of muscarinic signalling is frequently involved in various pathophysiological conditions, including neuropathic pain, neurological and psychiatric disorders, e.g. Alzheimer’s disease or schizophrenia, and some internal diseases, e.g. asthma or overactive bladder. To target these particular conditions, selective modulation of individual muscarinic subtypes is necessary to avoid undesired side effects. High homology of the orthosteric binding site among all muscarinic subtypes makes a finding of subtype-selective orthosteric agonists virtually unattainable. Selective targeting at a particular G-protein-mediated signalling pathway by biased agonists, exerted by agonist-specific conformation, can be the right way to achieve selectivity among individual subtypes of muscarinic receptors. On the other hand, bulky muscarinic antagonists, allosteric or bitopic ligands have a better chance to interact with less conserved areas of muscarinic receptors and achieve binding selectivity for individual muscarinic subtypes. Recently described muscarinic orthosteric agonists containing tetrahydropyridin and thiophene moieties display signalling bias toward Gi/o G-proteins and thus M2/M4 functional selectivity. Further, bitopic antagonists containing tetrahydropiridin moiety and O-hexyl chain act as M1 preferring long-acting antagonists. Accurate pharmacological analysis of the signalling profile and elucidation of mechanisms leading to the selectivity of these new compounds may facilitate the development of desired functionally selective agonists and antagonists. This project aims to perform a detailed binding and functional analysis of newly synthesized agonists and antagonists based on tetrahydropyridine. Further, we will employ site-directed mutagenesis of receptors and molecular modelling of ligand-receptor interactions to study the mode of action of these compounds.

Candidate’s profile (requirements):

We are seeking highly motivated independent candidate with a master’s degree or equivalent in pharmacology, biochemistry, molecular biology or related fields, or those expecting to obtain their degree this year. Essentially, candidate should be fluent in English and willing to travel to collaborating laboratories abroad to learn new techniques required for this project. Experience with in vitro cell culture, molecular biology techniques and basic programming skills are an advantage.

Supervisor: Jan Jakubik, PhD

References:

• Randáková A and Jakubík J, Functionally selective and biased agonists of muscarinic receptors. Pharmacol Res. 2021;169:105641. doi: 10.1016/j.phrs.2021.105641
• Randáková A, et al., Agonist-Specific Conformations of the M2 Muscarinic Acetylcholine Receptor Assessed by Molecular Dynamics. J Chem Inf Model. 2020; 27;60(4):2325-2338. doi: 10.1021/acs.jcim.0c00041.
• Randáková A, et al., Novel M2 -selective, Gi -biased agonists of muscarinic acetylcholine receptors. Br J Pharmacol. 2020;177(9):2073-2089. doi: 10.1111/bph.14970.
• Randáková A, et al, Novel long-acting antagonists of muscarinic ACh receptors. Br J Pharmacol. 2018; 175(10):1731-1743. doi: 10.1111/bph.14187

Department: Laboratory of Membrane Transport

PhD project: New regulatory mechanisms of the maintenance of monovalent-cation homeostasis crucial for the health of eukaryotic cells

Monovalent cations H+, K+, and Na+ are key elements of life required for all cellular functions. The intracellular concentrations of K+, Na+, and protons (pH) are determined via the activity of membrane proteins – transporters and channels mediating the continuous flux of cations and protons into and from cells with various transport mechanisms. Using the yeast Saccharomyces cerevisiae as a eukaryotic model organism, the PhD project will study new regulatory mechanisms maintaining monovalent-cation homeostasis in cells. The results will provide new insights into the regulation of cation homeostasis on the level of (i) particular cation transporters’ proteostasis (expression, biogenesis, function, and degradation) and (ii) their distribution/organization in the plasma membrane. The identification of new interactions among transporters and regulatory proteins will significantly advance our knowledge of molecular mechanisms required to maintain cation homeostasis and their physiological importance in healthy organisms.

Candidate’s profile (requirements):

The candidate should be highly self-motivated with master’s degree or equivalent (obtained before October 2024) in molecular biology, biochemistry, microbiology or related fields. Fluent English, as well as some experience in the basic laboratory (PCR, DNA and protein electrophoresis, bacteria transformation, plasmid isolation), bioinformatics (DNA and protein sequence search and comparison, sequenced fragments analysis, plasmid and primers design) as well as microscopic techniques are necessary.

Supervisor: Olga Zimmermannová, PhD. 

References:

1. Velazquez D. et al. Allosteric links between the hydrophilic N-terminus and transmembrane core of human Na+/H+ antiporter NHA2. Protein Science 31: E4460-E (2022); doi: 10.1002/pro.4460.

2. Papouskova K. et al. C5 conserved region of hydrophilic C-terminal part of Saccharomyces cerevisiae Nha1 antiporter determines its requirement of Erv14 COPII cargo receptor for plasma-membrane targeting. Mol Microbiol 115(1):41-57 (2021); doi: 10.1111/mmi.14595.

3. Smidova A. et al. The activity of Saccharomyces cerevisiae Na+, K+/H+ antiporter Nha1 is negatively regulated by 14-3-3 protein binding at serine 481. BBA – Mol Cell Re. 1866: 118534 (2019); doi: 10.1016/j.bbamcr.2019.118534.

4. Zimmermannova O. et al. Erv14 cargo receptor participates in regulation of plasma-membrane potential, intracellular pH and potassium homeostasis via its interaction with K+-specific transporters Trk1 and Tok1. BBA – Mol Cell Res 1866: 1376–1388 (2019); doi: 10.1016/j.bbamcr.2019.05.005.

Department: Laboratory of Biological Rhythms

PhD project: Development of circadian clocks in the fetal brain and their sensitivity to maternal stress

The mammalian circadian system aligns physiological functions with time of day. The system consists of principal clock located in the suprachiasmatic nuclei of the hypothalamus (SCN) that receives information about the external light/dark cycle and relays it to subordinate clocks in other brain regions and to clocks in various peripheral tissues. Stress is a lifestyle factor experienced by approximately 30% of pregnant women who report psychosocial stress in their daily lives. Despite previous extensive research on the effects of stress on the circadian system, studies on its effects on the circadian clock in the fetal SCN are sparse. The PhD project aims to determine the basic mechanisms of fetal SCN clock development and how glucocorticoids (and stress) affect immature brain clocks, with particular emphasis on the SCN. To achieve this goal, studies will employ the animal models such as laboratory rats and mice, including transgenic mouse models. A wide range of behavioral and molecular techniques used in the field of circadian clocks, including transcriptome/proteome/metabolome analyzes, real-time recording of clock gene expression in organotypic explants of brain areas and AAV transfection, will be employed.

Candidate’s profile (requirements):

The candidates should have the Master’s degree or equivalent in one of the fields: physiology, neuroscience, molecular biology, biochemistry, medicine or related fields, or they should be expecting to obtain their degree this year. Candidates should be fluent in English with good writing skills. Previous experience with biostatistics, in vivo models (mouse, rat) and molecular biology techniques is considered as an advantage.

Supervisor: Prof. Alena Sumova, DSc.

Reference:

Olejníková L., Polidarová L., Sumová A.: Stress affects expression of the clock gene Bmal1 in the suprachiasmatic nucleus of neonatal rats via glucocorticoid-dependent mechanism. Acta Physiol (Oxf). May;223(1):e13020, 2018. doi: 10.1111/apha.13020.
Greiner P., Houdek P., Sládek M., Sumová A.: Early rhythmicity in the fetal suprachiasmatic nuclei in response to maternal signals detected by omics approach. PLoS Biol. 2022 May 24;20(5):e3001637. doi: 10.1371/journal.pbio.3001637. eCollection 2022 May.

Department: Laboratory of Experimental Hypertension

PhD project: Mechanisms of gliflozins action in the treatment of non-diabetic experimental models of cardiovascular diseases

Gliflozins (inhibitors of sodium-glucose transporter 2 – SGLT-2) are a new class of antidiabetic drugs. Although they exert their hypoglycaemic effects through the inhibition of the sodium-glucose transporter at renal proximal tubule promoting glucose and sodium excretion, their potential goes far beyond. Thus, apart from the lowering of blood pressure and body weight, they are also renoprotective, cardioprotective and hepatoprotective both in diabetic but also non-diabetic patients. There are numerous experimental data on the effects of different gliflozins in diabetic kidney and heart disease. However, the experiments in non-diabetic animals are relatively scarce. Therefore, the aim of the PhD project will be to study molecular mechanisms of actions of these new class of antidiabetic drugs under non-diabetic conditions, with special focus on their combination with other drugs used in cardiovascular pathophysiology. 

Candidate’s profile (requirements):

We are looking for motivated candidates with master’s degree in molecular biology, biochemistry, physiology, or related fields. They should be fluent in English and interested in experimental research.

Supervisor: RNDr. Ivana Vaněčková, DSc. 

References:

Hüttl et al: Metabolic cardio- and reno-protective effects of empagliflozin in a prediabetic rat model, J Physiol Pharmacol, 71(5), 2020

Hojná S et al: Antihypertensive and metabolic effects of empagliflozin in Ren-2 transgenic rats, an experimental non-diabetic model of hypertension. Biomed Pharmacother.

2021;144:112246.

Malínská H et al: Beneficial Effects of Empagliflozin Are Mediated by Reduced Renal Inflammation and Oxidative Stress in Spontaneously Hypertensive Rats Expressing Human C-Reactive Protein. Biomedicines. 2022;10(9):2066.

Department: Laboratory of Pain Research

PhD Project: Neuroinflammation and pain

The main research interest of our department is to study mechanisms of pain and to explore new possibilities of pain treatment, especially in chronic states. Our experimental work is concentrated on the modulation of nociceptive information at the spinal cord level that is the first relay center between the periphery and higher brain areas. Our goal is to study these modulatory mechanisms in order to improve therapy for pain conditions such as neuropathic and cancer related pain. This project will be focused on the role of neuroinflammation in modulation of synaptic transmission and chronic pain development. Lately we are interested in the role of TRPV1 receptors, cannabinoids, endogenous lipids, opioids and inflammatory cytokines in this process. In our research we use mainly electrophysiological, optogenetic, OMICS analysis,  functional imaging, immunohistochemical, molecular and behavioral methods. In collaboration with clinics we aim to study human pathology in pain patients.

Candidate Requirements: 

The candidate should have a Masters’ degree in biological, medical or chemical sciences, or be due to complete their studies in this academic year. Experience in physiology, neurophysiology, cell biology, molecular biology or electrophysiology techniques would be an advantage. Candidates should be fluent in Czech or English.  

Supervisor:  Jiri Palecek, M.D., Ph.D.,

Selected relevant publications:

Li Y, Adamek P, Zhang H, Tatsui CE, Rhines LD, Mrozkova P, Li Q, Kosturakis AK, Cassidy, Harrison,.Cata,P. Sapire,K. Zhang,H. Kennamer, R. M. Jawad, A.B.  Ghetti, Yan, J., Paleček, J. Dougherty, P. M. The Cancer Chemotherapeutic Paclitaxel Increases Human and Rodent Sensory Neuron Responses to TRPV1 by Activation of TLR4. J Neurosci. 2015;35(39):13487-13500. IF=6.3

Nerandzic V, Mrozkova P, Adamek P, Spicarova D, Nagy I, Palecek J. Peripheral inflammation affects modulation of nociceptive synaptic transmission in the spinal cord induced by N-arachidonoylphosphatidylethanolamine. British Journal of Pharmacology 2018, 175, 2322-2356. IF = 6.8

Adamek P, Heles M, Palecek J, Mechanical allodynia and enhanced responses to capsaicin are mediated by PI3K in paclitaxel model of peripheral neuropathy. Neuropharmacology. 2019,146:163-174. IF=4.3

Heleš M, Mrózková P, Šulcová D, Adámek P, Špicarová D, Paleček J. Chemokine CCL2 prevents opioid-induced inhibition of nociceptive synaptic transmission in spinal cord dorsal horn. Journal of Neuroinflammation. 2021; 18(1)); 279 . IF = 9.6

Uchytilová; E, Špicarová D, Paleček J. Hypersensitivity Induced by Intrathecal Bradykinin Administration Is Enhanced by N-oleoyldopamine (OLDA) and Prevented by TRPV1 Antagonist. Int. J. Mol. Sci. 2021; 22(7)); 3712. IF = 6.2

P. Adamek, M. Heles, A. Bhattacharyya, M. Pontearso, J. Slepicka, J. Palecek. Dual PI3K-δ/γ Inhibitor Duvelisib Prevents Development of Neuropathic Pain in Model of Paclitaxel-Induced Peripheral Neuropathy. Journal of Neuroscience. 2022 Mar 2; 42(9):1864-1881. IF=6.7

Spicarova D, Nerandzic V, Muzik D, Pontearso M, Bhattacharyya A, Nagy I and Palecek J. Inhibition of synaptic transmission by anandamide precursor 20:4-NAPE is mediated by TRPV1 receptors under inflammatory conditions. Frontiers in Mol. Neuroscience 2023, 16:1188503,1-11, 2023,  IF = 6.2.

Department: Laboratory of Molecular Physiology of Bone

PhD project:
Studying bone marrow adiposity in mouse models of obesity: impact of sex dimorphism

Obesity is a metabolic bone disease accompanied with higher accumulation of bone marrow adipose tissue (BMAT) associated with increased risk of bone fractures and bone loss. With obesity, the function of key building blocks, bone marrow stromal cells (BMSCs) changes towards higher accumulation of BMAT, which is affected by diet and sex dimorphism. Men and women have unique nutritional needs based on physiological and hormonal changes across the life span, which may contribute to different prevalence of bone fractures among men and women. However, the exact molecular mechanism behind the sex-related differences in pathophysiology of bone are not well known. Thus, the aim of this project using different mouse models of obesity (B6, A/J mice and transgenic mice), is to investigate the impact of different diet interventions on BMAT expansion and BMSC molecular properties in relation to bone quality with respect to sex dimorphism.The project will employ in vivo phenotyping techniques (analyzing metabolic parameters, bone microstructure using different bioimaging methods microCT, contrast-enhanced CT, and specific program analysis), working with animal models, isolation of primary BMSC and applying several molecular, bioanalytical methods. Project will be conducted at the Institute of Physiology of CAS in collaboration with excellent laboratories abroad. The basic PhD
scholarship will be supported by the national grants.

Candidate’s profile (requirements):
We are seeking highly motivated, creative candidates with MSc degree or equivalent in molecular biology, biochemistry, physiology, medicine, pharmacology or related disciplines, or students expecting to obtain their degree this year. Experience with molecular biology techniques and in vitro cell culture methods are advantage.

Relevant publications:

• Benova A., et al. Novel thiazolidinedione analog reduces a negative impact on bone and mesenchymal stem cell properties in obese mice compared to classical thiazolidinediones. Mol Metab. 2022 Nov;65:101598. doi: 10.1016/j.molmet.2022.101598. Epub 2022 Sep 11
• Tencerova M, et al. Metabolic programming of bone marrow stromal stem cells determines lineage- differentiation fate. Bone Res. 2019 Nov 14;7:35. doi: 10.1038/s41413-019-0076-5.
• Tencerova M, et al. Obesity associated hypermetabolism and accelerated senescence of bone marrow stromal stem cells suggest a potential mechanism for bone fragility. Cell Rep. 2019 May 14;27(7):2050-2062.e6. doi: 10.1016/j.celrep.2019.04.066.
• Tencerova M, et al. High fat diet-induced obesity promotes expansion of bone marrow adipose tissue and impairs skeletal stem cell functions in mice. J Bone Miner Res. 2018 Feb 14. doi: 10.1002/jbmr.3408.
• Tencerova M, Kassem M. The Bone Marrow-Derived Stromal Cells: Commitment and Regulation of Adipogenesis. Front Endocrinol (Lausanne). 2016 Sep 21;7:127. Supervisor: Michaela Tencerova, Ph.D. (Michaela.Tencerova@fgu.cas.cz)