Presentation on theme: "Research Institute Facilities"— Presentation transcript:
1 Research Institute Facilities By Christine Andrews, Karen Gogala & Marja Simpson
2 Horticulture Centre Equipment Laboratory facilities with large working spaceTrial Site AreaPlant Growth CabinetsLarge Capacity Dehydrating OvenCool RoomVideo and scanner based image analysis systemGlasshouses with automatic heating and coolingSteam generatorAutomatic weather stationsList of Horticulture Centre facilities
3 Horticulture Centre Laboratory & Trial Site Slide shows the laboratory with large bench and floor space
4 Plant Growth Cabinets 1 large cabinet, 2 smaller cabinets Temperature and humidity controlledLighting intensity variable by switching lamps24 h timers provide control between instrumentsThree growth cabinets available, two smaller ones and one large more modern cabinet.All three cabinets are temperature and humidity controlled.Lighting is provided by different types of lamps and intensity can be varied by switching the lamps.All instruments can be controlled be 24h timers
5 Dehydrating Oven & Cool Room Operating range is +10oC to + 200oCThe first photo shows the large capacity dehydrating ovenIts operating range is +10 degrees Celsius to 200C.Second picture shows the coolroom.
6 Video and scanner based image analysis system Captures images with coloured video camera, Delta-T SCAN splash-protected flatbed scannerWinDIAS and Delta-T SCAN image analysis software analyse imagesUsage: WinDIAS- Measurement of the area of healthy and diseased plant leavesDelta-T SCAN- Leaf measurement, Root length measurement, object size analysis, eg. soil particles, seeds, measurements from photographs or copies, count objects, eg. seedsThis video and scanner based image analysis system can captures images with a coloured video camera or with a scanner. There is a splash protected flatbed scanner and a hand held scanner available.There are two software programs that allow images to be analysed.WinDIAS is used for measuring leaf areas, width and lengths of healthy and diseased plants and it can identify the percentage of healthy and diseased area.Delta-T Scan can also be used for measuring leaf areas but is very good for measuring root lengths, thickness, counting seeds or other objects.Samples can be scanned directly or first photographed and then scanned.
7 Glasshouses Glasshouse size 3m x 7.5m x 3m Automatic cooling and heating systemWinter heating capacity 10oC overnight, 20oC daySummer cooling 20-25oCLighting is provided by incandescent and fluorescent lamps which is 24 h timer controlledThe dimensions of the two new glasshouses are 3 high, 7.5 long and 2m wide.Both glasshouses are set up with an automatic cooling and heating system.The capacity of these units are to maintain in winter a minimum of 10 degrees C overnight and 20 degrees during the day. The cooling capacity for summer is to maintain a temperature of degrees.Lighting is provided by incandescent and fluorescent lamps which can be timer controlled.
8 Steam GeneratorSoil and plastic container treatment to control soil borne fungal diseases, nematodes and weedsThe Steam generator is used to recycle used potting mix and plastic pots with the aim to control soil borne fungal diseases, nematodes and weeds.
9 Automatic Weather Station 2 stationsRecords: Wind speed, wind direction, air temperature, rainfall, relative humidity, solar radiation, logger calculates evaporationData available online
10 Soil ShakerThe Endecotts EFL 2000 is a vibrating shaker that is used to carry out sieve tests in conjunction with sieve stacks for particle sizing of various material samples.Sizes of sieves available: 1.0mm2.0mm500micron250micron125micron63micron
11 Equipment – Research Lab Atomic Absorption SpectrometerUV/Visible SpectrometerScanning Electron MicroscopeFluorescence MicroscopePCR SystemAutomontage MicroscopeGIS SystemGC/MSHPLC
12 Atomic Absorption Spectrometer (AAS) Measures the amount of light absorbed by atomsLiquid sample aspirated, aerosolized & mixed with gasIgnited in flameAtoms reduced to free state which absorbs lightAAS measures the absorption spectrum of atoms as the name suggests. The instrument is used to identify and quantify the presence of atomic species which have an absorption pattern that is a fingerprint for each element. The fundamentals of operation are a beam of light is passed through a flame containing the atomic element. Certain wavelengths of the beam are absorbed. This is usually done with parallel beams -- one going through the gaseous sample; the other going directly to the spectrometer. The radiation that reaches the measuring part of the instrument passes through a narrow slit and impinges upon a grating (or prism) that separates the radiation spatially according to its wavelength. The separated wavelengths impinge upon a detector which compares the two beams and records the difference in the signal.The technique offers a quick, easy, accurate & highly sensitive means of determining the concentration of elements. Able to detect presence of up to 70 elements at levels ranging from very low (ppm) to the pure metalThe lamps we have presently are Al, Ca, Mg, Sr, Co, Cr, Cu, Fe, Mn, N, P, K,Na.Combustible gases such as acetylene & air or acetylene & nitrous oxideFlame 2100to 2800CFree atoms absorb light at characteristic wavelengths which are element specific & accurate to nm.To provide element specificity a light beam from a lamp whose cathode is made of the same element being determined is passed through the flame. A device eg photomultiplier detects the reduction of the light intensity due to absorption by the analyte & this can be directly related to the amount of element in the sample.Examples of use: The role of rubidium marked natural enemy refuge in the establishment and movement of Bemisia parasitoids.In this role refuge sites were treated with rubidium – insects were collected and the rubidium conc of insects was determined using flame emission spectroscopy. The aim was to show the movement of the parasitoids – if they came from the overwintering refuges adjacent to the crop or somewhere else.it is used for metals analysis in industrial areas dealing with environmental, chemical manufacturing, clinical, forensic, and food science disciplines.
13 UV/VIS Spectrophotometer Measures amount of light a sample absorbsA beam of light passes through onto a detectorAmount of molecules in a sample can be detectedBoth UV & visible spectraMeasures the amount of ultraviolet & visible light transmitted by a liquid sample. A beam of light is passed through the sample solution & the intensity of light is measured by a detector.By comparing absorbance data to standards of known concentration, the amount of molecules in the solution can be determined.UV/Vis contains a tungsten lamp (white light) & a deuterium light (UV)Used to detect molecules in solutions, presence & concentration, determine the purity of a sample & can look at the changes in a sample over time.Examples of use Mahmuda used this to measure the colour intensity in her flowers.Integrating sphere are a versatile accessory that allows measurements on virtually any solid or liquid. Minimal sample preparation is usually required, with samples often being measured in their original form. Integrating sphere collects light from a wide range of input angles, can correct for inaccuracies due to refraction or light scattering effects. Thick samples also cause problems due to light scatter, refraction and beam distortion. Again, an integrating sphere can compensate for these effects and provide extremely accurate results. An integrating sphere provides an ideal solution for accurate and reproducible measurements on a variety of difficult transmission samples. Even very thick samples and those which scatter and refract the beam can be readily measured in a controlled and precise way.
14 Scanning Electron Microscopy Creates magnified images by using electrons instead of light wavesShows 3D images at much higher magnificationSamples prepared – sputter coaterConventional microscopes use glass lenses to bend light waves & create a magnified image. Images are created without light waves are black & whiteSamples have to withstand vacuum, be dried & conduct electricityCoated with a thin layer of gold on a sputter coaterPut sample in vacuum column, pump out air, electron gun at the top emits a beam of high energy electrons. This travels downward thru a series of magnetic lenses that focus to a very fine spot. Near the bottom a series of coils moves the focussed beam back & forth across the specimenAs the electron beam hits the spot, secondary electrons are knocked loose from the surface. A detector counts these electrons & sends the images top an amplifierThe final image is built up from the number of electrons emitted from each spot on the sample
16 Fluorescence Microscopy Sample you want to study is the light sourceEnergy absorbed by atom; it gets excitedElectron jumps to a higher energy levelDrops back to ground state, emits a photon (fluorescing)Technique is based on the phenomenon that certain material emits energy detectable as visible light when irradiated with the light of a specific wavelength. Study specimens which can be made to fluoresce.Sample can be fluorescing in its natural form eg chlorophyll or be treated with fluorescing chemicalsThe fluorescing areas shine out against a dark background with high contrast.The researchers were able to track the movement of the actinomycete bacteria in the wheat plant by 'tagging' it with a gene for GFP which is picked up by fluorescence microscopy. The green areas show the colonisation of the endosperm of a wheat seed with the bacteria.Example of useKarilyn Gilchrist used this to study the evaluation of pollen tube growth in various hazelnut cultivars 24hrs after pollination in order to assess compatibilty/incompatibility between cultivars. Callose deposits in the pollen tube fluoresce following aniline blue staining of pistil squashes.
17 PCR RoomPolymerase Chain Reaction is a molecular biological technique for amplifying DNA without using a living organism.PCR is commonly used in medical and biological research labs for a variety of tasks.Amplifying means creating multiple copies ofTasks such as the detection of hereditary diseases, the identification of genetic fingerprints, the diagnosis of infectious diseases, the cloning of genes, and paternity testingThe PCR reaction is carried out in a thermal cycler. This is a machine that heats and cools the reaction tubes within it to the precise temperature required for each step of the reactionLeigh used this technique to determine the presence of phytoplasmas associated with Australian lucerne yellows. Getachew is continuing on with this work
18 Automontage Microscopy Perfectly focused 3D imagesIncreased depth of field softwareAllows images of small insects almost as good as the specimen itselfIs an image capture system for microscopy using software to produce a high quality 3D imageSoftware that receives a stack of digital images, examines each one for areas that are in focus, then stiches all the in focus bits together to make one image. In effect it allows you to make an image with as much depth of field as you want.Birgit uses this to look at leafhoppers. The scale is 1mm & the picture is clear.
19 GIS System Manages spatial data and associated attributes. It is a computer system capable of integrating, storing, editing, analysing, and displaying geographically-referenced information.In a more generic sense, GIS is a "smart map" tool that allow users to create interactive queries (user created searches), analyze the spatial information, and edit data.Geographic information systems technology can be used for scientific investigations, resource management, asset management, development planning, cartography and route planning. For example, a GIS might allow emergency planners to easily calculate emergency response times in the event of a natural disaster, or a GIS might be used to find wetlands that need protection from pollution.Brian Stone & Cilla Kinross use this equipment in their research.
20 HPLC and GC/MS High Performance Liquid Chromatograph Gas Chromatograph coupled with a Mass Spectrometer
21 High Performance Liquid Chromatograph Chromatography—what is it?Liquid ChromatographyBasic OperationEquipment usedTypes of ChromatographyApplications for HPLC
22 What is chromatography? Chromatography –’colour’ and ‘to write”Originally described by Tswett in 1906 who devised a method to separate plant pigments using a tube filled with CaCO3.Basically it is a broad range of physical methods used to separate and /or to analyse complex mixturesComponents to be separated are distributed between two phases:a stationary phase bed and a mobile phase which flows through the stationary bed.Individual species are retained by the stationary phase (packing) based on various interactions such as surface adsorption, relative solubility of the sample in the mobile phase and charge.
23 ChromatographyLC-mobile phase is a solvent and stationary phase is a packed bed of silica particles.
24 Liquid Chromatography HPLC is this process conducted at a high velocity and under pressure.Sample can be in an aqueous form or in an organic/aqueous form.Sample is injected onto the column and is pushed through by the mobile phase(eluent) under high pressure.Components are retained and separated on the column.They elute at different times depending on their chemical interaction with the packing in the column.The time at which they elute (retention time) is a characteristic of that compound.After compounds elute,they enter a detector(PDA) which creates an electronic signal. The greater the concentration of the compound, the greater the signal.
29 Carbohydrates in vegetables ApplicationsChemical separationsIdentificationQuantificationPurificationCosmetics,energy,food,life sciences pharmaceutical, biomedical, drug detection and identification.Carbohydrates in vegetablesHerbicides
30 Gas Chromatograph/Mass Spectroscopy (GC/MS) Mass Spectrometer
31 Gas Chromatograph Mobile phase is an inert gas such as helium Sample is injected into a heated injection port, becomes vapourised and travels onto the column by means of the carrier gas.Column is made of fused silica onto which is coated the liquid stationary phase and it is enclosed in a heated zone(oven)Compounds become separated as they interact with the columnVariables are temperature,gas flow, and column specifications.Separated compounds identified by specific detector.(FID.NPD,ECD)
33 Mass Spectrometer Creates charged particles (ions) from molecules. Analyzes those ions to provide information about the MW of the compound and it’s chemical structureMany types of MS which allow wide range of analyses.GC/MS is the coupling of GC with MS
34 GC/MSA. Capillary column interface which connects GC to mass spectrometerB. Sample enters ionization chamberIonization occurs. A beam of electrons impacts the sample molecules which lose an electron becoming positive (M+)C. A positive potential is applied to repel the + ions out of the ionization chamber and into the mass analyser.(filter)
35 GC/MSMass analyser separates the positively charged particles under vacuum according to their mass.Particles then enter a detector which sends information to the computer and resulting chromatograms give a mass spectrum of the sample components.Identification of the compound relies on the fact that every compound has a unique fragmentation pattern.