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Plant biotechnology experiments 4th semester
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Abhishek Kaushik
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Plant biotechnology experiments 4th semester
1.
1 2017 ABHISHEKKAUSHIK 01-Jul-17 PLANTBIOTECHNOLOGYEXPERIMENTS 4thSem
2.
2 Abhishekkaushik 1.AIM: To prepare Murashige
and Skoog (MS) mediaforplanttissueculture. PRINCIPLE: Thebasalmediumisformulatedsothatitprovidesallofthe compoundsneededforplantgrowthanddevelopment, includingcertaincompoundsthatcanbemadebyanintact plant,butnotbyanisolatedpieceofplanttissue.Thetissue culturemediumconsistsof95%water,macro-and micronutrients,vitamins,aminoacids,sugars.Thenutrients inthemediaareusedbytheplantcellsasbuildingblocksfor thesynthesisoforganicmolecules,orascatalysatorsin enzymaticreactions.Themacronutrientsarerequiredin millimolar(mM)quantitieswhilemicronutrientsareneeded inmuchlower(micromolar,μM)concentrations.Vitamins areorganicsubstancesthatarepartsofenzymesor cofactorsforessentialmetabolicfunctions.Sugaris essentialforinvitrogrowthanddevelopmentasmostplant culturesareunabletophotosynthesizeeffectivelyfora varietyofreasons.Murashige&Skoog(1962)medium(MS) isthemostsuitableandcommonlyusedbasictissueculture mediumforplantregeneration. MATERIALSANDREQUIREMENTS: · Distilledwater,sucrose,gellingagent,1M NaOHor1M HCl toadjustthepH,micronutrientsstock,macronutrientsstock, organiccompoundstock. · Equipment–Balance,pHmeter,autoclave,LAFcabinet. · Glassware–conicalflask,phytajars,beakers,pipettes. Preprationofmacronutrientstock MSmajorsalts mg/1Lmedium 500mlstock(20X) 1.NH4 NO3 1650mg 16.5gm 2.KNO3 1900mg 19gm 3.Cacl2 .2H2 O 440mg 4.4gm 4.MgSO4 .7H2 O 370mg 3.7gm 5.KH2 PO4 170mg 1.7gm Preprationofmicronutrientstock MSminorsalts mg/1Lmedium 500ml stock (200X) 1.H3 BO3 6.2mg 620mg 2.MnSO4 .4H2 O 22.3mg 2230mg 3.ZnSO4. 4H2 O 8.6mg 860mg 4.KI 0.83mg 83mg 5.Na2 MoO4. 2H2 O 0.25mg 25mg 6.CoCl2. 6H2 O 0.025mg 2.5mg 7.CuSO4. 5H2 O 0.025mg 2.5mg Preprationofvitaminstock MSVitamins mg/1Lmedium 500mlstock (200X) 1.Thiamine(HCl) 0.1mg 10mg 2.Niacine 0.5mg 50mg 3.Glycine 2.0mg 200mg 4.Pyrodoxine(HCl) 0.5mg 50mg PREPARATIONOFHORMONESTOCKS: · Weighout0.3gofIAA · SterilizetheIAAbyplacingunderUVlightfor30mins. Transfertoasterilevolumetricflask. · DissolvetheIAAinfewdropsofethanolandmakeupthe volumeto100mlusingsteriledistilledwater. · Weighout0.1mgofkinetinandsterilizeunderUVlight · Transferto a flaskand dissolvein 100 mlofsterile distilledwater · Add30mlofIAAstockand1.5mlofkinetinstocktoeach bottleaseptically.Mixwellandallowthecontentstosolidify anduseimmediatelyorstoreat4 0 C. PROCEDURE: 1. Dissolve the microelements,macroelements and organicsin800mlofdistilledwater. 2. Addtherequiredhormonesolutions. 3. Adjustthemedium pHto5.7byadding1M NaOHor 1MHCl. 4. Add additionaldistilled waterto adjustthefinal volumeto1litre. 5. Addtheagarandheatthemedium todissolvethe agar. 6. Dispensethemedium intoculturetubesorvessels andautoclavefor20minutesat121°C. 2.Aim: isolation ofprotoplastby mechanical method Principle: Protoplastcanbeisolatedfrom almostallplantparts:roots, leaves,fruits,tuber, rootnodules,pollenmothercelletc.Protoplastisolatedby mechanicalisacrudeand tediousprocedure. Cellsareplasmolysedcausingtheprotoplasttoshrinkfrom thecellwall.The protoplastobtainedfrom thismethodisthenculturedon suitableculturemedium.The principledeficiencyofthisapproachisthattheprotoplast
3.
3 Abhishekkaushik releasedisfewinnumber. Mechanicalisolationwasthatofonlyhistoricaleventnow. MaterialsRequired: 1.Plantleaves–Durantarepens 2.Mortarandpestle 3.PhosphatebufferpH-7.0 4.0.3Msorbitol 5.0.3Mmannitol 6.Glassslides 7.Microscope. Procedure: 1.Youngleaveswereobtainedfrom plantsgrowingoutdoors andinitiallywashed withtapwatertoremoveanydustparticles. 2.The leaves
were washed with phosphate bufferand homogenizedgentlywiththe mortarandpestle. 3.Thecrudeprotoplastsuspensionwascentrifugedatvery low50-100rpmfor10 minutes. 4.Thesupernatantcontainingintactprotoplastwascarefully pipettedoutandthe pelletcontainingcelldebrisandothercellorganelleswere discarded. 5.Smallvolumeofsupernatantwasplacedintheslidesand coveredwithcoverslip. 6.Theslidewasobservedinlightmicroscopetofindout viableprotoplast Result: Thesphericalshapedprotoplastswereobservedusingthe microscope. 3.AIM: isolation ofprotoplasts by enzymatic method PRINCIPLE: Protoplastsareisolatedbytreatingtissueswithamixtureof cellwalldegrading enzymeinsolution,whichcontainosmoticstabilizer.Amost suitablesourceof protoplastsismesophylltissuefrom fullyexpandedleavesof youngplantsornewshoots. Thereleaseofprotoplastisverymuchdependentonthe natureandcompositionof enzymesusedtodigestthecellwall.Therearethreeprimary componentsofthecellwall whichhavebeenidentifiedascellulose,hemicellulaseand pectinsubstance.Pectinase (macrozyme)mainly degrades the middle lamella while celluloseandhemicellulase degradesthecelluloseandhemicellulosiccomponentsofthe cellwall.Duringthis enzymatic treatment,the protoplastobtained should be stabilizedbecausethemechanical barrierofthecellwallwhichofferedsupporthasbeenbroken. Forthisreasonan osmoticm is added which prevents the protoplastfrom bursting. MATERIALSREQUIRED: 1.Youngleaves 2.70%ethanol 3.2%cellulose 4.13%mannitol 5.0.5%macrozyme 6.CPWsaltsolution: KH2PO4-27.2mg/l KNO3-101mg/l CaCl2-1480mg/l MgSo4-246mg/l KI-0.16mg/l CaSo4-0,026mg/l pH-5.8. PROCEDURE: 1.Theyoungleaveswerecollectedandwashedinsterile distilledwaterthrice. 2.Theleaveswerecutintosmallbits. 3.Thentheleaveswerekeptimmersedin13%mannitolfor1 hforpre-plasmolysis. 4.Mannitolwas removed afterincubation antsterilized enzymemixture(Cellulase+ macerozyme)wasaddedandincubatedat25ºCinashaker for12h 5.Thefiltratewascentrifugedat100gfor5mintosediment theprotoplast. 6.Thesupernatantwasremovedandtheprotoplastpellet wassuspendedin10mlof CPW+21%sucrosesolution. 7.Themixturewascentrifugedat100gfor5min.Theviable
4.
4 Abhishekkaushik protoplastwillfloatto thesurfaceofthesucrosesolution. 8.The supernatantwas collected
and viewed under microscope. 9.Theprotoplastswerevisualizedinmicroscope. RESULT: Protoplastswereisolatedbyenzymaticmethodandviewed underthemicroscope 4.AIM:Thepolymerasechainreaction(PCR)isa laboratorytechniqueforDNA Principle ThePCRinvolvesthe primermediatedenzymatic amplification ofDNA.PCRisbasedonusingtheability ofDNApolymerasetosynthesizenewstrandofDNA complementarytotheofferedtemplatestrand.Primer isneededbecauseDNApolymerasecanadda nucleotideonlyontoapreexisting3′-OHgrouptoadd thefirstnucleotide.DNApolymerasethenelongateits 3endbyaddingmorenucleotidestogeneratean extendedregionofdoublestrandedDNA. Materials BuffersandSolutions 10xAmplificationbuffer Chloroform dNTPsolution(20mM)containingallfourdNTPs(pH8.0) EnzymesandBuffers ThermostableDNApolymerase NucleicAcidsandOligonucleotides Forwardprimer(20μM)inH2O Reverseprimer(20μM)inH2O TemplateDNA. DissolvetemplateDNAin10mMTris-Cl(pH7.6)containinga low concentration ofEDTA (<0.1 mM)atthe following concentrations:mammaliangenomicDNA,100μg/ml;yeast genomicDNA,1μg/ml;bacterialgenomicDNA,0.1μg/ml; andplasmidDNA,1-5ng/ml. Method 1. Inasterile0.5-mlmicrofugetube,mixinthefollowing order: REAGENTS AMOUNT(μl) Deionizedwater 37.5μl Taqassaybuffer(10x) 5μl TemplateDNA 1μl dNTPsmix 2μl Forwardprimer 2μl Reverseprimer 2μl TaqDNApolymerase 5μl Thetablebelow providesstandardreactionconditionsfor PCR.Mg2+ (1.5 mM) ;KCl(50 mM) ;dNTPs (200 μM) ;Primers(1μM);DNApolymerase(1-5units);TemplateDNA(1 pgto1μg). 2. Ifthethermalcyclerisnotfittedwithaheatedlid,overlay thereactionmixtureswith1drop(approx.50μl)oflight mineraloil.Alternatively,placeabeadofwaxintothe tubeifusingahotstartprotocol.Placethetubesorthe microtiterplateinthethermalcycler. 3.Amplify the nucleic acids using the denaturation, annealing,and polymerization times and temperatures listedbelow. 4. Withdraw a sample (5-10 μl)from the testreaction mixtureandthefourcontrolreactions,analyzethem by electrophoresisthroughanagarosegel,andstainthegel withethidiumbromideorSYBRGoldtovisualizetheDNA. 5. Ifmineraloilwasusedtooverlaythereaction(Step2), removetheoilfrom thesamplebyextractionwith150μl ofchloroform.Theaqueousphase,whichcontainsthe amplifiedDNA,willform amicellenearthemeniscus. Themicellecanbetransferredtoafreshtubewithan automaticmicropipette. AmplificationBuffer: 500mMKCl. 100mMTris-Cl(pH8.3atroomtemperature). 15mMMgCl2. Autoclavethe10xbufferfor10minutesat15psi(1.05 kg/cm 2 )onliquidcycle.Dividethesterilebufferintoaliquots andstorethemat-20 o C. KCl DissolveanappropriateamountofsolidKClinH2O,autoclave for20minutesonliquidcycleandstoreatroom temperature. Ideally,this4Msolutionshouldbedividedintosmall(approx. 100μl)aliquotsinsteriletubesandeachaliquotthereafter usedonetime. Tris-Cl Dissolve121.1gofTrisbasein800mlofH2O.AdjustthepH tothedesiredvaluebyaddingconcentratedHCl. Base wavelength(nm) ExtinctionCoefficient(E)(M-1cm-1) A 259 1.54x10 4 G 253 1.37x10 4 C 271 9.10x10 3 T 267 9.60x10 3
5.
5 Abhishekkaushik pHHCl 7.470ml 7.660ml 8.042ml (1M)Allowthesolutiontocooltoroom temperaturebefore makingfinaladjustmentstothepH.Adjustthevolumeofthe solution to
1 litre with H2O.Dispense into aliquots and sterilizebyautoclaving.Ifthe1M solutionhasayellowcolor, discarditandobtainTrisofbetterquality.ThepH ofTris solutionsistemperature-dependentanddecreasesapprox. 0.03pH unitsforeach1oC increaseintemperature.For example,a0.05M solutionhaspHvaluesof9.5,8.9,and8.6 at5 o C,25 o C,and37 o C,respectively. dNTPSolution DissolveeachdNTP(deoxyribonucleosidetriphosphates)in H2Oatanapproximateconcentrationof100mM.Use0.05M TrisbaseandamicropipettetoadjustthepHofeachofthe solutionsto7.0(usepH papertocheckthepH).Dilutean aliquotoftheneutralizeddNTPappropriately,andreadthe opticaldensityatthewavelengthsgiveninthetablebelow. CalculatetheactualconcentrationofeachdNTP.Dilutethe solutionswithH2Otoafinalconcentrationof50mM dNTP. Store each separately at 70 o C in smallaliquots.For polymerasechainreactions(PCRs),adjustthedNTPsolution topH8.0with2NNaOH.Commerciallyavailablesolutionsof PCR-gradedNTPsrequirenoadjustment. Foracuvettewithapathlengthof1cm,absorbance=EM. 100mM stocksolutionsofeachdNTP arecommercially available. Precautions chloroformCHCl3 isirritatingtotheskin,eyes,mucous membranes,andrespiratorytract.Itisacarcinogenandmay damagetheliverandkidneys.Itisalsovolatile. Avoid breathingthevapours. Wearappropriateglovesandsafety glasses.Alwayswearachemicalfumehood. 5.AIM:Toisolateandinoculateanthersforhaploid production. PRINCIPLE: Haploidsrefertothoseplantswhichpossessa gametophyticnumberof chromosomesintheirsporophytes.Haploidsmaybe groupedintotwobroad categories: (a)monoploidswhichpossesshalfthenumberof chromosomesfromadiploid species. (b)Polyhaploidswhichpossesshalfthenumberof chromosomesfromapolyploidy species. Haploidproductionthroughantherculturehasbeenreferred toasandrogenesis whilegynogenesisistheproductionofhaploidplantsfrom ovaryorovuleculture wherethefemalegameteorgametophyteistriggeredto sporophyticdevelopment. MATERIALSREQUIRED:- 1.AnthersfromHibiscus 2.MSmedium 3.growthfactors 4.70%ethanol 5.2%mercuricchloride 6.Mesoinositol 7.Scissors 8.Scalples 9.Petriplates 10.Forceps. PROCEDURE: 1.FlowerbudsofHibiscuswerecollected. 2.Theflowerbudsaresurfacesterilizedbyimmersingin 70%ethanolfor60sec followedbyimmersingin2%sodiumhypochloridesolution for1minorin mercuricchloride. 3.Thebudswerewashedfourorfivetimeswithsterile distilledwater. 4.ThebudsweretransferredtoasterilePetridish. 5.Thebudsweresplitopenusingabladeandtheanthers wereremovedwithout damageandthefilamentswereremoved. 6.TheantherswereplacedhorizontallyontheMSmedium supplementedwith differentconcentrationofplantgrowthregulatorsor mesoinositol. 7.ThePetriplatesweresealedandincubatedindarkat28ºC. 8.ThePetriplateswereexaminedforthegerminationof anthers. RESULT: Theantherunderwentgerminationleadingtotheformation ofhaploidplantlets. 6.AIM-RandomamplifiedpolymorphicDNA(RAPD) PCRbasedtechniqueforidentifyinggenetic variation. Principle
6.
6 Abhishekkaushik The RAPD technique
is based on the polymerase chain reaction (PCR).A targetDNA sequence is exponentially amplifiedwiththehelpofarbitraryprimers,athermostable DNA polymerase,dideoxy nucleotide tri- phosphates, magnesium and reaction buffer.The reaction involves repeatedcycles,eachconsistingofadenaturation,aprimer annealingandanelongationstep(fig1).Inthefirststepthe DNAismadesinglestrandedbyraisingthetemperatureto 94C (denaturation).In thesecond step,lowering ofthe temperaturetoabout40to65Cresultsinannealingofthe primerto theirtargetsequences on the template DNA (annealingstep).Inthethirdcycle,temperatureischosen wheretheactivityofthethermostableTaqDNApolymeraseis optimal,i.e.,usually720C. Materialandreagents Instruments: PCR machine(PerkinElmer9600),microcentrifuge,100V powersupply,Gelelectrophoresistank,gelmouldandslot former,UVtransilluminator,Camera,autopipettes,vortex. Reagents: 1.TaqDNApolymerase 2.GenomicDNA(5ng/l) 3.dNTPmix(2mMeachofdATP, dCTP,dGTPanddTTP) 4.MgCl2(25mM) 5.BufferforDNApolymerase 6.10-meroligonuleotideprimers(5M) 7.Steriledistilledwater 8.Electrophoresisgradeagarose 9.0.5XTBEbuffer 10.Ethidiumbromidesolution(10mg/mll) 11.DNAlengthmarker 12.Loadingbuffer Miscellaneous:ThinwalledPCRtubes,tips,tissuepaper. Protocol 1.Each10lofreactionmixcontains Component Volume FinalConcentration GenomicDNA 3.0l 15ng Buffer 1.0l 1X dNTPs 1.0l 0.2mM Primer 0.6l 0.6M TaqDNApol 0.2l 1unit MgCl2 1.0l 2.5mM Water to10l Prepareamastermix(forallsamples+control)that containsalltheabovecomponentsexcepttheDNA. Thawallcomponentscompletely VortextheMgCl2vigorously Vortexthemastermixtomixallcomponentsbefore aliquoting 2.AliquotintoPCRtubesandaddthetemplateDNA.Mix well. 3.PlacethePCRplatecarryingthereactiontubesinthe sampleblockofthethermocycler. 4.Carryoutaninitialdenaturationstepat94Cfor4min followedby40cycleswiththefollowingcycleparameters: Step194Cfor1min Step235Cfor1min Step372Cfor2min Extendthe72Cstepofthefinalcycleby5min 5.Whentheamplificationhasfinished,add3loftheloading dyetoeachsample. 6.Preparea1.2%agarosegelin0.5XTBEbuffercontaining ethidiumbromide(5g/mlofgel).LoadtheDNAlength markerandthesamples.Runthegelin0.5xTBEbufferat 55Vfor4h. RESULTS VisualizethegelonaUVtransilluminator.Ifrequiredthegel canbephotographedusingPolaroid665or667filmand analysedfurther. 7Aim:TheprocessofDNAfingerprintingby RestrictionFragmentLengthPolymorphism(RFLP) method. Principle: Restrictionfragmentlengthpolymorphism(RFLP)analysisis extensivelyusedinmolecularbiologyfordetectingvariation attheDNAsequencelevel.RFLPfunctionsasamolecular markerasitisspecifictoasingleclone/restrictionenzyme combination.MostRFLPmarkersarecodominantandhighly locus-specific.In molecularbiology,restriction fragment lengthpolymorphism,orRFLPisatechniquethatexploits variations in homologous DNA sequences.RFLP is a difference in homologous DNA sequences thatcan be detectedbythepresenceoffragmentsofdifferentlengths afterdigestionoftheDNAsamplesinquestionwithspecific restrictionendonucleases.Thebasictechniquefordetecting RFLPsinvolvesfragmentingasampleofDNAbyarestriction enzyme,whichcanrecognizeanddigestDNAwherevera specificshortsequenceoccurs,in aprocessknown as restrictiondigestion.TheresultingDNAfragmentsarethen separatedbylengththroughaprocessknownas agarose gel electrophoresis. RFLP is specific to a single clone/restrictionenzymecombinationanditoccurswhen thelengthofadetectedfragmentvariesbetweenindividuals. Materials DNAsample –15.0μl 10XAssayBuffer –3.0μl MilliQwater* –10.0μl restrictionenzymes(EcoRIandPstI) Glasswares:Measuringcylinder,Beaker Reagents:Ethidiumbromide(10mg/ml) Other requirements: Electrophoresis, apparatus,UV Transilluminator,WaterBath,Micropipettes,Tips, Adhesivetape,Crushedice,Microwave/Hotplate/Burner Procedure: 1.Beforestartingtheexperiment,crushiceandplacethe vialscontainingDNAsamples, restrictionenzymesandassaybuffersontoit. 2.InthisexperimentthreereferenceDNAsamplesandthe testsamplearedigested simultaneouslywithtworestrictionenzymesEcoRIandPstI.
7.
7 Abhishekkaushik 3.Setupfourseparatereactionmixturesasfollows: DNAsample –15.0μl 10XAssayBuffer –3.0μl MilliQwater*
–10.0μl EcoRI –1.0μl PstI –1.0μl Total30μl 4.Afterpreparingthefourreactiontubes,mixthe componentsbygentlepipettingandtapping. 5.Takeplacethetubesinincubatorat37oCfor2-3hours. 6.Afterincubation,immediatelyadd5μlof6XDyetoeach tube. 7.Runthesamplesonagarosegelat100-120vcurrent supplyfor45-60minutes. 8.Observethegelunderauvtransilluminator. Result: VisualizetheDNAbandsusingUVtransilluminator. Lane1:1kbDNAladder Lane2:ReferenceSample1 Lane3:ReferenceSample2 Lane4:ReferenceSample3 1 2 3 4 8.AIM-PCR-amplificationofSSRfromPlants GenomicDNA principle Simple sequence repeats (SSRs), also known as microsatellites,aretandem repeatsoftwotofivenucleotide DNA coresequencessuchas(AT)n,(GT)n,(ATT)n,or (GACA)nspreadthroughouteukaryoticgenomes.TheDNA sequencesflankingmicrosatellitesaregenerallyconserved withinindividualsofthesamespecies,allowingtheselection ofpolymerasechainreaction(PCR)primersthatwillamplify theinterveningSSRinallgenotypes.Variationinthenumber oftandem repeats,n,results in differentPCR product lengths.Theserepeatsarehighlypolymorphic,evenamong closelyrelatedcultivars,duetomutationscausingvariation inthenumberofrepeatingunits.Differentallelescanbe detectedatalocusbythepolymerasechainreaction(PCR), using conserved DNA sequences flanking the SSR as primers.TheSSRassayisbeingincreasinglyappliedtoplant mappingprojectsduetoitsrelativeadvantages.First,SSRs arehighlypolymorphicandthushighlyinformativeinplants. Second,SSRscanbeanalyzedbyarapidandtechnically simple PCR-based assay.Third,SSRs are co-dominant markers.Finally,SSRsareboth abundantand uniformly dispersedinplantgenomes. Requerements 1.TaqDNApolymerase 2.GenomicDNA(5ng/l) 3.dNTPmix(2mMeachofdATP,dCTP,dGTPanddTTP) 4.MgCl2(25mM) 5.BufferforDNApolymerase 6.10-meroligonuleotideprimers(5M) 7.Steriledistilledwater 8.Electrophoresisgradeagarose 9.0.5XTBEbuffer 10.Ethidiumbromidesolution(10mg/mll) 11.DNAlengthmarker 12.Loadingbuffer 13.PCRmachine PREPRATIONOFPCRMIX Buffer10X 500μl MgCl25mM 300μl dTTP100mM 10μl dATP100mM 10μl dCTP100mM 10μl dGTP100mM 10μl ddH20 460μl Totalvolume 1.3ml PROCEDURE 1. Set-upa50-μlreactionintolabeledsterile0.25-ml tubes. 2. PrepareaMIXincludingthePCRMIX,theprimers, andtheTaqpolymerase.Keepthetubesinice. 3. Addthecomponentsinthefollowingorder:Water, DNA,MIX(PCRMIX+primers+Taq).Mixwelland seal 4. tubeswithsuppliedlids.Makesurethelidsareon tightly. 5. PlacethePCRplatecarryingthereactiontubesin thesampleblockofthethermocycler. 6. .Carryoutaninitialdenaturationstepat94Cfor 4minfollowedby40cycleswiththefollowingcycle parameters: Step194Cfor1min Step235Cfor1min Step372Cfor2min Extendthe72Cstepofthefinalcycleby5min 7. Whentheamplificationhasfinished,add3lofthe loadingdyetoeachsample. 8. Preparea1.2%agarosegelin0.5XTBEbuffer containingethidiumbromide(5g/mlofgel).Load theDNAlengthmarkerandthesamples.Runthegel in0.5xTBEbufferat55Vfor4h. RESULT
8.
8 Abhishekkaushik StaingelinethidiumbromideandVisualizethegelonaUV transilluminator.
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