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Department of Microbiology

WWW

http://micro.wbbib.uj.edu.pl/

Head

Prof. dr hab. Jan Potempa
room: B220 (3.1.24), phone: +48 12 664 63 43

Staff

Prod. dr hab. Jacek Międzobrodzki
room: C242 (2.1.32), phone: +48 12 664 63 71, e-mail: jacek.miedzobrodzki@uj.edu.pl
Dr hab. Joanna Kozieł
room: B204 (3.1.36), phone: +48 12 664 63 62, e-mail: joanna.koziel@uj.edu.pl
Dr hab. Dariusz Dziga 
room: B243 (3.1.32), phone: +48 12 664 65 40, e-mail: dariusz.dziga@uj.edu.pl
Dr hab. Piotr Mydel
room: C225 (2.1.29), phone: 12 664 61 10, e-mail: piotr.mydel@uj.edu.pl
Dr. Karina Adamowicz
room: B219 (3.1.23), phone: +48 12 664 63 77, e-mail: karina.adamowicz@uj.edu.pl
Dr. Małgorzata Benedyk-Machaczka 
room: C225 (2.1.29), phone: +48 12 664 61 10, e-mail: malgorzata.benedyk@uj.edu.pl
Dr. Ewelina Dobosz
room: C243 (2.1.31), phone: +48 12 664 61 29, e-mail: e.dobosz@uj.edu.pl
Dr. Aleksander Grabiec
room: B243 (3.1.32), phone: +48 12 664 65 40, e-mail: aleksander.grabiec@uj.edu.pl,  www.epiperio.wbbib.uj.edu.pl
Dr. Danuta Mizgalska
room: B219 (3.1.23), phone: +48 12 664 63 77, e-mail: danuta.mizglaska@uj.edu.pl
Dr. Zuzanna Nowakowska
room: C243 (2.1.31), phone: +48 12 664 61 29, e-mail: zuzanna.nowakowska@uj.edu.pl 
Dr. Magdalena Pilarczyk-Żurek
room: C243 (2.1.31), phone: + 48 12 664 61 29, e-mail: magdalena.pilarczyk-zurek@uj.edu.pl
Dr. Maja Sochalska 
room: B203 (3.1.37), phone: +48 12 664 63 78, e-mail: maja.sochalska@uj.edu.pl 
Dr. Kinga Wójcik
room: B201 (3.1.38), phone: +48 12 664 61 68, e-mail: kinga.wójcik@uj.edu.pl
Dr. Danuta Bryzek
room: C243 (2.1.31), phone: +48 12 664 61 29, e-mail: danuta.bryzek@uj.edu.pl
Dr. Anna Golda
room: B219 (3.1.23), phone: +48 12 664 63 77, e-mail: anna.b.golda@uj.edu.pl
Dr. Maja Kosecka-Srojek
room: B205 (3.1.35), phone: +48 12 664 63 65, e-mail: maja.kosecka-strojek@uj.edu.pl
Dr. Mirosław Książek
room: MCB 3/10, phone: +48 12 664 61 07, e-mail: książek.miroslaw@uj.edu.pl
Dr. Aleksandra Milewska 
room: MCB 1.32, phone: +48 12 664 79 62, e-mail: aleksandra.milewska@uj.edu.pl
Mgr Klaudia Puła
room: C241 (2.1.33), phone: +48 12 664 62 43, e-mail:Klaudia.pula@uj.edu.pl
Mgr Aneta Sroka 
room: B203 (3.1.37), phone: +48 12 664 63 78, e-mail: aneta.sroka@uj.edu.pl
Mgr Marta Kossowicz-Reroń
room: C225 (2.1.29), phone: +48 12 664 61 10, e-mail: marta.kossowicz-reron@uj.edu.pl
Mgr Magdalena Nowak 
room: B219 (3.1.23), phone: +48 12 664 63 77, e-mail: magdalena.lidia.nowak@uj.edu.pl
Mgr Agata Potempa
room: B203 (3.1.37), phone: +48 12 664 63 78, e-mail: agata.potempa@uj.edu.pl

PhD students

Grzegorz Bereta, room C241 (2.1.33), phone: +48 12 664 62 43, e-mail: grzegorz.bereta@doctoral.uj.edu.pl
Paweł Botwina, room: MCB 0/19, e-mail: pawel.botwina@doctoral.uj.edu.pl
Joanna Budziaszek, room: C241 (2.1.33), phone: +48 12 664 62 43, e-mail: joanna.budziaszek@doctoral.uj.edu.pl
Yuliya Chykunova, room MCB 1/32, e-mail: y.chykunova@doctoral.uj.edu.pl
Agnieszka Dąbrowska, room: MCB 0/19, e-mail: agnieszka.dabrowska@doctoral.uj.edu.pl
Katherine Falkowski, room: MCB 3/10, phone: +48 12 664 61 07, e-mail: katherine.falkowski@doctoral.uj.edu.pl 
Anna Gąsiorek, room: C241 (2.1.33), phone: +48 12 664 62 43, e-mail: a.gasiorek@doctoral.uj.edu.pl 
Anna Jacuła, room MCB 3/10, phone: +48 12 664 61 07, e-mail: anna.jacula@doctoral.uj.edu.pl
Marta Kamińska, room: MCB 3/10, phone: +48 12 664 61 07, e-mail: marta_kaminska@outlook.com
Katarzyna Kuśka, room: MCB 1/34, phone: +48 12 664 61 03, e-mail: katarzyna.kuska@doctoral.uj.edu.pl
Klaudia Lisowska, room: B205 (3.1.35), phone: +48 12 664 63 65, e-mail: klaudia.lisowska@doctoral.uj.edu.pl
Katarzyna Łagosz, room B243 (3.1.32), phone: +48 12 664 65 40, e-mail: kasia.lagosz@doctoral.uj.edu.pl
Mariusz Madej, room: MCB 3/10, phone: +48 12 664 61 07, e-mail: mariusz.madej@uj.edu.pl
Małgorzata Magoch, room: MCB 1/7, telefon: 12 664 63 87, e-mail: m.magoch@gmail.com
Agata Marczyk, room: C241 (2.1.33), phone: +48 12 664 62 43, e-mail: agata.twardzik@uj.edu.pl
Katarzyna Owczarek, room: MCB 1/32, phone: +48 12 664 79 62, e-mail: katarzyna.kosowicz@uj.edu.pl
Magdalena Pachota, room: MCB 1/32, phone: +48 12 664 79 62, e-mail: magdalena.pachota@uj.edu.pl
Laura Sąsiadek, room: MCB 3/10, phone: +48 12 664 61 07, e-mail: Laura.sąsiadek@doctoral.uj.edu.pl
Marta Słomka, room C241 (2.1.33), phone +48 12 664 6243, e-mail: marta.slomka@doctoral.uj.edu.pl
Artur Szczepański, room: MCB 1/32, phone: +48 12 664 79 62, e-mail: artur.szczepanski@uj.edu.pl
Katarzyna Szczęśniak, room C241 (2.1.33), phone: +48 12 664 62 43, e-mail: k.szczesniak@doctoral.uj.edu.pl
Irena Waligórska, room: MCB 3/10, phone: +48 12 664 61 07, e-mail: irena.waligorska@gmail.com
Aleksandra Wielento, room: C241 (2.1.33), phone: +48 12 664 62 43, e-mail: aleksandra.wielento@doctoral.uj.edu.pl
Valeria Napolitano, room: MCB 1/7, phone: +48 12 664 63 86,
Natalia Zubrzycka, room: B203 (3.1.37), phone: 12 664 63 78, e-mail: natalia.zubrzycka@doctoral.uj.edu.p

 

Research topics

  • Pathogenesis of autoimmune diseases, including rheumatoid arthritis
  • Role of posttranslational modifications in immune system regulation
  • Role of negative inflammatory regulators in bacterial infection
  • Role of kallikrein-related proteases in EGF-related signal transduction
  • Role of arginine citrullination in the protease-inhibitor interactions in the context of innate immunity system
  • Sigficance of bacterial citrullination of host proteins/peptides in pathogenesis of periodontal disease
  • Role of citrullination in healing and regeneration of periodontal tissues
  • Petiopathogenesis and novel approaches to therapy of gingival fibromatosis
  • Defense mechanisms of bacteria
  • Epigenetics of bacterial infections
  • Apoptosis of immune cells and its role in the development of periodontitis 
  • Molecular mechanisms of bacterial opportunistic infections
  • Genetic and phenotypic bacterial strains typing
  • Pathogens transmission between human and animal
  • Advanced molecular diagnostics for bacterial infections 
  • Next generation sequencing (NGS) in medical microbiology
  • The role of fibroblast in the pathogenesis of periodontitis
  • Significance of citrullination catalyzed by PPAD in the pathogenesis of periodontitis
  • Impact of citrullination on periodontal tissues healing and regeneration
  • Significance of the polymorphisms in the PPAD gene from P. gingivalis in the pathogenesis and prognosis of periodontal disease
  • Molecular mechanisms and novel attempts to therapy of gingival fibromatosis
  • Proteases and their protein inhibitors
  • Mechanisms underlying clinical and epidemiological connections between periodontitis (parodontosis) and bacteria responsible for the development of periodontosis and systemic human diseases
  • Microbiological degradation of cyanobacteria; environmental, biochemical, molecular and biotechnological aspects
  • Analysis of adaptation mechanisms (at the genetic, biochemical and physiological level) of toxic strains of cyanobacteria to selected stress factors
  • Interactions between toxic cyanobacteria strains and their specific cyanophages
  • Potential of purple bacteria for the synthesis of biohydrogen based on agricultural waste

Methods

  • Models of in vitro and in vivo infections (subcutaneous chamber model, paradontosis model, model of aspiration pneumonia, model of rheumatoid arthritis, sepsis model)
  • Flow cytometry
  • Cell death analysis, cytotoxicity, cell proliferation, differentiation
  • Primary tissue cultures/organotypic cultures of gingival mucosa
  • In vitro cultures of progenitors and neutrophils immortalized with the HoxB8 transcription factor
  • Histology, immunomorphology, immunohistology and immunohistochemistry of tissues
  • Computer analysis of immunofluorescent stained cells and tissues
  • Fluorescence microscopy
  • Immunofluorescence microscopy
  • Biochemical baterial strains typing
  • Genetic methods in bacteria typing
  • Next generation sequencing (WGS, RNASeq)
  • Gene expression analysis (qPCR)
  • Protein analysis (ELISA, Western Blot)
  • Elektrophoresis 2DE, proteins and DNA electrophoresis
  • Chromatography (FPLC, HPLC, LC-MS)
  • Computed tomography

Current projects

  1. Jan Potempa: Wyleczymy neutropenię (FIXNET): wykorzystanie identyfikacji zaburzeń funkcji proteaz granulocytów obojętnochłonnych jako nowych możliwości diagnostycznych i terapeutycznych. TEAMNET (2019-2023), FNP
  2. Joanna Kozieł: Identyfikacja czynników wirulencji Streptococcus anginosus. OPUS 15 konsorcjum (2019-2022) NCN
  3. Joanna Kozieł: Rola negatywnego regulatora stanu zapalnego MCPIP-1 w rozwoju paradontozy. OPUS 15 ( 2019-2022) NCN
  4. Jan  Potempa: Struktura i funkcja unikatowego dwuskładnikowego systemu regulatorowego periodontopatogennej bakterii P.gingivalis. OPUS 16 (2019- 2022) NCN.
  5. Maja Sochalska: Targeting deregulated expression of anti-apoptotic proteins belonginbg to the Bcl-2 family in neutrophils as a potential therapy against periodintal disease. In vitro and in vivo analysis. FIRST TEAM - 4/2017 (2019-2022), FNP.
  6. Aleksander Grabiec: Epigenetics of periodontitis: DNA methylation in disease development and as a potential therapeutic target. FIRT TEAM 5  (2018-2021), FNP.
  7. Magdalena Pachota: Novel inhibitors of herpes virus protease. PRELUDIUM (2018-2020), NCN.
  8. Jan Potempa: Structure and function characterization of newly discovered unique inhibitors of proteases. OPUS 11 (2017-2020), NCN.
  9. Małgorzata Benedyk-Machaczka: System sekrecji białek typu IX (T9SS) jako nowy cel w opracowaniu związków blokujących wirulencję Porphyromonas gingivalis. MINIATURA 1 (2018-2019), NCN.
  10. Anna Golda: Analiza antyzapalnego mechanizmu działania koniugatów peptydów będących analogami enkefaliny i temporyny. MINIATURA 1 (2018-2019), NCN.
  11. Katarzyna Owczarek: Analysis of human coronavirus OC43 and Zika virus internalization routes in cells. Inhibition of the early steps of infection by intracellular pH tuning. PRELUDIUM (2018-2019), NCN.
  12. Dominika Staniec: Strukturalna i funkcjonalna charakterystyka kalpaino-podobnej peptydazy Tpr, ważnego czynnika wirulencji Porphyromonas gingivalis. PRELUDIUM 13 (2018-2019), NCN.
  13. Mariusz Madej: Charakterystyka strukturalna i funkcjonalna unikatowego systemu pobierania peptydów ze środowiska przez Gram-ujemną bakterię Porphyromonas gingivalis. ETIUDA 6 (2018-2019), NCN.
  14. Ewelina Dobosz: Ocena roli MCPIP-1 w regulacji procesu apoptozy neutrofilii. PRELUDIUM 12 (2017-2019), NCN.
  15. Izabela Ciastoń: A novel, non-enzymatic mechanism of action of gingipains as potent major virulence factor ofPorphyromonas gingivalis. PRELUDIUM 11 (2017-2019), NCN.
  16. Maja Kosecka-Strojek: Development of a reference data set for identification of Streptococcus and Enterococcus species based on Next Generation Sequencing of 16S-23S rRNA region. PRELUDIUM 11 (2017-2019), NCN.
  17. Mariusz Madej: The role of PorX and PorY proteins in regulating the expression of proteins responsible for secreting major virulence factors of Porphyromonas gingivalis. PRELUDIUM 10 (2016-2019), NCN.
  18. Maja Sochalska: Deregulated apoptosis of neutrophils as a potential mechanizm underlying the pathobiology of periodontitis. HOMING -1/2016 (2016-2019), FNP.
  19. Dariusz Dziga: Investigation of alternative mechanisms of cyanotoxins biodegradation. OPUS (2015-2019), NCN.
  20. Aleksander Grabiec: Epigenetics of periodontitis: alterations in the host protein acetylation system as a potentially fundamental mechanism for disease development. POLONEZ 1 (2016-2018), NCN.
  21. Danuta Mizgalska: Application of SELEX methodology for selection of aptamers as research and diagnostic tools to study and potentially to treat periodontitis. (2015-2018). SONATA 8, NCN.
  22. Mirosław Książek: Insight into biochemistry, structure, evolution and biology of bacterial serpins on example of miropin from human pathogen Tannerella Forsytha. OPUS 9 (2015-2018), NCN

Selected publications

  1. The Bactericidal Activity of Temporin Analogues Against Methicillin Resistant Staphylococcus aureus. Golda A, Kosikowska-Adamus P, Kret A, Babyak O, Wójcik K, Dobosz E, Potempa J, Lesner A, Koziel J. Int J Mol Sci. 2019 Sep 25;20(19).
  2. Proteolytic processing and activation of gingipain zymogens secreted by T9SS of Porphyromonas gingivalis.Veillard F, Sztukowska M, Nowakowska Z, Mizgalska D, Thøgersen IB, Enghild JJ, Bogyo M, Potempa B, Nguyen KA, Potempa J. Biochimie. 2019 Jun 15. 
  3. Discovery of Novel Potential Reversible Peptidyl Arginine Deiminase Inhibitor. Aliko A, Kamińska M, Falkowski K, Bielecka E, Benedyk-Machaczka M, Malicki S, Kozieł J, Wong A, Bryzek D, Kantyka T, Mydel P. Int J Mol Sci2019 May 2;20(9).
  4. Triggering NETosis via protease-activated receptor (PAR)-2 signaling as a mechanism of hijacking neutrophils function for pathogen benefits. Bryzek D, Ciaston I, Dobosz E, Gasiorek A, Makarska A, Sarna M, Eick S, Puklo M, Lech M, Potempa B, Potempa J, Koziel J. PLoS Pathog2019 May 20;15(5):e1007773. 
  5. BET Bromodomain Inhibitors Suppress Inflammatory Activation of Gingival Fibroblasts and Epithelial Cells From Periodontitis Patients. Maksylewicz A, Bysiek A, Lagosz KB, Macina JM, Kantorowicz M, Bereta G, Sochalska M, Gawron K, Chomyszyn-Gajewska M, Potempa J, Grabiec AM. Front Immunol2019 Apr 30;10:933. 
  6. Porphyromonas gingivalis in Alzheimer's disease brains: Evidence for disease causation and treatment with small-molecule inhibitors. Dominy SS, Lynch C, Ermini F, Benedyk M, Marczyk A, Konradi A, Nguyen M, Haditsch U, Raha D, Griffin C, Holsinger LJ, Arastu-Kapur S, Kaba S, Lee A, Ryder MI, Potempa B, Mydel P, Hellvard A, Adamowicz K, Hasturk H, Walker GD, Reynolds EC, Faull RLM, Curtis MA, Dragunow M, Potempa J. Sci Adv2019 Jan 23;5(1):eaau3333. 
  7. The impact of Porphyromonas gingivalis peptidylarginine deiminase on biofilm formation, invasion and transcriptional landscape of epithelial cells. Aliko A, Kamińska M, Bergum B, Gawron K, Benedyk M, Hellvard A, Jonsson R, Lamont RJ, Malicki S, Potempa J, Delaleu N, Mydel P. Sci Rep. 2018 Sep 20;8(1):14144. doi: 10.1038/s41598-018-32603-y.
  8. Fibroblasts from recurrent fibrotic overgrowths reveal high rate of proliferation in vitro - findings from the study of hereditary and idiopathic gingival fibromatosis.Gawron K, Łazarz-Bartyzel K, Kowalska A, Bereta G, Nowakowska Z, Plakwicz P, Potempa J, Fertala A, Chomyszyn-Gajewska M. Connect Tissue Res. 2018 Sep 20:1-11. 
  9. A Novel Biological Role for Peptidyl-Arginine Deiminases: Citrullination of Cathelicidin LL-37 Controls the Immunostimulatory Potential of Cell-Free DNA Wong A, Bryzek D, Dobosz E, Scavenius C, Svoboda P, Rapala-Kozik M, Lesner A, Frydrych I, Enghild J, Mydel P, Pohl J, Thompson PR, Potempa J, Koziel J.. J Immunol2018 Apr 1;200(7):2327-2340. 
  10. The Bacteroidetes Q-Rule: Pyroglutamate in Signal Peptidase I Substrates.Bochtler M, Mizgalska D, Veillard F, Nowak ML, Houston J, Veith P, Reynolds EC, Potempa J. Front Microbiol2018 Mar 1;9:230. 
  11. Epigenetic regulation in bacterial infections: targeting histone deacetylases. Grabiec AM, Potempa J: Crit Rev Microbiol2018;44(3):336-350.
  12. Heterologous expression of mlrA in a photoautotrophic host - Engineering cyanobacteria to degrade microcystins. Dexter J, Dziga D, Lv J, Zhu J, Strzalka W, Maksylewicz A, Maroszek M, Marek S, Fu P. Environ. Pollut2018;237:926-935. 
  13. The case for periodontitis in the pathogenesis of rheumatoid arthritis. Nat Rev Rheumatol. Potempa J, Mydel P, Koziel J. 2017 Oct;13(10):606-620. doi: 10.1038/nrrheum.2017.132. Epub 2017 Aug 24. Review. 
  14. Inactive Gingipains from P. gingivalis Selectively Skews T Cells toward a Th17 Phenotype in an IL-6 Dependent Manner. Glowczyk I, Wong A, Potempa B, Babyak O, Lech M, Lamont RJ, Potempa J, Koziel J. Front Cell Infect Microbiol2017 Apr 27;7:140. doi: 10.3389/fcimb.2017.00140. 
  15. The outer-membrane export signal of Porphyromonas gingivalis type IX secretion system (T9SS) is a conserved C-terminal β-sandwich domain. de Diego I, Ksiazek M, Mizgalska D, Koneru L, Golik P, Szmigielski B, Nowak M, Nowakowska Z, Potempa B, Houston JA, Enghild JJ, Thøgersen IB, Gao J, Kwan AH, Trewhella J, Dubin G, Gomis-Rüth FX, Nguyen KA, Potempa J. Sci Rep2016;6:23123.
  16. Manipulation of neutrophils by Porphyromonas gingivalis in the development of periodontitis Sochalska, M. and J. Potempa (2017). Front Cell Infect Microbiol 7: 197
  17. Inhibition of herpes simplex viruses by cationic dextran derivatives. Pachota M, Klysik K, Synowiec A, Ciejka J, Szczubialka K, Pyrc K, Nowakowska M. (2017Journal of Medicinal Chemistry. 60(20):8620-8630.
  18. MCPIP-1, Alias Regnase-1, Controls Epithelial Inflammation by Posttranscriptional Regulation of IL-8 Production. Dobosz E, Wilamowski M, Lech M, Bugara B, Jura J, Potempa J, Koziel J. J Innate Immun2016;8(6):564-578. 
  19. Multiple-locus tandem repeat fingerprinting as a method for rapid and cost-effective typing of animal-associated Staphylococcus aureus strains from lineages other than sequence type 398. Kosecka-Strojek M, Ilczyszyn WM, Buda A, Polakowska K, Murzyn K, Panz T, Bialecka A, Kasprowicz A, Jakunbczak A, Krol J, Wieliczko A, Wladyka B, Międzobrodzki J. J Med Microbiol2016;65:1494.
  20. Clonal Structures and Characterization of Staphylococcus aureus Strains from Invasive Infections in Paediatric Patients from South Poland: Association between Age, spa Types, Clonal Complexes, and genetic Markers. Ilczyszyn WM, Sabat AJ, Akkerboom V, Szkarłat A, Klepacka J, Sowa-Sierant I, Wasik B, Kosecka-Strojek M, Buda A, Miedzobrodzki J, Friedrich A. PLoSOne2016; 11:e15448

Batchelor/master thesis topics

  • Identification of bacterial and virial virulence factors
  • The role of epigenetic mechanisms in pathogen-host interaction
  • Modulation of immunological response during infection
  • Potranslational protein modifications during inflammation
  • Characterization of new bacterial proteolytic enzymes and their protein inhibitors
  • The influence of apoptotic proteins on the function and survival of immune system cells in the development of periodontal inflammatory disease (in vitro, in vivo, ex vivo)
  • Genetic and enzymatic bacterial strains typing
  • Analysis of bacterial virulence and multidrug resistance genes
  • Changes in the transcription of toxic genes of cyanobacteria essential in response to oxidative stress
  • Adaptation of toxic cyanobacteria strains at the physiological level to selected stress factors 
  • Expression of the mlrA gene in the Synechocystis strain and analysis of the microcystin degradation efficiency
  • Analysis of nitrogenase expression and activity of purple bacteria in an environment enriched with cellulose degradation product

Requirements for candidates

  • High score in major cell biology/biochemistry and/or microbiology courses.
  • Techniques: basic biochemical methods, bacterial cultivation