Item 7. SAMPLING AND LMOs DETECTION 7.3. IDENTIFICATION OF LMOs Detection is required when: • By law in the country is required identification and/or labelling • Mixtures between GMOs + non-GMOs • Need to export to a country with strict legislation • Need to verify non-GMOs shipments • For environmental risk verifications In the international market • Important focus differences between commercial blocks: – USA does not require identification and GM crops are easily set free into the environment – EU requires labelling with 0.9% treshold “Historical” cans of GM tomato puree with long shelf life • First GM-food authorized 1994 • They were labelled… and people bought them!!! • The variety lost sensory characteristics and was retired from the market Extraction of: Sampling Immunostrips ELISA plates Protein PCR end point DNA RTq-PCR In order to detect proteins, specific antibodies are required. The antibodies are proteins with quaternary structure. Lateral flow test, IMMUNOSTRIP Control line. Antibodies antiIgG adsorbed Antibodies anti-antigen conjugated with enzyme Test line. Antibodies antiantigen adsorbed Lateral Flow test, IMMUNOSTRIP The antibodies are binded to their antigen in the sample and the complex antigen-antibody moves by capillarity towards the reaction lines. Lateral Flow test, IMMUNOSTRIP Antigen binds to the antibodies that are in the test line. Free antibodies bind to the antibodies anti-Ig present in the control line. Immunostrip procedure 1. Weigh 250 mg of fresh leaf (plantlet) 2. Insert the sample in the bag 3. Grind or crush the sample 5. Let stand for 10 minutes (vertical position) 4. Insert the immunostrip into the bag with SEB or MEB buffer. 6. Read results Qualitative immunoassay in strip. Ej. Cry9C QuickStixTM Envirologix Also by this technique can be detected CP4-EPSPS protein in samples with low % of transgenic maize IMMUNOSTRIP CP4 EPSPS IMMUNOSTRIP Cry 1Ab/Ac Maíz NK603 Maíz BT 11 10% 1% 0.1% 0.05 % 10% 1% 0.5 % 0.1 % ELISA: Enzyme-Linked-ImmunoSorbent Assay Format: DAS (Double Antibody Sandwich) The first Ac is adsorbed to the plate ELISA: Enzyme-Linked-ImmunoSorbent Assay Formato: DAS (Double Antibody Sandwich) Sample that contains protein is added Protein ELISA: Enzyme-Linked-ImmunoSorbent Assay Format: DAS (Double Antibody Sandwich) Second antibody is added. It is conjugated with a enzyme Enzyme Antibody ELISA: Enzyme-Linked-ImmunoSorbent Assay Formato: DAS (Double Antibody Sandwich) Colorless compound Product Colorless Product compound Enzyme Antibody ELISA plate, second antibody congujated to alkaline phospatase Quantitative Immunoassay (ELISA) Centrifugation to clarify samples Sample extraction. Preparation of ELISA plates ELISA cont. Incubation at room temperature Sample application Wash Substrate addition/ Colour development Spectrophotometric measurement - for quantification- Specificity assesment of antibodies in the ELISA test 1 2 3 A MEB Cry 1Ab/1Ac NK 603 B MEB Cry 1Ab/1Ac NK 603 C CP4 Cry 3A Bt 11 D CP4 Cry 3A Bt 11 E NPT II Cry 3Bb1 MON 810 F NPT II Cry 3Bb1 MON 810 G Cry 2A Cry 1C Chalqueño H Cry 2A Cry 1C Chalqueño KIT Cry 1Ab/1Ac KIT CP4 EPSPS 1 2 3 1 2 3 A B C D E F G H A B C D E F G H Quantitative Analysis by ELISA in detection of protein CP4-EPSPS 1 1 2 3 4 5 A A MEB 0.125 % B MEB 0.125 % Mon810 10% Nk603 10% Bt11 10% C 1% 0.062 % Mon810 1% Nk603 1% Bt11 1% C D 1% 0.062 % Mon810 1% Nk603 1% Bt11 1% D E 0.5% 0.031 % Mon810 0.1% Nk603 0.1% Bt11 0.1% F 0.5% G H Mon810 10% Nk603 10% Bt11 10% 0.031 % Mon810 0.1% Nk603 0.1% Bt11 0.1% Control 0.25% 0.015 % Chalqueño MEB Negativo Control 0.25% 0.015 % Chalqueño MEB Negativo B E F G H 2 3 4 5 Detection thresholds of three transgenic maize events CP4-EPSPS protein can be detected with high sensitivity in mixtures with low percentage of transgenic maize. Sensitivity for detection of CRY proteins is much lower. Considerations: Immunochemical methods • Immunochemical methods can be realized in fast ways, in situ, or in laboratory, few equipment is required. • Strip based methods are only qualitative. • ELISA can be quantitative but: – Different levels of protein expression are reflected in different sensitivity levels – No reference materials recognized. – No agreement between quantification units (% in weight or protein concentration) PCR principles Double chain opening (~90°C) –denaturation Primers that recognize specific sequences (50- 60°C) Synthesis of template complementary chains (74°C) 3’ 5’ 5’ 3’ Sequence of interest 3’ 5’ 5’ Synthesis of one copy 3’ Taq polymerase Amplification: Sequence of interest Taq Taq Amplification Taq Taq Number of PCR cycles 0 1 2 3 4 5 6 7 8 9 10 20 30 40 Number of DNA molecules 1 2 4 8 16 32 64 128 256 512 1024 1,000,000 1,000,000,000 1,000,000,000,000 Theoretical PCR products Real Cycle number Factors to consider • Specificity – primer design • Product length (DNA amplified fragment) • There are differences between qualitative and quantitative tests • Whether PCR is uniplex or multiplex • If the method is specific for a type of instrument Primer design P E G 1. Exploration 2. Gene specific target 3. Specific construct 4. Event specific target H P E G T Host genomic DNA Promoter element (CaMV 35S) Amplifying element Gene of interest (Cry, EPSPS) Terminator (NOS) T H LOW Target specificity H HIGH PCR for transgenic sequence detection Recombinant Gene 1 A 2 3 4 B 5 C Amplicons D DNA of GM grains Genomic DNA Recombinant gene Specific-specie primers recognize genomic DNA DNA of non-GM grains Genomic DNA Specific-GMO primers do not interact No amplification Intrinsic factors of the sample that affect the amplification • Integrity of template DNA – Size of the amplicon • Presence of inhibitory substances – Humic substances – Proteins Others: – EDTA – NaOH – SDS and other detergents A 1 2 3 4 5 6 7 8 2000 bp 1000 bp 1 Ladder 2A Seeds B 1500 bp 500 bp Load: 100ng Dye: SYBR Green 2B Commercial nixtamal flour 1 2 3 4 5 6 7 8 3 4 5 6 7 8 Dough Nixtamal flour Tortilla Tortilla chips Corn chips Dry Corn chips DNA Extraction • Extraction yield – Tissue • DNA purity • Quality for amplification Amplification – effect of the purity of the DNA template A M S E HJ HJS HM HMS Es P C- 225 pb C C- M HM HMS HJ HJS S E P B C- M HM HMS HJ HJS S E Es P 225 pb 225 pb Amplification of a fragment of the Invertase gene. Limit of Detection MON810 B M 10 1 0.1 C-1 C-2 C-3 C-4 300 pb 100 pb Detection of the specific event MON810 in different proportions (10%, 1% y 0.1%). C-1, negative control with BT11 maize seed DNA 100% transgenic; C-2, negative control with NK603 maize seed genomic DNA; C-3, negative control with chalqueño maize seed DNA; C-4, negative control without DNA. M, 50 bp ladder. Identity verification: Restriction analysis Amplicons of CamV35S promoter and restriction products with Asp700. Lane 1: 50bp ladder, lanes 2 and 3: Bt176 control, lanes 4 and 5: canned corn grains, in 2% agarose gel. Quantitative PCR qPCR – RTQ-PCR PCR products 100 10 2 1 0.1 0.01 Cycle number Ct m=-3.32 Log conc. Ct = number of cycles needed for the amplification signal to be statistically different from the background signal Number of PCR cycles Number of DNA molecules 1 2 3 2 4 8 21 22 23 10 2 3.32 16 32 64 128 24 ... ... ... 4 5 6 7 Lineal dynamic range Efficiency (-1/m) Efficiency = ([10 ]-1) * 100 Results are accepted when the efficiency is higher than 95% (m = 3.45 a 3.3) More common system probes Some results in PCR real time Specificity of primers and probes designed for RTQ-PCR Maíze % GM O Primers and Probes Bt11 Primers and Probe MON810 Primers and Probe Promoter 35S CaMV Primers and Probe Endogenous gene No. muestras/ reacciones positivas Promedi o de Ct No. muestras/ reacciones positivas Promedio de Ct No. muestras/ reacciones positivas Promedio de Ct No. muestras/ reacciones positivas Promedio de Ct Bt11 10 3/3 29.2+0.1 0/3 - 8/8 26.1+0.2 10/10 23+0.33 MON810 10 0/3 37.9 * 6/6 27.4+0.1 5/5 26.4+0.1 10/10 22.9+0.5 NK603 10 0/3 39.8+0.5 * 0/3 - 4/4 25.7+0.2 6/6 23+0.16 Chalqueño 0 0/3 - 0/3 - 0/6 35.9+0.3* 10/10 23+0.42 NTC - 0/3 - 0/3 - 0/4 - 0/10 - Effect of the extraction system Figure 26. Standard curves of the events MON810 y Bt11 from DNA extracted with the commercial systems A, B and C. 1, curve of the event Bt11 with extraction system A. 2, curve of the event MON810 with extraction system A. 3, curve of the event MON810 with extraction system B. 4, curve of the event Bt11 with extraction system B. 5, curve of the event Bt11 with extraction system C. 6, curve of the event MON810 with extraction system C. A B C D E F G H Figure 27. Amplification curves generated with 100% transgenic DNA from event MON810, extracted with the system B. A, 20 ng. B, 10 ng. C, 5 ng. D, 2.5 ng. E, 1.25 ng. F, 0.625 ng. G, 0.313 ng. H, 0.156 ng. Figure 29. Amplification curves generated with 100% transgenic DNA of the event MON810, extracted with the system A. Serial dilutions were performed however, the amplification generated with each dilution does not allow to clearly establish to each curve the initial DNA concentration. Effect of the extraction method over the quantification Mixture of MON810 (%) B Extraction method C A 10 1 0.1 11.48 + 0.327 0.91 + 0.186 0.11 + 0.032 16.15 + 1.118 2.11 + 0.154 0.12 + 0.016 13.96 + 0.140 Without amplification Without amplification Effect of the primers and probes design Linearization Data Kit comercial OGMs Transgene Diseño Endogenous Gene Kit comercial OGMs Diseño Curve with event Slope Intercept R2 Efficiency (%) Bt11 -3.537 28.253 0.999 91.7 MON810 -3.375 29.712 0.999 97.8 NK603 -3.836 30.512 0.999 82.3 Bt11 -3.382 27.673 0.998 97.5 MON810 -3.326 28.411 0.998 99.8 NK603 -3.429 29.592 0.992 95.7 Bt11 -3.685 29.003 0.993 86.8 MON810 -3.516 29.466 0.996 92.5 NK603 -3.731 30.187 0.985 85.4 Bt11 -3.111 28.593 0.997 109.6 MON810 -3.326 28.228 0.995 99.8 NK603 -3.193 29.103 0.995 105.7 Sybr green A B First negative derivate of the dissociation curves of Amplicons obtained for A. MON810 and B. endogenous gene Non-specific amplification Effect of the DNA quality over Sybr green quantification Mixture of MON810 (%) Extraction method 10 1 0.1 B 10.3±0.007 1.1±0.021 0.25±0.006 C 10.8±0.018 2.3±0.017 0.10±0.077 A 48.5±0.157 53.8±0.149 0.03±0.011 Other example: • Detection of transgenic maize in processed foods: – Nixtamal Flour – Dough – Tortilla – Fried tortilla (tostada) – Fried dough M. Quirasco, B. Schoel, J. Plasencia, J. Fagan & A. Gálvez. 2004. Suitability of RTQ-PCR and ELISA for Cry9C detection in Mexican corn tortillas: fate of DNA and protein after alkaline cooking. Journal of AOAC International. 87:639-646 A 1 2 3 4 5 6 7 8 2000 bp 1000 bp 1 Ladder 2A Semillas B 1500 bp 500 bp Carga: 100ng Tinción: SYBR Green 1 2 3 4 5 6 7 8 2B Harina de nixtamal comercial 3 Masa 4 Harina de nixtamal 5 Tortilla 6 Tortilla frita 7 Masa frita 8 Masa seca frita Content of GMO, determined by RTQ-PCR, in different nixtamalized products prepared with white maize non – transgenic and different percentages of StarLinkTM . StarLinkTM 0.1% (w/w) Sample Granos de maíz Masa Media, % (w/w) 0.19 RSD CV, % 0.018 9.3 0.10 0.005 4.8 Harina de nixtamal Tortilla 0.10 0.001 0.7 0.31 0.004 1.4 Tortilla chip Corn chip ND - - 0.10 0.002 1.5 Corn chip secos ND - ND = No detectado StarLinkTM 1% (w/w) Sample RSD CV, % 0.121 9.8 1.16 0.002 0.2 Harina de nixtamal Tortilla 1.03 0.016 1.5 1.41 0.015 1.0 Tortilla chip Corn chip 0.52 0.001 0.3 1.16 0.023 2.0 0.079 12.4 Granos de maíz Masa Corn chip secos Media , % (w/w) 1.23 0.63 StarLinkTM 10% (w/w) Sample RSD CV, % 0.166 1.2 12.64 0.090 0.7 Harina de nixtamal Tortilla 9.35 0.017 0.2 9.47 0.254 2.7 Tortilla chip Corn chip 6.64 0.175 2.6 14.29 0.119 0.8 0.053 0.6 Granos de maíz Masa Corn chip secos Media, % (w/w) 14.12 8.28 LOD = Limit of Detection =.01% en RTq-PCR LOQ = Limit of Quantification = 0.1% en RTq-PCR Immunochemical methods are adequate to detect the protein in grains and materials without too much processing Protein DNA Seed Primary Processed ingredient foods Highly processed foods ... However DNA can be detected in highly processed foods Sampling Pre-treatment GenScan Halving 1 Halving 2 Composite samples “ 1 2 UNAM 3 Detection and cuantification of exogenous DNA by RTQ-PCR ELISA p35S Detection of authorized and unauthorized transgenic events in Mexico by RTQ-PCR Heterologous protein detection Event Specific Immunostrips Results Cd. Juárez Piedras Negras Nuevo Laredo Matamoros Altamira Customs where maize samples were obtained Veracruz 430 Veracruz Centro Coatzacoalcos 1) 2) 3) 4) Subsampling by dividing into four parts (“halving”) Food authorization status of GM varieties of maize TRANSFORMATION EVENT Authorized in Mexico U.S.A. Europe MON-00021-9 (GA21) Yes Yes Yes MON-00603-6 (NK603) Yes Yes Yes MON-00810-6 (MON810) Yes Yes Yes DAS-01507-1 (TC1507) Yes Yes Yes MON-00863-5 (MON863) Yes Yes Yes DAS-59122-7 Yes Yes Yes MON-88017-3 (MON88017) Yes Yes No ACS–ZM002-1 / ACS-ZM003-2 (T14, T25) Yes Yes Yes SYN-BTØ11-1 (BT11 (X4334CBR, X4734CBR)) Yes * Yes Yes REN-00038-3 (LY038) Yes * Yes No SYN-IR604-5 (MIR604) Yes * Yes No * vents Approved in october of 2007 Immunological methods commercially available for heterologous protein detection ELISA • CP4-EPSPS (RR) • Cry3Bb1 • Cry1Ab/1Ac • Cry1F Immunostrips • CP4-EPSPS (RR) • Cry3Bb1 • Cry1Ab/1Ac • Cry1F • Cry34Ab1 • Cry9C • PAT Possible presence of transgenic events by immunoassay (ELISA + strips) Protein Port 1 Port 2 Port 3 Poprt 4 Port 5 Port 6 Port 7 Port 8 Cry1Ab/Ac MON810 Bt11 MON80100* MON802* MON809* MON810 Bt11 MON80100* MON802* MON809* MON810 Bt11 MON80100* MON802* MON809* DBT418** MON810 Bt11 MON80100* MON802* MON809* MON810 Bt11 MON80100* MON802* MON809* DBT418** MON810 Bt11 MON80100* MON802* MON809* DBT418 ** MON810 Bt11 MON80100* MON802* MON809* MON810 Bt11 MON80100* MON802* MON809* Cry3Bb1 MON88017 MON863 MON88017 MON863 MON88017 MON863 MON88017 MON863 MON88017 MON863 MON88017 MON863 MON88017 MON863 N/D Cry1F DAS01507 DAS01507 DAS01507 DAS06275 *** DAS01507 DAS01507 DAS06275*** DAS01507 DAS06275 *** DAS01507 DAS01507 Cry34Ab1 DAS59122 DAS59122 DAS59122 DAS59122 DAS59122 DAS59122 DAS59122 ND ND ND ND ND ND ND ND NK603 MON88017 MON80100* MON802* MON809* NK603 MON88017 MON80100* MON802* MON809* NK603 MON88017 MON80100* MON802* MON809* NK603 MON88017 MON80100* MON802* MON809* NK603 MON88017 MON80100* MON802* MON809* NK603 MON88017 MON80100* MON802* MON809* NK603 MON88017 MON80100* MON802* MON809* NK603 MON88017 MON80100* MON802* MON809* ND MON863 DAS59122 T14/T25 DAS06275*** DBT418** MS6 ND MON863 DAS59122 T14/T25 DAS-06275*** DBT418** MS6 MON863 DAS59122 T14/T25 DAS06275*** DBT418** MS6 ND ND Cry9C CP4EPSP S PAT† ND ND, non detected protein * Events not containing Cry1Ab/Ac + CP4EPSPS ** Event containing Cry1Ab/Ac + PAT *** Event containing Cry1F + PAT † StarLink contains Cry9C + PAT. Cry9C not detected, its presence is discarded in PAT positive samples Potential presence of MON80100 y MON809 because they were not commercialized. DNA verification required. Specific presence of transgenic events in maize grains, by RTQ-PCR Event MON810 T25 GA21 NK603 DAS-01507-1 MON863 MON88017 DAS-59122-7 Third party analysis (Gene Scan) • Confirmed the results obtained in Lab. 312, Dept. of Food Science and Biotecnhnology, Faculty of Chemistry, UNAM • Confirmed the absence of the eventMON88017 “Possible” events are discarded • Immunodetection is insufficient for specific-event detection. • Do not encompass the totality of authorized events (GA21), as well as nonauthorized ones (676/678/680, DLL25, LY038, MIR604, MS3 y MS6) • By PCR was confirmed the presence of MON810, MON862, DAS01507, DAS59122 and NK603 • It was also discarded the presence of MON88017, possible event according to the immunodetection. • Technological development is needed for the detection of possible unauthorized events. 60 50 40 % 30 20 10 0 Events Customs Quantification (RTQ-PCR) of transgenic events authorized in Mexico prior to may 2007* * Bt11 y LY038 approved in july andy MIR604 in october of 2007 140 120 100 % 80 60 40 20 0 C Aduana ua ah u hi h i la hu a Co as l ip u ma Ta Estado uz rac e V e o rt N a n Fro ter d lfo o G o ic éx M e Región Total content (%) of GM material in each one of the analyzed samples “Stacked” varieties of Maize Event 1 x Event 2 ACS-ZMØØ3-2 x MON-ØØ81Ø-6 DAS-59122-7 x NK603 DAS-59122-7 x TC1507 DAS-Ø15Ø7-1 x MON-ØØ6Ø3-6 BT11 x MIR604 BT11 x MIR604 MON-ØØ6Ø3-6 x MON-ØØ81Ø-6 MON-ØØ81Ø-6 x LY038 MON-ØØ863-5 x MON-ØØ6Ø3-6 MON-ØØ863-5 x MON-ØØ81Ø-6 MON-ØØ863-5 x MON-ØØ81Ø-6 MON-ØØØ21-9 x MON-ØØ81Ø-6 MON89034 x MON88017 MON8903 x NK603 SYN-BTØ11-1 x MON-ØØØ21-9 TC1507 x DAS-59122-7 MIR604 x GA21 MON810 x MON88017 x Event 3 x NK603 x GA21 x MON-ØØ6Ø3-6 Copia 1 ADN Copia 2 ADN Copia 3 ADN Copia 4 ADN Copia 5 ADN Evento “Stack” DAS59122-7 x 100% NK603 100% 200% ? Copia 1 ADN Copia 2 ADN Copia 3 ADN Copia 4 ADN Copia 5 ADN Evento “Stack” DAS59122-7 x 80% NK603 100% 180% ? Copia 1 ADN (No-GM) Copia 2 ADN Copia 3 ADN Copia 4 ADN Copia 5 ADN Evento “Stack” DAS59122-7 x 80% NK603 80% 160% ? Normalizing genes from developers´ certified methods* • MON810: hmg (high mobility group) • MON863: adh (alcohol dehydrogenase) • NK603: adh (alcohol dehydrogenase) * Only recomended gene Use of normalizing gene in tests performed in the laboratory: RT-PCR • % OGM = (transgene/normalizing gene) x 100 • MON810 with hmg • MON810 with adh 15.25 x 100 = 43.8 34.84 15.25 x 100 = 23.1 66.01 • If the amount of endogenous gene increases (denominator), the amount of GMO will be underestimated. 90 80 70 1 2 60 3 % 50 4 40 5 6 30 7 20 8 10 0 hmg adh MON810 hmg adh MON863 hmg adh NK603 Quantification of three events using two different normalizing • adh could be present in the genome of the maize in more than one copy. • Quantification with adh could underestimate the results 140 120 100 Eventos 80 p35S % 60 40 20 8 7 6 5 4 3 2 1 0 Quantification of GM material (total) according to specific events or promoter 35S Hipotesis about the diferent quantification of the endogenous gene • Poor characterization of the endogenous gene (number of copies in the genomic DNA not specified) • Sequences of primers or probes provided by the developer are not specific enough • Low astringency PCR programme • ¿Which endogenous gene should choose? • ¿Differences between cultivars? Conclusions • Exists a high income of GM material in the analyzed customs. • The most abundant events were: MON810 > NK603 > DAS1507-1 • The presence of “stacked” variety makes more complex the transgenic material quantification. • Standardization is required (at international level) regarding which normalizing genes should be used. • An inter- governmental information exchange system is required in order to harmonize maize commerce between the USA and Mexico • The event MON88017 (authorized variety) was not detected Abraham Acatzi1 Javier Magaña1 Carlos Moles2 Carolina Peña2 Marcela Castillo2 Maricarmen Quirasco1 Javier Plasencia3 Marcelo Signorini4 Amanda Gálvez1, 2 1 Programa Universitario de Alimentos. PUAL-UNAM Dept. Alimentos y Biotecnología. Facultad de Química. Universidad Nacional Autónoma de México (UNAM) 3 Dept. Bioquímica. Facultad de Química. UNAM 4 Comisión Federal para la Protección contra Riesgos Sanitarios. Secretaría de SALUD 2