Department of Molecular Biophysics and Pharmacology

1. UV/VIS Raman Spectrophotometer (Jobin-Yvon, Model T64000).
2. Microcalorimeters Microcal (differential scanning and isothermal titration calorimeters)
3. FUJIFILM bio-imaging analyzer (AIDA image analyzer software).
4. Varian AA240Z Zeeman atomic absorption spectrometer equipped with a GTA 120 graphite tube atomizer.
5. LZC-4V illuminator (photoreactor) (Luzchem, Canada) with temperature controller.

This instrumentation belongs to a basic equipment of the Department making it possible to perform molecular biophysics and biology research of DNA affected by anticancer metallodrugs on a good international level. This instrumentation is relatively old (5-15 years), but still in a good shape having technical parameters sufficient for topical research in the area in which the Department is currently involved.

Department of Biophysical Chemistry and Molecular Oncology

1. Multifunctional electrochemical analyzers Autolab (Ecochemie/Metrohm Autolab BV, The Netherlands); potentiostat-EQCM Model 440A (CH Instruments, USA); potentiostat/galvanostat PalmSens (Palm Instruments BV, Holandsko) and electrochemical analyzer IM6 (ZAHNER - Elektrik GmbH & Co.KG, Německo):  key instrumentation for the research on biopolymer electrochemistry, studies of DNA and protein structure and interactions at interfaces and development of electrochemical biosensors and bioassays.

2. AFM/STM Multimode 8 electrochemical system (Veeco, USA) has recently been purchased and will be available for IBP as a core facility for the imaging of surfaces and molecular layers deposited on them. 3. The Department is involved in the CEITEC project where new equipment with the total costs of about 0,8 mil Euro has been required and should be installed in our Institute.

Department of Molecular Epigenetics

The laboratory has a greenhouse (20m²) and shares unique instrumental facilities at IBP with the others. The most important devices located at DME are listed below:

1. Real-time PCR system 7300 (Applied Biosystems) – new equipment, standard parameters.
2. Five thermal cyclers including four gradient ones.
3. Pulsed-field gel electrophoresis system Gene Navigator (GE Healthcare)

Outlook: Replacement of an old (20 yrs) deep -70ºC freezer is expected in a short term (worth ~1000 EURO), and a Plant Growth chamber (worth ~2000 EURO), in a long term.

Department of Molecular Cytology and Cytometry

1. Spinning disc confocal microscopy. Leica upright microscope, DMSTC motorized stage, Piezzo z-movement, MicroMax CCD camera, CSU-10 confocal unit, Ar-Kr laser, 2.5W with AOTF. The equipment is controlled by the corresponding software using PC and software developed in collaboration with MasarykUniversity.

Laser scanning confocal microscopy (LSCM). In 2009, we established new Central

2. Laboratory of Cellular Biophysics that involves sorter Aria II and Leica TSC SP-5 X, equipped with WLL (470-670 nm); argon laser (488 nm) and 2 UV lasers (355 nm and 405 nm). The laboratory enables advanced studies of many biological aspects of normal and tumour cells. Advanced software is used for data acquisition, 3D-analysis and FRAP (Fluorescence Recovery After Photobleaching) evaluation. Leica microscope represents a unique equipment for studies related to the biology of chromatin. The equipment is a part of Core facility for cellular biophysics.

3.⁶⁰Co gamma-irradiator Chisostat. Essential for experimental irradiation of various biological systems with ionizing radiation. The device is technically in good condition, though old, but needs a new radioactive cobalt load to increase its exposure rate. The facility is used by many scientist in the Brno region.

Department of Cytokinetics

Flow-cytometry (FCM) is one of principal methodologies routinely used in our Department. DC members together with the DMCC belong to the one of leaders systematically introducing advanced technology for the measurement of the cells and cell processes at the Institute and CR (see also part…). Thus one of the first analytical flow cytometers in Brno(FACS Calibur) was installed in our Department. Although this instrument is still used in the DC on a daily basis, during recent two years, we have worked on the modernization of FCM. We participated on the establishment of the novel core facility “Laboratory of Cellular Biophysics” (LCB) at IBP, equipped with confocal microscope and advanced high-speed sorter. We were able to introduce the latest generation fluorescence-activated cell sorter FACS Aria II, which fundamentally improves our technological means in the area of cell sorting. Specially ordered configuration of our sorter represents state-of-the-art flow cytometry equipment. It is equipped with 17 fluorescence detectors and unique combination of four lasers for fluorochrome excitation including 355 nm UV laser. Four way sorting into various tube, glass and plates formats including 384 well plate is available. This system has advanced control of the setup and quality of the instrument. Such instrument together with well trained operators is flexible and allows wide range of applications. Our department guarantees operation and support for this equipment.

Department of Free Radical Pathofyziology

1. NO meter ISO-NO Mark II (WPI, USA): The NO meter is the up to date and essential instrument for the Department. The NO meter is an electrically isolated nitric oxide potentiostat. The sensors provide fast, accurate and stable NO-measurements over a wide concentration range. The system is designed for direct measurement of NO in aqueous solutions, tissues and gas mixtures. The sensors are amperometric; whereby nitric oxide diffuses rapidly through the electrode’s selective membrane and is oxidized at the “working” electrode, resulting in the generation of an electrical (redox) current.

2. Luminometers Immunotech (Immunotech, Czech Republic) and Orion II (Berthold detection systems, Germany): Luminometers enable the measurement of reactive oxygen species generation by phagocytes, the detection of antioxidative activity, ATP concentration, reporter gene assay etc. The detector of ORION II is operated in photon counting mode, which guarantees the lowest signal background for unsurpassed signal to noise ratio and the highest linearity.

Department of Structure and Dynamics of Nucleid Acids

Two high-performance computer clusters. The first contains 50 nodes with 280 primitive (core) CPUs (AMD DualCore Opteron 285 and 2220; Intel QuadCore Xeon 2.66 GHz) and is used for long-timescale molecular dynamics simulations. This cluster is equipped by terabyte disk array and data storage. The other cluster contains 43 nodes with 344 core CPUs (Intel QuadCore Xeon 2.66 GHz) while each node is equipped by large memory (4-64 GB) and disk space (1-6 TB). This cluster is designed for demanding quantum chemical calculations.

This equipment is reasonable for our purposes at present. Both clusters contain nodes purchased in the period 2006-2010. Due to the fast development of hardware the equipment is outdated within 2-4 years since the purchase date and must be continually upgraded.

Department of CD Spectroscopy of Nucleid Acids

The main method of the laboratory is circular dichroic spectroscopy. Thus, the most important apparatuses are two CD spectrometers Jobin Yvon, Mark VI, one of which was bought thanks to the support of an NIH grant, USA. Regrettably, the dichrographs are already old and their repairs and maintenance are very expensive. Within the CETTEC project, we have been promised a new dichrograph which, unlike the present ones, will be capable of measuring up to the area of wavelengths shorter than 200 nm. This will enable to study proteins and DNA-protein interactions. CD spectroscopy is extraordinarily suitable for the study of biophysical properties of biopolymers. Both apparatuses are also amply used by workers of other laboratories of the Institute and by other institutes.

Another important apparatus is aVarian Cary 4000 UV-VIS spectrophotometer. It is primarily used for the measurement of melting curves, which represent the basic thermodynamic characterization of the structures studied.

Department of Plant Developmental Genetics

The laboratory is equipped with adequate instrumentations for molecular genetics and cytogenetics (PCR cyclers, electrophoretic and gel dokumentation systems, flowbox,  centrifuges, thermostats, hybridization ovens, crosslinkers, water-baths, deep-freezers, nanodrop, speedvac etc). Our laboratory has been recently rebuilt, it is appropriately equipped, and greenhouse facilities are readily available. Several unique instruments bring new quality and significantly wide our horizons.

1. The CellCut Plus (MMI, Olympus) machine is a unique tool enabling select, cut and collect cells, subcellular components and specific chromosomes by laser microdissection. The microdissected chromosomes are used as a template for generating chromosome specific libraries and as a cytogenetic tool used for flourescence in situ hybridization.

2. The Olympus AX70 research grade microscope for both fluorescence and visible light applications, including Differential Interference Contrast observation of unstained specimens. This microscope is equipped with motorised X/Y scanning stage (Märzhäuser Wetzlar) enabling repeated fluorescence in situhybridizations or immuno-localisations and FISH. For the acquisition of images we use highly sensitive monochrome CCD camera (Zeiss AxioCam MRm).

3. Cryomicrotome Leica CM1800 is used for the preparation of tissue sections and subsequent detection of gene expression during various stages of plant tissue development.