Research equipment

Research equipment

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National Institute of Biology (NIB) is located at two premises: headquarters and 4 research groups are located in Ljubljana, while Marine Biology Station is situated in Piran, Slovenia. Its highly skilled and flexible scientific staff has advanced and up-to-date research instrumentation and facilities at their disposal. Laboratories operate according to a quality management system certified under ISO 9001 and selected laboratories are accredited according to ISO/IEC 17025. Acquisition of Good Laboratory Practice Certificate is in progress.

Below is the list of most important laboratory equipment at NIB, grouped according to the specific research field:

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ANIMAL ECOPHYSIOLOGY
Equipment Key applications
  • Experimental set-up with PreSens optical oxygen sensors and
    thermostatic incubator for open-flow and close bottle respiration
    measurements of biofilms and aquatic invertebrates
  • ecophysiological studies – responses of aquatic animals to environmental gradients and stressors (temperature, pH, toxic substances)
BIOCULTURES
Equipment Key applications
INSECTS:
  • Insect quarantine laboratory
  • Honeybee colonies
  • Bee SCAN Lowland Electronics (bee counter)
  • Insect tents for semi-field experiments (3x7 m, 2x)
  • rearing of quarantine insects
  • investigating effects of pesticides and diseases on behaviour and underlying physiology of pollinators
  • investigation of insect pollination
  • assessing impact of pesticides on foraging behaviour and learning abilities of honeybees
  • developing techniques for monitoring pollinators (distribution and population dynamics)
  • applying bees as entomo-vectors for control agents
PLANT GROWTH
  • 2 quarantine greenhouses
  • 4 plant growth chambers, 2 plant tissue culture chambers,
  • nethouse
  • plant growth and multiplication
  • physiological and ecological studies
  • plant transformation
  • virus maintenance
  • work with quarantine pathogens
AQUACULTURE
  • Thermostatic incubators for experimental set-ups for aquatic invertebrates
    (crayfish, Daphnia, Niphargus, Gammarus)
  • Breeding of aquatic invertebrates in the water-tank facilities
  • ecophysiological studies – responses of aquatic animals to environmental gradients and stressors (temperature, pH, toxic substances)
  • Growth chambers and incubators for algae and cyanobacteria
  • (eco)toxicity studies (OECD TG201)
  • taxonomy studies
  • ecophysiological studies
  • Animal models - Zebrafish (Danio rerio):
    maintenance of stock/breeding in the fish tank facility and established protocols
    for eco-toxicology studies and (transgenic) human cell injection studies.
  • genetic toxicology studies in zebra fish embryos; protein miss-expression (functional) studies in zebra fish embryos via transgenic cells’ (over-expressing or siRNA silenced) injections, etc.
CELL & TISSUE CULTURE
Equipment Key applications:
  • Cell & tissue culture laboratories equipped with laminar flow hoods, cryo tanks,
    deep freezers automatic parameter monitored freezers, centrifuges and CO2 incubators
  • plant tissue culture chambers
  • bacteria culture laboratories equipped with laminar flow hoods, incubators
  • culturing of established cancer (stem) cell lines, normal (stem) cell lines and plant cultures (cell, tissue)
  • isolation of primary (spheroids) cultures of cancer (stem) cells & normal (stem) cells from tumour and adipose/umbilical cord tissue,
  • intercellular cross-talk studies,
  • glioma tissue bio-banking
  • mutagenicity/genotoxicity studies
  • plant growth and multiplication, plant transformation, virus maintenance
CHROMATOGRAPHY AND SPECTROMETRY
Equipment Key applications
  • Liquid Scintillation Counter
  • Perkin Elmer
  • LSC TriCarb 4200
  • measurements of primary production and bacterial carbon production
  • Fluorometer, Turner Designs
  • Trilogy laboratory fluorometer
  • measurement of chlorophyll a in the water samples
  • High Performance Liquid Chromatography
  • Agilent
  • qualitative and quantitative measurements of pigments
  • Spectrometer
  • Perkin Elmer
  • Spectrum one FT-IR
  • structural characterization of compounds
  • Continuous Segmented Flow Analyzers (SFA)
  • Seal Analytical (model QuAAttro 39)
  • nutrient analysis in the water,
  • CHNS elemental analyzer, Elementar, Vario Micro Cube
  • CHNS analysis in the water and sediments,
  • Gas chromatograph for identification of microorganisms using
    fatty acid methyl esters analysis (Sherlock Microbial Identification System)
  • microorganism identification
  • Fast protein liquid chromatography AKTA Purifier UPC 100
  • purification of proteins and other small particles
  • IC chromatograf 761 Compact (Methrom) +
  • analysis of cations and anions in freshwater samples
  • Agilent Mass spectrophometer/Gas chromatograph (5973 MS/6890N GC)
  • for metabolomic analysis (Lipids, Amino Acids) or detection of pesticides
  • ELISA reader Tecan Sunrise
  • Flow cytometer (Calibur BD)
  • Spectrofluorimeter with luminometer for microtitre plates (Tecan Genios)
  • Spectrofluorimeter - multidetection reader SynergyMX(BioTech Instruments)
  • monitoring cellular processes at protein expression/activation level
EQUIPMENT FOR ACOUSTIC ANALYSIS
Equipment Key applications
  • Laser vibrometer Polytec: controller 2200-L, controller head OFV-353
  • Laser vibrometer Polytec: controller OFV-5000, controller head OFV-505
  • Vibration exciters Bruel & Kjǽr (9x)
  • SINUS Acoustic Real-time Analysis Instrument, Samurai 2.0
  • registration and analysis of insect communication signals (acoustic-vibratory signals)
  • investigations of the adaptive nature of insect vibratory communication in relation to host plant mechanics
  • characterisation of mechanical properties of solid materials: determination of resonant properties of wood, etc.
EQUIPMENT FOR IMAGE ANALYSIS
Equipment Key applications
STEREOMICROSCOPES
  • SZX12 with digital camera and Imaging Software cellSens (Olympus)
  • Stereozoom SMZ1500 (Nikon)
BRIGHT FIELD MICROSCOPES
  • BX50, BX51 with digital kamera (Olympus)
  • Axioscope 2 plus (Zeiss)
  • Eclipse 80i with digital camera and Imaging software NIS Elements (Nikon)
  • inverted AxioObserver Z1 (Zeiss)
  • inverted Diaphot (Nikon)
FLUORESCENCE MICROSCOPES
  • DMRB/E with digital camera (Leica)
  • E800 with digital camera (Nikon) and Imaging software Comet Assay IV (Perceptive Instruments)
  • Inverted EclipseTE300 with digital camera and Imaging software NIS Elements (Nikon)
ELECTRON MICROSCOPY
SPECIAL APPLICATION SYSTEMS
  • Confocal fluorescent macroscope (Leica TCS LSI)
  • Zooscan (Hydroptics)
  • Axioskop 2 FS with laser ablation system (Zeiss)
  • Inverted Eclipse Ti with digital cameras and Imaging software NIS Elements (Nikon);
  • upgraded with MMI CellEctor Plus system:
  • MMI CellPump,
  • 3D cellRobot,
  • MMI CellExplorer Software (MMI AG)
  • taxonomical, biodiversity and biogeographical studies
  • immuno-cytochemistry
  • immuno-histochemsitry
  • live monitoring of cellular processes with labeled (fluorescent) substrates
  • comet-assay, micronucleus test
  • morphological cell analysis
  • qualitative and quantitative analysis of phytoplankton, phytobenthos and zooplankton
  • studying cell-cell interactions, cell function and cell lineages (embryonic development of nervous and muscular systems)
  • analysis of fluorescent staining preparations, morphological cell and tissue analysis
  • isolation of single cells in a format suitable for further in vitro culture and downstream molecular analysis in nanolitre volume mixtures (automated deposition of cells onto reaction slides or directly into PCR tubes, IBIDI style chambers (FISH, ICC) or into micro-fluidic devices)
FIELD EQUIPMENT
Equipment Key applications
  • Research vessel Sagita, SEA ARK, USA
  • Fast sampling boat, Carolina Skiff DLV – 258
  • Oceanographic buoy Vida, Prototype, own development
  • Remote controlled sampling boat, Prototype Henigman d.o.o.
  • Quadkopter, Kopterworks, Quad H2O waterproof RTF
  • Scientific diving station, Specialized workshop
  • Under water communication kit, Aquacom + Posedion diving system STX-101, STX-101M
  • Rosette, CTD SeaBird + Ocean test equipment (Niskins)
  • WTW Multiset 3430 for water pH, oxygen and conductivity measurements up to 40 m in depth
  • Laser particle size analyzer, LISST 100X, Sequoia Scientific
  • Laser system for the detection of jellyfish, Prototype Salvi sp.
  • Acoustic velocimeter, Nortek Vector
  • Drifter, Prototype Henigman d.o.o.
  • Microstructure multiparametric probe, Sea & Sun Technology GmbH
  • Wessel mounted Acoustic Doppler Current profiler, Rdi, Teledyne
  • Bottom mounted Acoustic Doppler Current profiler, Nortek Vector
  • OTT Acoustic Digital Current meter (ADC)
  • Delta T device – metereological station
  • Portable laser vibrometer Polytec PDV 100 (3x)
  • Various sampling devices for freshwater, marine and terrestrial organisms
  • Ornithological field observation equipment
  • fast measurements of surface temperature and salinity
  • quadkopter survey of the sea surface with built-in camera
  • measurement and analyses of the particles size
  • jellyfish detection and counting
  • turbulence measurements
  • tracking of surface water mass
  • water and sediment sampling
  • continuous measurements of various parameters
  • infrastructure for scientific diving, divers support and communication among divers and divers – surface
  • environmental vertical profiling (CTD, DO, CHLa, PAR, pH) + turbulence profiling (fluctuations of T, C, vertical shear)
  • vertical profiling of currents
  • automated water column sampling
  • on-line availability of atmospheric and marine environment data + possibility to mount additional sensors on the oceanographic buoy
  • flow velocity and discharge measurements in running waters
  • sampling of marine, freshwater and terrestrial organisms
  • detection of insect pests in biological materials (early detection of pest and invasive species of beetles in trees, cut wood, wood packaging material; detection of insect pests in organic objects of cultural heritage)
  • bird ecology research
NEUROBIOLOGY ANALYSIS
Equipment Key applications
  • Electrophysiology set-up for insect neurobiology (2x)
  • researching neuronal basis of vibratory signal processing and evolution
    of neuronal networks and underlying behavioural decisions
  • extracellular recording, intracellular recording, staining techniques
PROTEIN & BIOCHEMICAL ASSAYING
Equipment Key applications
  • 2D gel electrophoresis system with image analysis software (Image Master 2D Platinum)
  • Flow cytometer (Calibur BD)
  • monitoring cellular processes at protein expression/activation level
  • Set-up for biochemical assays (Ultrasonic Homogenizer Cole&Palmer;
    Sigma 2K15 Centrifuge, thermostatic incubator, Perkin Elmer Lambda
    25 UV/VIS Spectrophotometer)
  • measuring of respiratory potential and stress response in aquatic and
    terrestrial invertebrates and aquatic biofilms
QUANTITATIVE ANALYSIS OF NUCLEIC ACIDS
Equipment Key applications
  • Real-time PCR (Applied Biosystems 7900HT, ViiA7;
    Roche Light Cycler 480, Cephid Smart Cycler)
  • Digital PCR (nanofluidic Fluidigm BioMark HD System and
    droplet digital PCR System BioRad QX200)
  • gene expression, miRNA analysis, SNP genotyping, protein expression, copy number variation, high-resolution melt, sample quantification for sequencing, pathogen detection
  • Isothermal LAMP amplification (GenieII)
  • pathogen/pest detection, on-site application, SNPs typing, quantitative method
  • Next-generation sequencing (Ion Torrent, Roche GS Junior)
  • targeted sequencing, sequence capture, exome sequencing, whole genome sequencing of microbial organisms, metagenomics and pathogen discovery, transcriptome sequencing.
  • pipetting robot (Perkin Elmer MultiProbe II),
  • homogenizers: MP Biomedicals FastPrep-24, Qiagen Tissue Lyzer,
    Seward Stomacher Stomacher 80 Biomaster),
  • Thermo KingFisher mL, KingFisher duo,
  • Agilent 2100 Bioanalyzer
  • automated liquid handling
  • various biological material homogenization
  • automated magnetic-based nucleic acids extraction
  • analysis of nucleic acids, proteins and cells (QC, quantifications)
OTHER
Equipment Key applications
  • Denaturating Gradient Gel Electrophoresis (DGGE),
    C.B.S. Scientific
  • separating double stranded PCR products of similar length
    but differing sequence composition
  • Cytometer, BD Biosciences, BD Accuri C6
  • detection of fluorochromes (FITC, PE, PerCP and APC), cell counting,
    viability assays, detection of cynobacteria
  • Rotating table, BAMS Podnart
  • geophysical lab experiments
  • ArcGIS 9.0 sofware for spatial analysis
  • environmental analysis of spatial data