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Department of Analytical Biochemistry

Webpage

www.zba.wbbib.uj.edu.pl

Head

Prof. Andrzej Kozik, PhD, DSc
room: 4.0.25 (A104), phone: +48 12 664 65 25

Staff

  • Adam Dubin, professor emeritus
    room: 4.0.21 (A118), phone: +48 12 664 65 11
  • Paweł Mak, PhD, DSc
    room: 4.0.22 (A119), phone: +48 12 664 65 38
  • Ibeth Guevara–Lora, PhD, DSc
    room: 4.0.26 (A103), phone: +48 12 664 65 27
  • Benedykt Władyka, PhD, DSc
    room: 4.0.21 (A118), phone: +48 12 664 65 11
  • Emilia Bonar, PhD, Eng
    room: 4.0.21 (A118), phone: +48 12 664 65 11
  • Karolina Hyz, PhD, Eng
    room: 4.0.7 (A124), phone: +48 12 664 65 06
  • Michał Bukowski, PhD
    room: 4.0.8 (A125), phone: +48 12 664 65 44
  • Mariusz Gogól, PhD
    room: 4.0.24 (A135), phone: +48 12 664 65 44
  • Oliwia Bocheńska, PhD
    room: 4.0.27 (A101), phone: +48 12 664 65 24

PhD students

  • Marcin Hydzik, room: 4.0.8 (A125), phone: +48 12 664 65 44
  • Monika Janczak, room: 4.0.7 (A124), phone: +48 12 664 65 06  
  • Anna Niewiarowska-Sendo, room: 4.0.8 (A125), phone: +48 12 664 65 44  
  • Dorota Zając, room: 4.0.8 (A125), phone: +48 12 664 65 44
  • Gabriela Zielińska, room: 4.0.8 (A125), phone: +48 12 664 65 44

Research topics

  • Molecular mechanisms of the host-pathogen interactions in bacterial and fungal infections
  • Biochemical and structural characterization of the virulence factors (mainly secreted proteases and cell-surface adhesins) of pathogenic bacteria (e.g. Staphylococci) and fungi (e.g. Candida yeasts)
  • Biochemical and structural characterization of proteinase inhibitors
  • Biochemical and structural characterization of antimicrobial peptides
  • Structural and functional modifications of proteins during inflammation
  • Functionality of the kinin-generating and blood-coagulation systems during inflammation and infections
  • Biochemistry of vitamins and coenzymes

Methods and specialistic equipment

  • A broad spectrum of liquid chromatography methods. The Department is equipped with several low-pressure chromatographs (Pharmacia, BioRad), medium-pressure FPLC systems (Pharmacia, Knauer) and high-performance liquid chromatographs (Dionex, Shimadzu, Waters) with spectrophotometric and fluorimetric detectors.
  • Sequencing of proteins and peptides: The Department is equipped with an automatic protein sequencer Procise 491 (Applied Biosystems).
  • Mass spectrometry: The Department is equipped with a HCT Ultra ETDII (Bruker) mass spectrometer with ESI ion source and ion trap analyzer. This spectrometer is coupled with an ultrahigh-performance chromatograph Ultimate 3000 (Dionex). This LC-MS system allows to identify a variety of biologically active compounds by precise measurements of their molecular masses - directly or after enzymatic fragmentation. In our laboratories the spectrometer is applied for proteomic studies and for the identification and characterization of biologically active peptides.
  • Electrophoretic techniques. Proteins and peptides are analyzed using one- and two-dimension polyacrylamide gels (1D and 2D), both in mini and big formats. The comparative 2D electrophoresis is applied in studies concerning changes in intracellular and secretory proteomes of microorganisms, treated with different environmental factors. Selected proteins and peptides are then identified by direct automatic sequencing or mass spectrometry.
  • Molecular biology. We routinely perform nucleic acid amplification, molecular cloning, qualitative and quantitative determination of gene expression, construction of plasmid vectors, gene manipulations (introduction and knock-out). Additionally, we produce recombinant proteins in prokaryotic (Escherichia coli, Bacillus subtilis, Staphylococcus spp.) and eukaryotic (Pichia pastoris) hosts.
  • Dynamic light scattering (DLS). The Department is equipped with a DLS spectrometer (model DynaPro, Protein Solutions). This equipment allows to estimate the hydrodynamic radius of molecules in solutions. This parameter can then be used to calculate the molecular mass of the molecule, to determine homogeneity of the analyzed compounds as well as to trace changes in the size of molecules during aggregation or ligand binding.

Current projects

  1. Monika Janczak: An investigation of the chromosomally encoded PemIKSp toxin-antitoxin system of Staphylococcus pseudintermedius. (2016-2018). Preludium 10, National Science Centre (NCN).
  2. Benedykt Władyka: Toxin-antitoxin systems as regulators of gene expression in Staphylococcus. (2015-2018). Opus 7, National Science Centre (NCN).
  3. Paweł Mak: Studies on bacteriocins and virulence factors of animal strain Staphylococcus pseudintermedius 222. (2014-2017). Opus 6, National Science Centre (NCN).
  4. Oliwia Bochenska: Susceptibility of human antimicrobial peptides to the action of aspartic proteases secreted by pathogenic yeast Candida albicans. (2014-2016). Preludium 5, National Science Centre (NCN).
  5. Andrzej Kozik: Identification of adhesins of the pathogenic fungi Candida "non-albicans". (2013-2016). Opus 4, National Science Centre (NCN).
  6. Benedykt Władyka: Identification and studies of factors involved in staphylococcal virulence using genomics and proteomics. (2013-2016). Sonata 4, National Science Centre (NCN).
  7. Aleksandra Pęcak: Elaboration of ssDNA molecules having ability to bind the cellular receptor of hialuronic acid. (2013-2016). Preludium 4, National Science Centre (NCN).

Selected publications

  1. Bonar E, Wojcik I, Jankowska U, Kedracka-Krok S, Bukowski M, Polakowska K, Lis MW, Kosecka-Strojek M, Sabat AJ, Dubin G, Friedrich AW, Miedzobrodzki J, Dubin A, Wladyka B (2016) Identification of secreted exoproteome fingerprints of highly-virulent and non-virulent Staphylococcus aureus strains. Front Cell Infect Microbiol 6:51.
  2. Pieta P, Majewska M, Su Z, Grossutti M, Wladyka B, Piejko M, Lipkowski J, Mak P (2016) Physicochemical studies on orientation and conformation of a new bacteriocin BacSp222 in a planar phospholipid bilayer. Langmuir 32:5653-5662.
  3. Wladyka B, Piejko M, Bzowska M, Pieta P, Krzysik M, Mazurek Ł, Guevara-Lora I, Bukowski M, Sabat AJ, Friedrich AW, Bonar E, Międzobrodzki J, Dubin A, Mak P (2015) A peptide factor secreted by Staphylococcus pseudintermedius exhibits properties of both bacteriocins and virulence factors. Sci Rep 5:14569.
  4. Bochenska O, Rapala-Kozik M, Wolak N, Kamysz W, Grzywacz D, Aoki W, Ueda M, Kozik A (2015) Inactivation of human kininogen-derived antimicrobial peptides by secreted aspartic proteases produced by the pathogenic yeast Candida albicans. Biol Chem 396:1369-75.
  5. Kozik A, Gogol M, Bochenska O, Karkowska-Kuleta J, Wolak N, Kamysz W, Aoki W, Ueda M, Faussner A, Rapala-Kozik M (2015) Kinin release from human kininogen by 10 aspartic proteases produced by pathogenic yeast Candida albicans. BMC Microbiol 15:60.
  6. Kozik A, Karkowska-Kuleta J, Zajac D, Bochenska O, Kedracka-Krok S, Jankowska U, Rapala-Kozik M (2015) Fibronectin-, vitronectin- and laminin-binding proteins at the cell walls of Candida parapsilosis and Candida tropicalis pathogenic yeasts. BMC Microbiol 15:197.
  7. Karkowska-Kuleta J, Kozik A. (2014) Moonlighting proteins as virulence factors of pathogenic fungi, parasitic protozoa and multicellular parasites. Mol Oral Microbiol 29:270-283.
  8. Guevara-Lora I, Stalinska K, Augustynek B, Labedz-Maslowska A. (2014) Influence of kinin peptides on monocyte-endothelial cell adhesion. J Cell Biochem 115:1985-1995.
  9. Pustelny K, Zdzalik M, Stach N, Stec-Niemczyk J, Cichon P, Czarna A, Popowicz G, Mak P, Drag M, Salvesen GS, Wladyka B, Potempa J, Dubin A, Dubin G. (2014) Staphylococcal SplB serine protease utilizes a novel molecular mechanism of activation. J Biol Chem 289:15544-15553.
  10. Bukowski M, Lyzen R, Helbin WM, Bonar E, Szalewska-Palasz A, Wegrzyn G, Dubin G, Dubin A, Wladyka B. (2013) A regulatory role for Staphylococcus aureus toxin-antitoxin system PemIKSa. Nat Commun 4:2012.

Batchelor/master thesis topics

  • Isolation and biochemical characterization of proteolytic enzymes
  • Protein expression in heterological bacterial expression systems
  • Cloning, expression and purification of recombinant proteins
  • Antibacterial peptides: isolation, purification, sequencing and biochemical characterization
  • Bacteriocins: isolation, purification, sequencing and biochemical characterization
  • New techniques in protein and peptide chemistry
  • Interaction of the contact system proteins – kininogen, prekallikrein and factor XII – with the surface of selected Candida spp.
  • Kinin generation by secreted proteinases from Candida spp.
  • Mechanism of kinin generation in various cell models
  • Expression of genes and proteins involved in the regulation of inflammation, especially in relation to the kinin generation system

Requirements for candidates

Interests in theoretical aspects and in experimental work concerning biochemistry, genetic engineering and physicochemistry.