Infrastructure

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Laboratory of molecular systematics

In this laboratory we generate data addressing scientific questions of taxonomy, phylogeny, phylogeography and related evolutionary processes across different groups of vascular and non-vascular plants. Methods applied are focused on the study of differences and changes on the DNA level among organisms using several methods such as AFLP (Amplified Fragment Length Polymorphism), SSRs (microsatellites – simple repetitions) or sequencing of selected loci. Most of the currently used molecular methods are based on variations of the PCR (Polymerase Chain Reaction) and the analyses of the relevant products. The laboratory is also equipped for DNA extraction from plant material dried in silica gel or from herbarium specimens. In case when direct sequencing of specific loci is problematic, we use methods such as SSCP (Single-Strand Conformation Polymorphism) or cloning of PCR products into the bacterial cells, separating different alleles from diploid and especially from polyploid individuals. Currently we implement also new methods based on the NGS (Next Generation Sequencing), such as a Hyb-Seq and RAD-Seq. Here we are sequencing only selected loci and not the whole genome, which decreases price per sample and gives the opportunity to sequence more individuals. The laboratory of molecular systematics possess all necessary equipment for standard methods used in molecular systematics such as DNA extraction, PCR based methods (PCR-RFLP, AFLP, SSR), DNA purification, as well as cloning of PCR products (centrifuges, mixer mill, PCR thermocyclers, thermoblocks, incubators, PCR and flow boxes, spectrophotometer and fluorometer, temperature controlled electrophoresis apparatus, electrophoresis power supplies, blue light and UV-transilluminators with imaging system, etc.). The Institute owns or hires licenses for all relevant programs needed for molecular data evaluation (Geneious, PAUP, MacClade, SYN-TAX, SAS, DAx).

 

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The laboratory is equipped by following instruments:

  • Thermomixers Eppendorf (type “comfort” and “compact”)
  • Shaking incubator N-BIOTEK (NB-205)
  • Centrifuges Eppendorf (5804, 5427R, 5415R), Hettich (Rotanta 460R)
  • Mixer mill Qiagen (TissueLyser II)
  • Thermal cyclers Eppendorf (Mastercycler pro S and ep gradient S)
  • Electrophoresis power supplies Consort (EV243), Biometra (PS305T)
  • Electrophoresis apparatus Elchrom Scientific (Origins 2100E)
  • Imaging system Kodak (Gel Logic 200)
  • Blue light transilluminator Herolab (UVT-20 BE)
  • Spectrophotometer Thermo Scientific (NanoDrop 2000)
  • Fluorometer Life Technologies (Qubit 2.0)
  • Reverse osmosis system Werner (RO3 PLUS)
  • UV/UF ultrapure water system Werner (EASY pure II)
  • Biological Safety Cabinet ESCO Class II BSC
  • DNA/RNA UV-cleaner box BIOSAN (UVT-S-AR)
  • Autoclave sterilizers Nüve (OT 032), Tuttnauer (3850EL)
  • Incubator Binder (APT.Line)

 

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Laboratory of karyology and flow cytometry

Regarding karyological research, the Institute possesses a karyological laboratory equipped by a microscope Axioscope 2 (Zeiss) and two flow cytometers equipped by a green laser with488 nm excitation wave and an HBO mercury arc lamp for UV excitation, respectively. Flow cytometers allow to detect relative (DNA ploidy level) as well as absolute DNA amount in plant material. Two cytometers running in parallel offer a possibility of simultaneous measurements of relative and absolute DNA amounts of the same sample and thus i.a. estimation of the proportion of AT/GC bases in the studied genome.

 

Morphometric laboratory

All instrumental and software equipment required for the application of multivariate morphometrics is available. This consists of several high-quality stereomicroscopes (Olympus SZ 61) with digital cameras to output image to PC, and A3 scanner allowing observation, digitalization and subsequent evaluation of the investigated material. Software accessories comprise licenses of statistical programs and packages (SAS, SYN-TAX) needed for evaluation of the biostatistical data.

 

Mycological laboratory – analyses and isolation

This laboratory serves for basic analyses of anatomy, morphology and chemistry fungal material – non lichenized as well as lichenized fungi. We perform basic analysis of secondary chemistry here (thin layer chromatography – TLC), and to prevent potential and very probable contamination, also preparatory steps for DNA extraction (PCR and post-PCR steps are carried out in the Laboratory of molecular systematics). It is equipped by following instruments:

  • UV lamp and UV box Camag, development tanks
  • shredder Retsch MM 200
  • thermal chamber: KCB 25 W
  • optical instruments for micro-morphological observations and identifications of fungi: light microscopes Zeiss Axio Scope.A1 with digital camera Axiocam 105 and visualisation software AxioVision SE64 Rel. 4.9.1, light microscopes Olympus CX41 and BX51 with ARTRAY Artcam 300MI camera and visualisation software Quick Micro Photo 2.3 and Deep Focus 3.1, stereomicroscope Olympus SZ61
  • digital camera Sony DSLR-A200 with Tamron 17-50 mm F/2,8 DiII and Kodak Easy Share Z 650 objectives for photo-documentation of samples
  • deep-freezers for disinfection of herbarium specimens
  • freezers for storage of biological material and chemical reagencies

 

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Mycological, phytopathological and algological cultivation labs

The laboratories serve for isolation of the material from the substrate (microscopic fungi from host plant tissues, algae and cyanobacteria from water), inoculation and cultivation of the material for further analyses (e. g. molecular analyses). The laboratories are equipped by following instruments:

  • sterile box, Thermo Scientifific MSC-Advantage and ESCO biohazard II laminar flow box for isolation of fungi and lichen photobionts and for routine lab work in sterile condition
  • universal cultivation box and Biological termostat BT120 with regulated temperature and humidity for cultivation of fungi and lichen photobionts
  • laboratory autoclaves for sterilisation of culture media and lab supplies
  • Hettich EBA 270 centrifuge for routine work with algae and cyanobacteria
  • Lovibond thermostatically controlled cabinet for cultivation of microorganisms

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Laboratories of plant physiology – abiotic stress, plant physiology, electrophysiology, cell biology and light and electrone microscopy

In our laboratories we use mainly the methods as a ROS determination, electrophoresis, root respiration, determination of different enzymes activities, methods for obtaining physiological status of  investigated plants, gene expression and semiqantitative RT-PCR. The laboratories are equipped by following instruments:

  • centrifuges: Eppendorf and Sartorius
  • spectrophotometers: BECKMAN COULTER DU 730 and Nanodrop 2000C Thermo Scientific
  • vertical electrophoresis
  • Clark oxygen electrode
  • fluoromether: SYNERGY HT
  • hybridiser HB-2D Techne
  • ultraviolet corsslinker UVC-T08 Ultra Lum
  • fluorescent magnifier BellPhotonics
  • high performance liquid chormatograph Bio Logics, Bio Rad
  • gel documentation system 212PRO Lel Logic
  • confocal microscope FV1000 Olympus
  • thermocyclers Eppendorf and Biorad C1000
  • DNA analyser 4300 Licor
  • automatic DNA analyser Maxell Pormega
  • pipetting robot: epMotion 5075 vac Eppendorf
  • electrophoresis with termal gradient DCode Biorad
  • autoclave Tuttnauer 2540EL
  • ultrasound USC 1700TH VWR
  • distillation apparatus: Medihum
  • Cryotome Leica CM 1510 S
  • Fluorescence stereomicroscope Zeisse Pentafluor Discovery V12
  • Rotofor System- IEF BioRad
  • Electro-eluter Model 422 BioRad
  • ultracentrifuge Beckman L8–M

 

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Pedological laboratory

Chemical analyses of soil samples serve to complement datasets gathered for studies in plant communities. The results represent additional datasets for characterization of ecological requirements of particular plant assamblages.

  • dryer of laboratory glass KBC G – 100/250
  • dryer of plant material HS 402 A
  • stereoscopic video-microscope DSTM 722 3.0

 

Institute of Botany – detached unit in Banská Bystrica

Laboratory for identification of plant material

The laboratory is used for study of microscopic, anatomical preparations and herbarium specimens for scientific and educational purposes.

  • binocular: Olympus SZ61, 3,35-90x with digital camera 3Mpxi CMOS
  • microscopes: Carl Zeiss Axioscope A1 with digital camera 5Mpxi CMOS
  • USB microscope: AM 13T Dino-Lite Pro
  • digital photoscaner: Pentacon Scan 6000 S

 

Plant systematic laboratory 

The laboratory is used for detection of ecological requirements and eco-physiological properties of plants, and for preparation of karyological preparations for scientific or educational purposes.

  • device for water analysis: WTW Multi 3430 SET F
  • digital meter of soil moisture: Delta-T ML2x ThetaKit, 4 ks
  • digital conductivity meter Delta Porometer AP-4, 2 ks
  • metal detector Minelab X-TERRA 305
  • soil conductivity meter Geonics EM38-MK2
  • Geographic information system (GIS) – layers: 1. Digital model of relief , 2. Average daily air temperature in 2 m, 3. Monthly rainfall, 4. Total monthly of photosynthetically-active solar radiation, 5. Soil cover, 6. Land cover