GMO Investigator Kit Is your food genetically modified?

2. GMO Investigator KitIs your food genetically modified?

3. GMO Investigator KitInstructors Stan Hitomi Coordinator – Math & Science San Ramon Valley Unified School District Danville, CA Kirk Brown Lead Instructor, Edward Teller Education Center Science Chair, Tracy High School and Delta College, Tracy, CA Sherri Andrews, Ph.D. Curriculum and Training Specialist Bio-Rad Laboratories Essy Levy, M.Sc. Curriculum and Training Specialist Bio-Rad Laboratories

4. Whyteach GMO testing? • Inquiry-based • Real-world test • Environmental Science • Plant Physiology • Genetics and biotechnology • Bioinformatics/Data Mining • Standards-based

6. GMO Investigator Kit Advantages • Extract and amplify DNA from different food samples • Perform genuine diagnostic procedures • Use PCR and electrophoresis to find GMO foods • Sufficient materials for 8 student workstations • Complete the activity in three 45 minute lab sessions • Laboratory extensions: Real-Time PCR

7. GMO Workshop Time Line • Introduction to GM foods • DNA extraction of food products • Set up PCR reactions • Electrophorese PCR products • Analysis and interpretation of results

8. GMO InvestigatorProceduresOverview

9. What is a GMO? "genetically modified organism (GMO)" an organism in which the genetic material has been altered in a way that does not occur naturally by mating and/or natural recombination

10. US Approval for GM food crops • Corn • Soy • Papaya • Canola • Potato • Chicory • Rice • Squash • Sugarbeet • Tomatoes • Approval does not necessarily mean these crops are distributed • Database of GM crops: www.agbios.com Which foods contain GM product?

11. Which foods contain GM product? Sources: 1996-1999 Fernandez and McBride, 2000-2004: USDA, National Agriculture Statistics Service, Acreage.

12. Which foods yield viable plant DNA?

13. Why test for GMO’s? • Legislation • US: food labeled “GM-Free” <5% GM • EU: food labeled “GM” if >1% GM • Japan: food labeled “GM” if >5% • Export • What about unlabeled food?

14. How to test for GMOs ELISA: Test for presence of proteins expressed from genetic modifications Pro: Quick, cheap, low tech Con: Crop specific, protein stability PCR: Test for presence of inserted foreign DNA Pro: ID different GM crops, DNA stability Con: Expensive, timely

15. How to test for GMOs • Test for GMOs by PCR: • Grind food • Extract DNA from sample • Test sample DNA for viable plant DNA • Test sample DNA for genetic modifications

16. Kit Controls • Bio-Rad certified non-GMO food • Verify PCR is not contaminated • GMO positive control DNA • Verify GMO-negative result is not due to PCR reaction not working properly • Primers to universal plant gene(Photosystem II) • Verify viable DNA was extracted

17. Why amplify a plant gene? To confirm that viable DNA was extracted and that negative GM result isn’t due to a non-viable template. Use highly conserved chloroplast gene from Photosystem II – part of the light reaction of photosynthesis.

18. Why use CaMV 35S and NOS? CaMV 35S – Sequence for the promoter of 35S transcript of the Cauliflower mosaic virus. Used because it functions in every plant cell NOS- Sequence fornopaline synthase terminator from soil bacterium Agrobacterium tumefacians Used because it evolved to be recognized in most plants

19. Laboratory Quick Guide

20. Extract DNA from food

21. 50 μl Volumetric Measurements

22. Why these steps? • Grinding food to release DNA • InstaGene chelates divalent ions (e.g. Mg2+) necessary for DNA degrading enzymes (e.g. DNases) • Only 50 μl of food transferred otherwise InstaGene is overwhelmed (~ 5 mg of original material) • Boiling releases DNA from food into the InstaGene solution • Pellet InstaGene and food debris because InstaGene inhibits PCR reaction (Taq needs Mg++) Mg++ Mg++ Mg++ Mg++ Mg++ Mg++ Mg++ Mg++ InstaGene

23. Set up PCR reactions

24. What is needed for PCR? The PCR ReactionWhat do you need? • Template -the DNA to be amplified • Primers -2 short specific pieces of DNA whose sequence flanksthe target sequence • Forward • Reverse • Nucleotides -dATP, dCTP, dGTP, dTTP • Magnesium chloride -enzyme cofactor • Buffer -maintains pH & contains salt • Taq DNA polymerase – thermophillic enzyme from hot springs

25. Polymerase Chain Reaction PCR Animation http://www.bio-rad.com/LifeScience/jobs/2004/04-0522/04-0522_PV92_PCR.html

26. The PCR ReactionHow does it work? Heat (94oC) to denature DNA strands Cool (59oC) to anneal primers to template Warm (72oC) to activate Taq polymerase, which extends primers and replicates DNA Repeat 40 cycles

27. Why have GM crops? • Growing human population • Loss of farmable land • Remediation of soil • Enrich nutrient content

28. Desirable Traits • Pest Resistance • Herbicide Tolerance • Viral Resistance • Drought Resistance • Increased Nutritional Value • Improved Fruit • Altered Ripening

29. Opponents argue • Creation of super pests • Creation of super weeds • Loss of biodiversity • Biotechnology companies control agriculture • Health concerns

30. Method for Genetic Modification of Crops • Choose desirable trait • Clone the gene • Engineer the gene • Transform gene into plant • Backcross GM plant into high yield crops

31. Choose desirable trait • Pest Resistance: Bt crops • Bacillus thuringiensis protein is a delta endotoxin kills corn borers • HerbicideTolerance: Round Up Ready crops • Agrobacterium tumifaciens protein with resistance to Round Up herbicide (glyphosate) Bacillus thuringiensis Delta endotoxin crystal

32. Bacillus thuringiensis Clone the gene Delta endotoxin crystal Bt gene ori Ti plasmid Ti genes

33. GO STOP Engineer the gene Bt gene ori Ti plasmid Ti genes Antibiotic resistance

34. Transform gene into plant Isolate plant cells Grow undifferentiated callus Transform cells Select cells Grow transgenic plant Redifferentiate callus

35. Backcross GM plant into high yield crops YYgg x yyGG YyGg YYgG YygG YYgg Yygg YYgg x YyGg GM plant = yyGG High yield plant = YYgg YYgG YYgg YYGg YYGG YYgG x YYgG

36. 1: non-GMO food with plant primers 2: non-GMO food with GMO primers 3. Test food with plant primers 4: Test food with GMO primers 5: GMO positive template with plant primers 6: GMO positive template with GMO primers 7: PCR MW Ruler 1 2 3 4 5 6 7 Analysis of Results GMO positive 1 2 3 4 5 6 7 GMO negative

37. GMO Investigator KitLab Extensions • Independent studies • Data Mining/Bioinformatics for specific genes • E.g. Design primers to the cry genes in Bt corn • Quantitative Real-Time PCR

38. Trouble shooting • False Positives • Contamination-sterile technique; 10% bleach to clean pipette barrels, mortars & pestles, bench tops; barrier tips for all steps. • False Negatives • No DNA extracted • Possible food type or possibly primers do not work on that plant species • InstaGene matrix transferred to PCR reactions

39. GMO Investigator Kit Contents • Bio-Rad certified Non-GMO food • InstaGene • Master Mix • GMO primers • Plant PSII primers • GMO & PSII positive control DNA • PCR MW Ruler • DPTPs, microtubes, PCR tubes, foam floats • Manual • Not Included but required: • Thermal cycler • Water bath/heat block • Electrophoresis Module (agarose, TAE buffer & Fast Blast DNA stain) • Electrophoresis equipment & power supply • 2-20 ul pipettes & barrier tips