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doi 10 1111 eea 12090 technicalnote aneconomicalandeffectivehigh throughputdna extraction protocol for molecular markeranalysis in honeybees betha holloway matthewr tarver thomase rinderer usdahoneybeebreeding genetics andphysiologylaboratory molecularbiology 1157benhurroad batonrouge la70820 usa accepted ...

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                                                                                                                  DOI:10.1111/eea.12090
                                     TECHNICALNOTE
                                     Aneconomicalandeffectivehigh-throughputDNA
                                     extraction protocol for molecular markeranalysis in
                                     honeybees
                                     BethA.Holloway*,MatthewR.Tarver&ThomasE.Rinderer
                                     USDAHoneyBeeBreeding,Genetics,andPhysiologyLaboratory–MolecularBiology,1157BenHurRoad,BatonRouge,
                                     LA70820,USA
                                     Accepted:7May2013
                                     Key words: Apismellifera,Hymenoptera,purification,nucleicacid
               Introduction                                                   allow for consistent and reproducible yields, yet can cost
                                                                              several dollars per sample. Chelating agents purify DNA
               The honeybee is becoming an increasingly important             with high quality but may require long incubations and
               organism in the realm of laboratory-based genetics. As         preparations with additional proteinase K (Giraffa et al.,
               honey bee health around the world is declining, measures       2000; Casquet et al., 2012). Traditional phenol-chloro-
               are being taken to understand the genetic basis of a multi-    formextractionsrequirehandling,storage,anddisposalof
               tudeoftraitsincludingbehavior,diseaseresistance,surviv-        hazardous organic solvents. Honey bee DNA has recently
               ability, honey production, and pollination efficiency.          beeneffectively extracted and purified by homogenization
               Quantitative Trait Loci (QTL) studies and mapping              and utilizing proteinase K and ‘salting-out’ methods to
               projectsareelucidatingthecomplexinteractionsofgenetic          remove proteins (Bourgeois et al., 2008, 2010; Bourgeois
               loci that dictate the important traits being bred for by       &Rinderer,2009). However,we developed a simple, cost-
               beekeepers, queenproducers,andresearchersalike.Quan-           effective, and fast method using only sodium chloride and
               titative Trait Loci for foraging behavior and aggression       sodiumdodecylsulfate(SDS)toextractcleanDNAdirectly
               were identified nearly 15 years ago (Hunt et al., 1995,         useable for PCR without additional dilution as is typically
               1998), long before the advancements of the current and         required. This method is particularly useful for high-
               ongoing honey bee genome project (Honey Bee Genome             throughput extraction of DNA from large numbers of
               Sequencing Consortium, Baylor College of Medicine,             individual bees while minimizing labor, plastic consum-
               Houston,TX,USA).Morerecentstudieshaveidentifieda                ables, and reagent requirements. The resulting DNA is of a
               single QTL for chalkbrood disease resistance (Holloway         highenoughqualityandquantitytodirectlyamplifybands
               et al., 2012) andhaveutilizedthegenomedatatofinemap             formolecularmarkeranalysis.
               the interval to contain just two genes of potential interest
               (Holloway et al., 2013). As QTL studies are becoming           Materialsandmethods
               more commonplace in the understanding of honey bee             Beesamples
               genetics, DNAextractionmethodsareneedingtobefaster,            Freshly emerged adult bees or purple-eyed pupae individu-
               moreeffective,andmoreeconomicaltokeeppacewiththe               ally pulled from honeycombs were frozen at 20 °C. Bee
               analysesofthepopulationsbeingstudied.                          samplesforagedDNAweremaintainedat20 °Cfor1year
                  Honey bee QTL studies are generating information on         or fresh samples were processed immediately after a lethal
               potential gene or allele functionality relevant to mapping     freezing. Body segments from fresh or aged samples were
               populations. Yet, narrowing the intervals and pinpointing      separated and processed with any associated appendages
               the genes of interest for eventual marker-assisted selection   (headwithantennae,thoraxwithlegsandwings,abdomen).
               requires hundreds or even thousands of phenotyped bees
               to be processedfor DNAextractionandgenotyping.Typi-            Processingmethodology
               cally, the extraction processes yield good qualities and       1. Individual bees, pupae, or body segments (or 100 llof
               quantities of DNA per individual sample, yet are costly in                   1
               time and materials. Commercial DNA extraction kits                250 mg ml     control BSA) were placed in 96-well
                                                                                 racked 1.2-ml microtiter tubes (Genesee Scientific, San
                                                                                 Diego, CA, USA) containing a single 3.2-mm stainless
               *Correspondence:E-mail:beth.holloway@ars.usda.gov                 steel bead (Next Advanced, Averill Park, NY, USA). A
               196      Published2013.ThisarticleisaUSGovernmentworkandisinthepublicdomainintheUSA. EntomologiaExperimentalisetApplicata148:196–200, 2013
                                                                                               HighthroughputDNAextractioninhoneybees         197
                          second3.2-mmsteelbeadwasloadedintothetubeson                  squares (LS) means, was used to distinguish differences
                          top of the tissue and tubes were capped with a silicone       amongtreatments.Tukey’sHSDtestwasusedforseparat-
                          capmat(USAScientific,Ocala,FL,USA).                            ingmeansbytreatment.
                       2. Tissues were homogenized by a TissueLyser (Qiagen,
                          La Jolla, CA, USA) in 285 llof6M NaCl (or in water,           Resultsanddiscussion
                          0.5, 1, 2, 3, 4, or 5 M NaCl) (Fisher Scientific, Pitts-
                          burgh, PA, USA). Tissue maceration was attained by            Increasedsodiumchlorideconcentrationsmoreeffectively‘salt-out’
                          homogenizing at 30 strokes per s for 2 min; microtiter        proteins
                          plates wererotated,andthehomogenizationrepeated.              It is known that the anion products of dissolved salts indi-
                       3. Plateswerebrieflycentrifuged(BeckmanCoulterAlleg-              vidually affect the aggregation or precipitation of proteins
                          ra X-15 Centrifuge; Beckman Coulter, Brea, CA, USA)           fromsolutions such that the efficacies can be described by
                          to collect the homogenate away from the cap mat. A            the Hofmeister series (Zhang & Cremer, 2006; Kunz,
                          volume of 15 ll of 20% SDS (Amresco, Solon, OH,               2010). Although many DNA extraction protocols (Bour-
                          USA)wasadded,tubesre-capped,andhomogenizedat                  geois et al., 2008, 2010; Bourgeois & Rinderer, 2009) and
                          20strokes per s for 30 s, microtiter plates were rotated,     kits use acetate salts (potassium or ammonium), we chose
                          andthehomogenizationrepeated.                                 to focus on sodium chloride due to its availability and
                       4. Homogenates were incubated at room temperature for            universal use in a variety of laboratories. Chloride anion is
                          15 min,thencentrifugedat4 800 gfor20 minat4 °C.               considered a marginally functional salting-out factor,
                       5. Aliquots of 150 ll of cleared supernatant were trans-         somewhat less effective than acetate on the Hofmeister
                          ferred to a 96-well PCR plate containing 150 llof             series. Typical NaCl concentrations used for fast DNA
                          20 °Cisopropanol(FisherScientific),andgentlypip-              extraction range from less than 1 M (Chen et al., 2010;
                          ettedupanddownseveraltimes.                                   Margamet al.,2010)toupwardof4 M(Aljanabi&Marti-
                       6. Plateswerecentrifugedasinstep4topellettheDNA.                 nez, 1997). We homogenized whole adult bees, whole
                       7. Supernatant was removed by inverting the plates to            pupae, and BSA control protein in a concentration series
                          decant the liquid and floating gelatinous conglomerate         of 0–6 M NaCl (where 0.5 M served as a comparison for
                          fromthewells.                                                 the protocol presented in Margam et al., 2010). During
                       8. DNApellets were washed twice with 200 llof20 °C              this process, we noted an interesting phenomenon follow-
                          70%ethanol(FisherScientific),followedbycentrifuga-             ing the mixing of bee supernatant with isopropanol: the
                          tions as above in step 4 but modified to 10 min per            aggregated protein formed a gelatinous disk at the surface
                          spin, andsupernatantdecanted.                                 of the supernatant rather than as a pellet at the bottom of
                       9. DNApellets were dried for 10 min in a 37 °Cincuba-            the well, once initial NaCl concentrations reached 5 M.
                          tor, then resuspendedin25 llpurifiedwater.                     This resulted in an overall decrease in protein contamina-
                                                                                        tion of the extracted DNA and an easily removable con-
                       DNAquantificationandqualification                                  glomerate during decanting. The BSA control samples
                       Resuspended DNA was analyzed by NanoDrop (Nano-                  fromtheNaClconcentrationserieswereanalyzedforpro-
                       Drop, Willimgton, DE, USA) for absorbance at k = 260/            tein contamination by measuring absorbance at 280 nm,
                                                            1                                                                  1
                       280 nm ratios, dsDNA yield at lg ll     , and protein con-       where1absorbance is equal to 1 mg ml       of protein. The
                                                                    1
                       tamination by absorbance 280 = 1mgml .Statistical                protein contamination sharply decreases as NaCl concen-
                       analyseswereperformedusingJMP8.0(Cary,NC,USA).                   tration increases to 2 M (Figure 1). Bee DNA quantity and
                                                                                        quality measurements following resuspension of the dried
                       PCRamplification                                                  DNA show that the overall DNA yield also decreases
                       Extracted DNA using 6 M NaCl from frozen samples,                somewhat (Figure 2). However, it remains unclear if the
                       either undiluted or diluted in water (1:20) regardless of        260/280 nmabsorbancemeasurementsusedtodetermine
                       yield, wasamplifiedbystandardPCRmethods.A155-base                 extraction efficiency are artificially skewed toward higher
                       segment of honey bee beta-actin was amplified using               DNAyield when protein contamination is high. Regard-
                       primers F-TGCCAACACTGTCCTTTCTG and R-AGA-                        less, the quantity and quality are more than sufficient for
                       ATTGACCCACCAATCCA, then electrophoresed on a                     downstreamPCRtechniques.
                       2%agarosegel,andimaged.
                                                                                        ComparablequantitiesandqualitiesofDNAoffreshorhistorical
                       Statistical analysis                                             tissue samples
                       All statistical analyses were performed using JMP software       Comparisons were made between DNA extractions using
                       (Version 8). A two-way ANOVA, with adjusted least                6 M NaCl on bees frozen for 1 year and freshly collected
                198 Hollowayet al.
                                                                                 A
                                                                    1
                Figure 1 Average( SD;n = 12)proteincontent(mg ml )              B
                remainingafterextracting25 mgofBSAusingaconcentration
                seriesofNaCl[0.5,1,2,3,4,5,6M,and0(water)].
                bees. In addition to whole bees, body segments were
                processed to determine whether the yield and quality
                are dependent on the type of sample. In a tissue-specific
                manner,theextraction protocol yielded comparable DNA
                regardless of the age of the sample (Figure 3); however,
                only in whole bee or abdomen tissues did the disk form,
                float, and easily decant (data not shown). Quantity and
                qualityofDNAextractedinthedifferentsamplesweresig-
                nificantly different across tissue types (ANOVA; DNA
                amount retrieved: whole model, F        = 9.53, P<0.0001;
                                                    4,95
                condition,   F    = 0.0021,    P = 0.96;   body    region,
                              1,95                                               Figure 2 Average( SD;n = 6)quality(solidsymbols)and
                F    = 12.7, P<0.0001; DNA quality retrieved: whole
                 3,95                                                            quantity(opensymbols)ofDNAextractedfrom(A)wholebees
                model, F     = 50.69, P<0.001; condition, F       = 0.988,
                         4,95                                 1,95               and(B)pupaeusingaNaClconcentrationseries.DNAquality
                P = 0.32; body region, F      = 67.27, P<0.0001; protein
                                          3,95                                   remainsrelativelyconstantregardlessoftheNaClconcentration
                contamination: whole model, F         = 2.78, P = 0.032;
                                                  4,85                           usedduringtheextraction,whereasoverallDNAyielddecreases
                condition, F     = 0.11, P = 0.74; body region, F        =
                             1,85                                   3,85         astheNaClconcentrationincreases.
                 3.65, P = 0.015. In all cases, n = 12). Despite the remain-
                ingextraneousproteinintheheadandthoraxsamples,the
                quality and quantity of the extracted DNA is sufficient for       wastes for reagents and consumables, while reducing the
                subsequentPCRapplicationsonlywhendiluted.Thehead                 hazards associated with handling organic solvents. This
                and thorax DNA samples failed (or partially failed) to           protocol essentially uses common, inexpensive, dispos-
                directly amplify and required dilution for successful            able, and non-hazardous chemicals (NaCl, SDS,isopropa-
                amplification (Figure 4A and B), thereby requiring                nol, and ethanol). The price of consumables and reagents
                additional steps and plastic consumables to make such            per 96-well plate of processed DNA is about USD 8.00, or
                dilutions. The extraction from abdomens or whole bees            8.5 ¢ per individual bee [with the majority of the price (ca.
                resulted in relatively low yield, yet highly purified DNA         80%) determined by the plastic consumables], as com-
                such that no dilution step was needed to perform PCR             pared to several dollars per extract with commercial kits.
                (Figure 4CandD).                                                 In addition, sample preparation time is decreased because
                                                                                 wholebeescanbeprocessedasopposedtoindividualbody
                Generalremarks                                                   segments. The protocol presented here employs a modifi-
                We developed a fast, affordable, and eco-friendly DNA            cation to other protocols in that the saturated concentra-
                extractionprotocolforhighthroughputanalysisofmolec-              tionofNaClfunctionstoreduceproteincontaminationto
                ular markers in honeybees. The goal of developing this           negligible amounts. Importantly, this method allows high-
                DNA extraction protocol was to reduce the costs and              throughput 96-well-platform extractions as are necessary
                                                                                                                      HighthroughputDNAextractioninhoneybees                    199
                             A                                                                               A
                                                                                                             B
                                                                                                             C
                                                                                                             D
                             B                                                                               Figure 4 PCRamplificationofa155-bpbeta-actinfragment
                                                                                                             usingDNAextractedusing6 MNaClfromindividualtissue
                                                                                                             sampleseitherdirectlyfromtheresuspendedpellet(sixlaneson
                                                                                                             left) or a 1:20 dilution of the samesamples(sixlanesonright)of
                                                                                                             frozen(A)heads,(B)thoraxes,(C)abdomens,or(D)wholebees.
                                                                                                             Centerlanesare50-bpladder.Theamplifiedbandsalign
                                                                                                             approximatelywiththe150-bpbandoftheladder.
                                                                                                             sufficient to perform downstream standard PCR reactions
                                                                                                             that enable marker analyses such as cleaved amplified
                                                                                                             polymorphisms          (Holloway       et al.,   2013),     amplicon
                                                                                                             sequencing,andcloningwithhoneybeeDNA.
                                                                                                                The quantity of the DNA retrieved is more than suffi-
                             C                                                                               cient for standard practices. A return of >5 lgofDNA
                                                                                                             fromonetotalindividualbeecanbeexpectedthatismore
                                                                                                             than enoughtoperformdozensorhundredsofPCRreac-
                                                                                                             tions. Calculations of the total available DNA present in a
                                                                                                             whole honeybee suggest that this protocol retrieves only a
                                                                                                             portion. Based on the average mass of a nucleotide base-
                                                                                                                                  9               
                                                                                                             pair (1.029 9 10         pg) (Dolezel et al., 2003), the widely
                                                                                                             accepted typical dimensions of a eukaryotic cell (assume
                                                                                                             10-lm-diameter sphere, or ca. 0.5 pl), the diploidy of
                                                                                                             female bees, and the volume of a newly emerged worker
                                                                                                             bee (ca. 100 ll), if the bee were a solid mass of cells (ca.
                                                                                                             800 000 cells) then the total mass of DNA contained
                                                                                                             would be ca. 92 lg, an extremely gross overestimation
                                                                                                             based on the volume of bee that is non-cellularized
                            Figure 3 Thetimefromsamplecollectiontoprocessingdoesnot                          (hemolymph) or proteinaceous (exoskeleton) in nature.
                            affect the (A)overall yield,(B)quality,or(C)purity(protein                       Regardless, the minimum amount of DNA retrieved is
                            contamination)oftheextractedDNAafterpurificationwith6 M                           likely to be at least 5–10% of the total, which is plenty for
                            NaCl.NostatisticaldifferencesinDNAyield,quality,orpurity                         standard PCR use. However, because we did not perform
                            werefoundbetweenfrozen(storedfor1 yearat20 °C)and                               massspectrometryoranyothermeansofpuritymeasure-
                            freshlycollectedsamplesforanyofthetissuetypes(head,thorax,                       ments of the pelleted DNA, we cannot assume that the
                            abdomen,orwholebody).QuantityandqualityofDNA                                     quantity of DNA calculated by the NanoDrop is entirely
                            extractedweresignificantlydifferentacrosstissuetypes;different                    accurateascontaminantsmayalsoaffecttheabsorbanceat
                            letters onbars withinapanelindicatesignificantdifferences                         260 nm used for the determination. Understanding the
                            (Tukey’sHSDtest:P<0.05).                                                         formation of the gelatinous floating disk is beyond the
                            for a growing array of honey bee genetic studies such as                         scope of our research, yet the components of it may be
                            QTLand fine mapping, phylogenetic studies, population                             sequestering some of the DNA that is lost during the
                            studies, and the like. The quality of the DNA retrieved is                       decanting.
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...Doi eea technicalnote aneconomicalandeffectivehigh throughputdna extraction protocol for molecular markeranalysis in honeybees betha holloway matthewr tarver thomase rinderer usdahoneybeebreeding genetics andphysiologylaboratory molecularbiology benhurroad batonrouge la usa accepted may key words apismellifera hymenoptera purication nucleicacid introduction allow consistent and reproducible yields yet can cost several dollars per sample chelating agents purify dna the honeybee is becoming an increasingly important with high quality but require long incubations organism realm of laboratory based as preparations additional proteinase k giraffa et al honey bee health around world declining measures casquet traditional phenol chloro are being taken to understand genetic basis a multi formextractionsrequirehandling storage anddisposalof tudeoftraitsincludingbehavior diseaseresistance surviv hazardous organic solvents has recently ability production pollination efciency beeneffectively extra...

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