Core Facility

Head
Alicja Żylicz, PhD, Professor

Vice Head
Roman Szczepanowski, PhD

Senior Staff Scientists
Katarzyna Misztal, PhD
Krzysztof Skowronek, PhD, DSc Habil
Tomasz Węgierski, PhD





 

 

 

 

The goal of the Core Facility is to support innovative research at IIMCB, giving investigators access to a broad range of cutting-edge research technology platforms that are extensively used in such diverse areas as structural biology, bioinformatics, and molecular and cell biology. The Core Facility is run by experienced scientists who devote their time to maintaining the most sophisticated equipment and are top authorities in research applications for such equipment. More than 50 pieces of equipment are grouped into several units according to leading technologies or applications.


Bruker X8 PROTEUM X-ray diffraction system

 

The Macromolecule Crystallography Unit is one of the most advanced in Poland. Proteins are purified with several chroma­tographic FPLC systems and subjected to crystallization using two crystallization robots and ~1,000 crystallization conditions (buffers). The crystallization process is performed in a crystallization hotel at 4°C or 18°C, and progress is tracked by a CCD camera. The crystals are analyzed using an X-ray generator (Proteum Bruker) that is equipped with a CCD detector (Platinum 135) and cryostream cooler (Oxford Cryosystem series 700). This facility allows the collection of a complete set of diffraction data within a few hours.
The Biochemical and Biophysical Analysis of Proteins and Nucleic Acids Unit is equipped with analytical instruments for in-depth analyses of proteins and nucleic acids using different methods. Interactions between molecules are studied using several complementary techniques: microcalorimetry (VP-DSC and VPI-TC), analytical ultracentrifugation AUC (Beckman Coulter ProteomeLab Xl-I), and surface plasmon resonance (Biacore 3000). The size of the macromolecular complexes is measured by SEC-MALS (size exclusion chromatography with multiangle light-scattering detector) and analytical ultracentrifugation. We are also equipped with a wide selection of spectrophotometric instruments, including spectrophotometers, spectrofluorimeters, a CD spectropolarimeter, and a FT-IR spectrometer. Recently, the list of instruments has been broadened by a new Anton Paar DMA 5000 M and rolling-ball viscometer Lovis 2000 M, the world’s most accurate density meter.
The Mass Spectrometry of Proteins and Nucleic Acids Unit has two mass spectrometers: MALDI-TOF-TOF (ultrafleXtreem, Bruker) and LC-ESI-Ion Trap (amaZon speed ETD, Bruker). In addition to prompt standard proteomics analysis (protein identification and protein integrity assays) for internal users, which are vital for crystallography projects, we provide non-standard analyses of macromolecules other than proteins, particularly analyses of RNA samples. The use of MS analysis for RNA targets makes this facility a unique entity nationwide.


Spinning-disk microscope Andor Revolution XD
 
The Microscopy Bioimaging Unit offers fluorescence-based imaging systems that are suited for cell biology applications. Our microscopes either work in wide-field mode or use one of several optical sectioning techniques: confocal, two-photon, lightsheet, and TIRF. The newest acquisitions are a Zeiss LSM800 confocal microscope with high-resolution Airyscan detector and an electrophysiology and fluorescence imaging station based on a Zeiss Examiner.Z1 upright stand Other equipment includes a Zeiss LSM710 NLO dual confocal/multiphoton microscope for the live imaging of cells and tissues, a Leica TCS SP2 confocal microscope for live cell imaging and FRAP experiments, an Andor Revolutions XD system for real-time spinning-disk confocal microscopy and TIRF imaging, a Zeiss Lightsheet Z.1 single-plane illumination microscope (SPIM) for the imaging of fluorescently labeled zebrafish larvae, an Olympus CellR/ScanR imaging station for intracellular calcium measurements and the semi-high-throughput quantitative analysis of fluorescence signals, and a Nikon 80i Eclipse microscope with a scanning stage for the mosaic imaging of histochemically or fluorescently stained tissue sections. The unit also has a BD FACSCalibur for the quantitative analysis of fluorescence signals in suspension cells.

The Next Generation Sequencing Unit is equipped with a NextSeq 500 sequencer (Illumina). The Core Facility also provides instrumentation for complete sample preparation for sequencing, including a system for precise DNA/RNA and chromatin shearing and size selection (Covaris M220 and BioRuptor Pico, BluePippin) and system for nucleic acid quality and quantity measurements (TapeStation, NanoDrop 3300 Fluorospectrometer and Quantus). The NGS system is already used for the genomic, transcriptomic, and genome methylation sequencing of higher eukaryotes. The purchase of the NSG unit was supported by a Polish Ministry of Science and Higher Education equipment grant for the scientific consortium of IIMCB and Museum and Institute of Zoology PAS.



Illumina Next-Generation Sequencing (NGS NextSeq 500)
 
The Core Facility provides flexible assistance with methodological principles, experimental design, initial training, procedures that are needed for specific experiments, data analysis, and final interpretation, serving as a link between scientists and state-of-the-art technology. The Core Facility is also available to scientists from other institutes. IIMCB emphasizes cooperation with rapidly developing biotech companies in Poland. Within the framework of bilateral agreements, IIMCB laboratories collaborated with biotech companies, such as Adamed, Celon Pharma, Fermentas, BIOVECTIS, Glia, Polfa, and OncoArendi.