Laboratory of Instrumental Analysis and Preparation

The Laboratory of Instrumental Analysis and Preparation of IITD PAS is equipped with MALDI-TOF/TOF Bruker ultrafleXtreme mass spectrometer, with a set for nano-LC chromatography, and gas chromatographs coupled with mass spectrometry: Thermo Focus GC equipped with Ion-Trap ITQ 700 tandem mass spectrometer and Thermo Trace GC equipped with Thermo TSQ Quantum XLS Triple-Quad tandem mass spectrometer. The equipment provides IITD employees with access to mass spectrometry techniques for both proteomic studies and bacterial and eukaryotic glycoconjugate studies, immunology, biochemistry, microbiology, cancer research and vaccine design. In the structure of LIAP we have the electron microscopy laboratory, equipped with JEOL JEM F-200 transmission electron microscope, enabling STEM microscopy mode with BF (bright-field) and HAADF (high-angle annular dark-field) detectors and additional devices: vitrobot for the repetitive preparation of suspension freezing preparations, Plasma Cleaner for the preparation of carrier media, Boeckeler EMP5160 RMC tissue processor, allowing for the repetitive preparation of chemically fixed preparations, high vacuum atomizer with the ability to vaporize carbon and metal and a dedicated GPU workstation for processing data from TOMO and SPA methods, as well as 3D modeling of biological structures. The laboratory does not performs own research.

Laboratory Head

Head: dr hab. Jacek Rybka ORCID: 0000-0003-4499-1574

Structural and immunochemical studies of bacterial endotoxins, immunological properties of Gram-negative bacterial outer membrane components, methods of analysis of chemical markers of bacteria, microsystemic and micromechanical methods in bacterial and bacterial endotoxin detection, endotoxin detection using luminescent techniques. Functions: Head of the Laboratory of Instrumental Analysis and Preparation (2009 – currently), deputy director of IITD PAS for scientific affairs (2011-2015), director of IITD PAS (2015-2020)

Team
  • dr Katarzyna Kapczyńska, ORCID: 0000-0003-2722-9596
  • dr Anna Jarząb, ORCID: 0000-0002-1059-9147
  • mgr Eva Krzyżewska, ORCID: 0000-0002-5581-1690
Research methods
  • mass spectrometry: MALDI-TOF, GLC-MS, GLC-MSMS
  • transmission electron microscopy
Key equipment
  • MALDI-TOF/TOF Bruker ultrafleXtreme
  • nano-LC Easy-nLCII with Proteineer fc
  • GLC-MSMS: Thermo Focus with Ion-Trap ITQ 700
  • GLC-MSMS: Thermo Trace GC with Thermo TSQ Quantum XLS Triple-Quad
  • Transmission electron microscope JEOL JEM F-200
  • Automatic Plunge Freezer     Leica EM GP2
  • Plasma Cleaner PIE Scientific Tergeo EM
  • Tissue prcessor RMC Boeckeler EMP5160
  • Thermal evaporator Quorum Technologies K975X
Most important projects (during the last 10 years)
The laboratory does not perform its own research. Examples of projects using mass spectrometry techniques in the IIET PAS include biochemical characterization of macromolecules involved in immune processes, immunochemical studies of bacterial endotoxins, studies of surface structures of glycoconjugate and protein antigens, studies on mechanisms of pathogenicity of certain diseases of bacterial etiology, studies on the role of glycolipids in tumor progression, or studies on the properties of macro- and nanoparticles as carriers of therapeutic substances. The electron microscopy laboratory, provides access to traditional TEM sample preparation techniques, including fixation, resin embedding, preparation and imaging of samples at cryogenic conditions, three-dimensional imaging, using electron tomography and SPA (single particle analysis) techniques, as well as performing chemical composition microanalyses using EDS on the nanoscale, also on cryogenic samples.
Selected publications
  • Rollenske T., Szijarto V., Łukasiewicz J., Guachalla L.M., Stojkovic K., Hartl K., Stulik L., Kocher S., Lasitschka F., Al-Saeedi M., Schröder-Braunstein J., von Frankenberg M., Gaebelein G., Hoffmann P., Klein S., Heeg K., Nagy E., Nagy G., Wardemann H.: Cross-specificity of protective human antibodies against Klebsiella pneumoniae LPS O-antigen. Nat Immunol., 2018, 19(6):617-624 IF 23,530 (50 pkt MNiSW); https://pubmed.ncbi.nlm.nih.gov/29760533/
  • Razim A., Pacyga K., Aptekorz M., Martirosian G., Szuba A., Pawlak-Adamska E., Brzychczy-Włoch M., Myc A., Gamian A., Górska S.: Epitopes identified in GAPDH from Clostridium difficile recognized as common antigens with potential autoimmunizing properties. Scientific Rep. 2018, 8:13946 IF 4,011 (40 pkt MNiSW); https://pubmed.ncbi.nlm.nih.gov/30224677/
  • Palusiak A., Maciejewska A., Ługowski C., Różalski A., Kaszowska M.: The new structure of core oligosaccharide presented by Proteus penneri 40A and 41 lipopolysaccharides. Int J Mol Sci., 2018, 19(3) IF 4,183 (30 pkt MNiSW); https://pubmed.ncbi.nlm.nih.gov/29495556/
  • Man-Kupisińska A., Świerzko A.S., Maciejewska A., Hoc M., Różalski A., Siwinska M., Ługowski C., Cedzynski M., Łukasiewicz J.: Interaction of mannose-binding lectin with lipopolysaccharide outer core region and its biological consequences. Front Immunol., 2018, 9: 1498 IF 4,716 (35 pkt MNiSW); https://pubmed.ncbi.nlm.nih.gov/30008719/
  • Kaszowska M., Wójcik M., Siednienko J., Ługowski C., Łukasiewicz J.: Structure–activity relationship of Plesiomonas shigelloides lipid A to the production of TNF-α, IL-1β, and IL-6 by human and murine macrophages. Front. Immunol, 2017; 8: 1741 IF 6,429 (35 pkt MNiSW); https://pubmed.ncbi.nlm.nih.gov/29321776/
  • Górska S., Sandstrőm C., Wojas-Turek J., Rossowska J., Pajtasz-Piasecka E, Brzozowska E., Gamian A.: Structural and immunomodulatory differences among lactobacilli exopolysaccharides isolated from intestines of mice with experimentally induced inflmmatory bowel disease. Scientific Reports, 2016; 6: 37613 IF 5,228 (40 pkt MNiSW); https://pubmed.ncbi.nlm.nih.gov/27869188/
  • Dudek B., Krzyżewska E., Kapczyńska K., Rybka J., Pawlak A., Korzekwa K., Klausa E., Bugla-Płoskońska G.: Proteomic analysis of outer membrane proteins from Salmonella enteritidis strains with different sensitivity to human serum. PLoS One, 2016;11(10), doi: 10.1371/journal.pone.0164069 IF 3,057 (40 pkt MNiSW); https://pubmed.ncbi.nlm.nih.gov/27695090/
  • Paściak M., Dacko W., Sikora J., Gurlaga D., Pawlik K., Miękisiak G., Gamian A.: Creation of an In-House Matrix-Assisted Laser Desorption Ionization-Time of Flight Mass Spectrometry Corynebacterineae Database Overcomes Difficulties in Identification of Nocardia farcinica Clinical Isolates. J Clin Microbiol, 2015; 53(8):2611-21. doi: 10.1128/JCM.00268-15 IF 3,993 (35 pkt MNiSW); https://pubmed.ncbi.nlm.nih.gov/26041903/
  • Roszkowiak J., Jajor P., Guła G., Gubernator J., Żak A.M., Drulis-Kawa Z., Augustyniak D. Interspecies Outer Membrane Vesicles (OMVs) Modulate the Sensitivity of Pathogenic Bacteria and Pathogenic Yeasts to Cationic Peptides and Serum Complement, International Journal of Molecular Sciences, 2019, https://doi.org/10.3390/ijms20225577, IF 4,556, (140 pkt MNiSW); https://pubmed.ncbi.nlm.nih.gov/31717311/
  • Maldonado-Carmona N., Marchand G., Villandier N., Ouk T.S., Pereira M., Calvete M.J., Calliste C.A., Żak A., Piksa M., Pawlik K.J, Matczyszyn K., Lhez S. Porphyrin-loaded lignin nanoparticles against bacteria: a Photodynamic Antimicrobial Chemotherapy and environmentally friendly application, Frontiers in Microbiology, 2020, doi: 10.3389/fmicb.2020.606185, IF 4.235 (100 pkt. MNiSW); https://www.frontiersin.org/articles/10.3389/fmicb.2020.606185/abstract (praca jeszcze nie posiada linku do PubMed)