SAFRA Photonics

Laboratories

SAFRA Photonics counts with a fully equipment and cutting edge scientific infrastructure, which is shared with the Center for interdisciplinary biosciences at the P. J. Safarik University.
We have in disposition the following laboratories/facilities:

Laboratories

SAFTRA Photonics counts with a fully equipped and cutting edge scientific infrastructure, which is shared with the Center for interdisciplinary biosciences at the P. J. Safarik University. We have in disposition the following laboratories/facilities:

LABORATORIES OF CHEMISTRY AND CHEMICAL TECHNOLOGY

Research

Preparation and characterization of samples

Methodology

  • Basic methodologies for samples preparation and characterization
LABORATORIES OF CHEMISTRY AND CHEMICAL TECHNOLOGY

Equipment

  • fume hood
  • pure water production system
  • dryer
  • centrifuge
  • autoclave
LABORATORIES OF CHEMISTRY AND CHEMICAL TECHNOLOGY

LABORATORY OF BIOENERGETICS

Research

Main objective

The mechanism of proton pumping by respiratory oxydase is awaiting a solution on a molecular level. Our laboratory is focused on the elucidacion of the mechanism of proton pumping by the class of heme-cooper oxidases that is represented by cytochrome oxidases.

Methodology

  • The proton pumping by CcO is studied by using the purified bovine heart enzyme, bacterial (Rhodobater sphaeroides) wild type and mustants of oxidases and oxidases incorporated into phospolipid vesicles.

Equipment

  • Combination of the rapid kinetic method (stopped-flow)
  • Spetroscopic (UV-Vis, fluoroscence, magnetic circular dichroism, electron paramagnetic spetroscopy)
  • Biochemical methods of molecular biology are applied to reach the main goal
LABORATORY OF BIOENERGETICS

LABORATORY OF BIOTHERMODYNAMICS AND OPTICAL SPECTROSCOPY

Research

1. Construction and characterisation of targeted drug delivery system

main objective

Development of a new drug delivery system based on lipoproteins nanoparticles for the tergeted delivery of hydrophobic/amphiphilic drug to cancer tissues

2. Thermodynamics of drug biomacromolecule interactions

main objective

Complex chracterization of thermodynamics chracteristics of biomacromolecule-drug complexes (bindiing constants, number of binding sites, stability of the complex) aiming for medical application of the studied drugs

Methodology

  • UV-VIS and fluoroscence spectroscopies
  • Isothermal titration calorimetri
  • Stpped-flow technique
  • Measurements of cellular
LABORATORY OF BIOTHERMODYNAMICS AND OPTICAL SPECTROSCOPY

Equipment

  • Isothermal titration calorimeters iTC200 (MicroCal)
  • Stopped-flow instrument SX-20 (Applied Photophysics)
  • Seahorse XF-96
  • Absorption & fluorescence spectroscopy (Shimadzu)
LABORATORY OF BIOTHERMODYNAMICS AND OPTICAL SPECTROSCOPY

LABORATORY OF CELL CULTURES

Research

1. Cell culture – Sample preparation

2. Cell viability and Proliferation

3. Labeling and Flow cytometry

Methodology

  • 96 well plate
  • Colorimetric assays
  • Fluorescent assay
  • Luminiscence
  • Apotosis assays
  • Mitochondrial assays
  • Protein detection
LABORATORY OF CELL CULTURES

Equipment

  • Excitations 405 nm, 488 nm, 635 nm
  • Automatic arm with sample uptake port
  • Fluid containers and their holders
  • MACS Mini Sampler and tube raks
  • Control of cell proccesing
LABORATORY OF CELL CULTURES

LABORATORY OF CELL PHYSIOLOGY

Research

1. Cell physiological responses to various stimuli – electrical, ligand, photochemical.

2. Fluorescently tagged proteins – distribution, structure- function relationship.

Methodology

  • Patch clamp
  • FRET

Equipment

  • Patch clamp set up for electrophysiology recordings in whole cell configuration.
  • Set up consists of Olympus IX71 fluorescent microscope
  • CCD camera Hamamatsu ORCA R-2
  • micromanipulator MP-285
  • Axopatch™ 200B Capacitor Feedback Patch Clamp Amplifier for ultra low-noise patch clamp recordings
  • Axon Digidata® 1440A Digitizer a low-noise high-resolution 16-bit data acquisition system for electrophysiology recordings,
  • pCLAMP 10 Electrophysiology Data Acquisition
  • Analysis Software - user-friendly electrophysiology data acquisition and analysis software
LABORATORY OF CELL PHYSIOLOGY

LABORATORY OF CONFOCAL MICROSCOPY

Research

1. Inrtacellular localization of photosensitizers

2. Detection of pro- and antiapoptotic markers in cells

Methodology

  • Fluorescence imaging in living and fixed cells
  • Co-localization analysis
LABORATORY OF CONFOCAL MICROSCOPY

Equipment

  • Confocal microscope system (LSM 700 Zeiss, Germany)
  • Excitation: 488 nm
  • 555 nm, O2/CO2 module
  • mini-incubator for living cells imaging
  • Zen 2011 software (Zeiss, Germany)
LABORATORY OF CONFOCAL MICROSCOPY

LABORATORY OF FLOW CYTOMETRY

Research

Cellular uptake of drugs, cell viability and proliferation

Methodology

  • Flow-cytometry analysis

Equipment

  • MACSQuant Analyser
  • Excitation: 405 nm, 488 nm, 635 nm
LABORATORY OF FLOW CYTOMETRY

LABORATORY OF LASER SPECTROSCOPY

Research

Drug transport in biologycal systems

Diffusion of drug molecules (and aggregates) is studied in aqueous environment, in artificial bilayer lipid membranes and in live cells.

Detection of singlet oxygen

Methodology

  • Absorbtion, fluorescence and Raman measurements using modular experimental setups of our own design.
LABORATORY OF LASER SPECTROSCOPY

Equipment

  • Set of cw lasers: 488 nm, 532 nm, 596 nm, 633 nm, 785 nm
  • Laser tweezers setup combined with a Raman spectrometer
  • Apparatus for singlet oxygen detection: Q-switched Nd:YAG laser, OPO, NIR PMT.
  • Pulsed dye laser
LABORATORY OF LASER SPECTROSCOPY

LABORATORY OF MOLECULAR BIOLOGY

Research

1. DNA isolation and analysis, site-directed mutagenesis

2. Protein identification and analysis

Methodology

  • MacVector DNA and protein sequence analysis
  • DNA isolation and purification
  • Restriction enzyme analysis
  • Site-directed mutagenesis
  • DNA horizontal electrophoresis
  • Protein vertical electrophoresis
  • Western blot
LABORATORY OF MOLECULAR BIOLOGY

Equipment

  • Eppendorf centrifuge 5430R
  • Eppendorf centrifuge 5810R
  • Eppendorf PCR Mastercycler Nexus Gradient
  • water bath, pH meter
  • incubator shaker
  • small incubator for bacteria
  • horizontal and vertical electrophoresis
  • gel photoimage system, etc
LABORATORY OF MOLECULAR BIOLOGY

LABORATORY OF PROTEIN ENGINEERING

Research

1. Protein engineering

2. Directed evolution of proteins

3. Protein purification

4. Protein chemistry

5. Study of thermodinamics and kinetic stabilities of proteins

6. Enzymology

Methodology

  • Conventional methods of molecular biology, biocheistry and biophysics
  • display technologies such as ribosome and yeast displays
LABORATORY OF PROTEIN ENGINEERING

Equipment

  • Gene Pulser Excell Electroporation System (Bio Rad)
  • Visible spectrophotometer Novaspec III (Amersham Biosciences)
  • spectrophotometer NaNoVue (GE Healthcare)
  • Thermostated Incubator Titramax 1000 (Heidolph)
LABORATORY OF PROTEIN ENGINEERING

LABORATORY OF RAMAN SPECTROSCOPY

Research

1. Material characterization

2. Drug-biomacromolecule characterization

3. Detection of environmental pollutants

4. Cultural Heritage Analysis

5. Bioimaging

Methodology

  • Conventional Raman spectroscopy
  • Surface-enhanced Raman spectroscopy (SERS)
  • Macro and micro measurements
  • Measurements with cell incubator which allows to control temperature and O2/CO2 concentration
  • Raman mapping and imaging (spot(s), line, depth profile, area, 3D)
LABORATORY OF RAMAN SPECTROSCOPY

Equipment

  • Confocal Raman spectrophotometer Renishaw inVia Reflex
  • Upright Leica microscope DM2500 M
  • Inverse Leica microscope DMI3000 M
  • 3 excitation lasers (785nm - RL785 Renishaw diode (cw); 633nm - RL633 Renishaw HeNe (cw); 532nm -Cobolt CW DPSS laser)
  • CCD detector (1024 x 256 pixels-1 pixel: 26x26 μm; spectral range:200 nm – 1025 nm /100 – 10 000 cm-1; Peltier cooled to -70 °C)
LABORATORY OF RAMAN SPECTROSCOPY

LABORATORY OF TIME RESOLVED MICROSCOPY

Research

1. Drug-biomaromolecule interaction in vitro / in vivo

2. Detection of pO2 in cells during PDT

Methodology

  • Time-resolved fluorescence and phosphorescence
  • Mappinng the spatial distribution of drugs
LABORATORY OF TIME RESOLVED MICROSCOPY

Equipment

  • BECKER & HICKL DSC-120 Dual Chanel Confocal Scanning System
  • Zeiss AxioObserver Z1 microscope
  • NKT-Super-K Extreme Laser (40MHz, 430 - 1100 nm)
  • HPM-100-40 Hybrid detector (LP485, ns - μs)
LABORATORY OF TIME RESOLVED MICROSCOPY
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