Equipment and Expertise

Expertise

DNA and RNA analysis

  • DNA cloning
  • PCR analysis and qPCR analysis
  • Agarose electrophoresis
  • DNA and RNA isolation
  • FISH analysis
  • RNA-protein PLA
  • RNA and DNA pull down
  • Crosslinking
  • RNA-RNA interactions (PARIS method, COMRADES method)

Protein analysis

  • SDS PAGE and Western Blot 
  • Microscale thermophoresis
  • Immunoprecipitation/co-immunoprecipitation
  • Immunocytochemistry
  • ELISA
  • Protein-protein interactions (PLA, BioID, APEX)
  • Protein labelling
  • Glycoproteomics

Recombinant protein expression and purification

  • Bacterial expression systems (Escherichia coli, Lactococcus lactis)
  • Mammalian expression systems
  • Mutagenesis
  • Purification systems: Affinity chromatography, 4C gel filtration chromatography, ion-exchange chromatography – Fast Protein Liquid Chromatography (FPLC) research scale and small-scale preparatory chromatography
  • Ultrafiltration set-up (up to 500 mL)

Cell biology

  • Human cell lines and primary cell cultures (IPS, fibroblasts,
    neuronal cells, cancer cells, immune cells, intestinal cells, cancer
    stem cells, …)
  • Differentiation assays
  • Protein silencing and overexpression (transfection, lentiviral transduction)
  • CRISPR Cas gene editing
  • 3D cell models (multicellular spheroids)
  • Migration and invasion functional assays
  • Indirect (transwell chambers) and direct cell cocultures (monolayers and spheroids)
  • Bacterial-host cell interaction (adhesion, invasion, proliferation)

Flow cytometry and cell sorting

  • Phenotypic and functional analysis of immune cells
  • Cytotoxicity assays
  • Cell death analysis
  • Viability assays
  • Proliferation and cell cycle analysis
  • Isolation and phenotypic characterization of cancer stem cells

Biotechnology of bacteria

  • Genetic engineering of bacterial cells
  • Protein surface display
  • Bacterial viability determination
  • Bacterial growth kinetics
  • CRISPR-based tools for genomic engineering of Lactococcus lactis
  • Electroporation of Gram-positive bacteria
  • GMO biosafety risk assessment

Microbiology of bacteria and fungi

  • Bioassays for antibacterial compounds
  • Antiadhesion and antibiofilm compound analysis by fluorescent microscopy (effects on viability, biofilm composition and structure)
  • Biofilm cultivation systems (static and dynamic)
  • Microfluidics
  • Bacterial protein profiling (cytoplasm, surface proteins)
  • Bacterial genomics

Glycobiology

  • Extraction and characterization of complex bacterial and fungal glycans (teichoic acids, capsule, peptidoglycan, etc.)
  • Extraction of native lectins from environmental samples
  • Lectin characterization and application for labelling
  • Glycoproteomics (differential staining of glycans, deglycosylation)
  • Lectin probed western blot for detection of glycans and glycoproteins

    Evaluation of enzymes and inhibitors

    • Low-molecular weight inhibitors
    • Natural protein inhibitors
    • Enzyme kinetics
    • Zymography analysis and development (proteolytic, L-amino acid oxidase, cholinesterase activity)
     

    Equipment 

    Flow Cytometer

    Attune™ NxT Flow Cytometer, blue/red/violet/yellow
    ThermoFischer
     

    Cell Sorter

    S3e Cell Sorter
    BioRad
     

    Microscale Thermophoresis

    Monolith NT115.pico Red
    Nanotemper Technologies
     
    Contact Person: Ana Mitrović, PhD

    IXplore Spin High Resolution microscope system

    more

    (1) fully motorized Olympus IX83 inverted imaging platform equiped with

    (2) CSU-W1 spining disc confocal scanner, 2 digital sCMOS cameras, live-imaging chamber and CellSens Dimension with 3D Deconvolution solution Imaging

    Confocal laser scaning microscope

    Confocal laser scaning microscope LSM710
    Carl Zeiss
     

    Fluorescence inverted microscope

    EVOS M5000 Imaging System
    Thermo Fisher
     
    Contact Person: Ana Mitrović, PhD

    Compact cell culture microcope

    Olympus CKX53
    Olympus
     
    Contact Person: Nika Janež, PhD

    Fluorescence inverted microscope

    AxioObserver Z1
    Carl Zeiss
     
    Contact Person: Nika Janež, PhD

    Imaging System

    ChemiDoc Imaging System
    BioRad
     
    Contact Person:

    Western Blot Analysis

    SDS PAGE and Western Blot system
    BioRad
     

    Contact Person:

    Spectrofluorimeter

    Infinite M1000
    Tecan
     

    Contact Person: Ana Mitrović, PhD

    Fast protein Liquid Chromatography System (FPLC)

    AKTA Fast Protein Liquid Chromatography System
    GE Healthcare Life Sciences
     

    Contact Person:

    PCR

    Mastercycler Nexus X2
    Eppendorff

    Contact Person:

    Cell culture laboratories

    1st and 2nd biosafety level laboratories
     

    Contact Person: Milica Perišić Nanut, PhD, assist. prof. Helena Motaln, PhD

    Live Cell Imaging System

    Live Cell imaging Chamber for Confocal microscope
    Tokai
     

    Microfluidic system

    Microfluidic flow control system (FlowEZ 1000 mbar, 15 ml P-Caps, CO2 mixer, thermoblock, M-switch)
    Fluigent
     

    Hybridization Oven and UV Crosslinker 

    UPV HL-2000 Hybrilinker 230V and 254nm crosslinker
    UPV Life science equipment
     

    Contact Person: Urša Čerček, MSc

    Crosslinker 

    CL-1000 Ultraviolet Crosslinker 
    UPV Life science equipment
     
    Contact Person: Urša Čerček, MSc

    Electroportation System

    BTX Gemini X² – Twin Waveform Electroportation System (holds two cuvettes)
    Harvard Apparatus BTX

     

    BeadBeater