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PCR Detection of GMOs 1 PCR Detection of GMOs (Genetically Modified Organisms) Ashley Pan Shiwei Sun, Darrell Harvey, Nader Mehregani Biology 210A San Diego Mesa College 5/13/15

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Page 1: PCR Detection of GMOs (Genetically Modified Organisms ...€¦ · Polymerase Chain Reaction is the second method to determine if a food is a GMO or a non-GMO. Instead of using antibodies

PCR Detection of GMOs 1

PCR Detection of GMOs (Genetically Modified Organisms)

Ashley Pan

Shiwei Sun, Darrell Harvey, Nader Mehregani

Biology 210A

San Diego Mesa College

5/13/15

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PCR Detection of GMOs 2

Abstract (5 points):

To find if an organism is genetically modified, PCR testing was conducted in three

separate experiments: Isolation of genomic DNA, amplification of target sequence using PCR,

and analysis of PCR products using gel electrophoresis. The test sample, fresh corn, is predicted

to be genetically modified. If the sample is a GMO, then a 200 bp band will appear in lane four

of the gel. After conclusive testing, there was no band at 200 bp, but there was evidence of

primer dimers, which means the test sample cannot be identified as GMO or a non-GMO.

Introduction/Background/Scientific Concepts (10 points):

Genetically Modified Organisms (GMOs) are often the center of controversy in the world

of agriculture. From changing the genetic makeup of organisms unnaturally without genetic

recombination or mating, these new hybrid plants are created to withstand harsh climate changes,

pesticides, or even add nutritional value to plants. This way, farmers can grow crops without

worrying if they will survive certain seasons or not. On the other hand, some argue that these

GMOs are unknown and possibly detrimental to humans since they are chemically synthesized in

a laboratory and are not “natural.”

Since around 1996 and afterwards, GM foods have reached “67.7 million hectares in

2003” (Ag Biotech). The United States has grown the most amount of GMOs, with 63% of its

crops being genetically modified. Argentina comes second with 21%, Canada with 6%, and

Brazil with 4% of its crops classified as genetically modified.

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PCR Detection of GMOs 3

Compared to the rest of the world, the United States is more lax when it comes to

mentioning what has been genetically modified and what is not. Corn, soybean, cotton, and

canola are the most commonly grown GMO plants GMO positive plants (Noga 3). Often plants

are GMOs to be its own pesticide and being able to produce its own toxin to kill off insects that

try and eat it. People have argued that allergic reactions to these new substances can create new

detrimental diseases with adverse effects. Supporters of GMOs have said that GMOs can “reduce

the stress on land” by modifying them to be grown in any kind of environment.

Two methods are used to find if a food is a GMO or a non-GMO. One method is called

enzyme-linked immunosorbent assay, or ELIZA. This method includes finding proteins that are

made by GMO crops with particular antibodies. Unfortunately, since this so specific to a certain

plant, it cannot be used to test anything but fresh produce since the proteins inside could have

been destroyed through factory processing. On the bright side, ELIZA is a simple process that

can be used in the field. This means that the process is also inexpensive.

Polymerase Chain Reaction is the second method to determine if a food is a GMO or a

non-GMO. Instead of using antibodies to determine if the food is a GMO or a non-GMO, PCR

looks at sequences of DNA. This means that this method can be used for 85% of plants as well as

some processed foods since DNA is a constant for each individual plant. Sequences such as a

stop and start are used to control DNA sequences. These promoter and terminator sequences

allow certain genes to be expressed. The 35S promoter from cauliflower mosaic virus and the

nopaline synthase (NOS) terminator from Agrobacterium tumefaciens are the two most common

regulatory sequences and will be used in this experiment to identify if the test sample is a GMO

or a non-GMO food.

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PCR Detection of GMOs 4

In this lab, it is important to use a sample that is fresh produce. Even though the PCR test

can be used to find GMOs, it will produce more definite bands with the gel electrophoresis

process. Corn and wheat products are more likely GMOs because they are produced in such large

quantities. Day One of this lab will be to extract the DNA from the two samples, the certified

non-GMO and the test sample. DNA isolation is necessary because this helps the PCR react

“target and amplify a specific sequence” (Day One lecture). The non-GMO sample should be

prepared first to ensure that it stays pure from the test sample in case the test sample is a GMO.

It is important to thoroughly clean the mortar and pestle after the grinding the non-GMO sample

to ensure that each sample is contained. Keep tubes closed unless needed and make sure work

surfaces stay clean.

Grinding the samples is important to the lab to extract the cells for the experiment. To

help grind the samples, DNase- and RNase- free water is needed to help grind the sample. This

special type of water is used to prevent DNases (harmful enzymes) from degrading the extracted

DNA. These samples will then be put into a solution with InstaGene matrix. InstaGene matrix

has negatively-charged microscopic beads that attach to positive cations to stop them from

binding with enzymes. This helps the sample stay intact and prevent denaturing. After

stabilization, the samples can be denatured by boiling to neutralize the DNases.

The samples will then be removed from the water bath and then put into a centrifuge.

This is so the heavier pellet will be separated from the supernatant and will sink to the bottom of

the tube. The supernatant contains the DNA needed for Day Two while the pellet contains the

InstaGene matrix beads to stop the denaturation process.

Day Two of the lab entails the PCR amplification of the lab because it can be used for

85% of plants to test whether or not they are GMOs are non-GMOs. By identifying a specific

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PCR Detection of GMOs 5

sequence of DNA and replicating or “amplifying” the sequence, the process can take a small

amount of DNA and analyze the DNA on a larger spectrum. To do this, primers are needed to

“amplify” the sequence for replication. A forward and reverse primer are used to start and stop

DNA sequences and bind on complementary DNA sequences for these primers. After, the

complementary strands are copied by DNA polymerase from reading those strands, the target

sequence can then be used to read the template DNA and “add nucleotides to the 3’ ends of the

primers” (Day 2 Lecture).

Taq DNA polymerase is used because it is a thermostable DNA polymerase that can

protect the DNA’s integrity after the double-stranded DNA is separated from heating. Specific

primers, such as CaMV promote, NOS terminator, and PSII gene are used to control which

sections are needed for the target sequence for the experiment. CaMV 35S is used in the

experiment because it is found in every plant cell while NOS terminator is used because it is

“evolved to be recognized in most plants” (Biotechnology Explorer). PS II is tested to make sure

that the sample is plant based since plants undergo photosynthesis to grow. The size of the PCR

that results is much longer than the initial sequence since the process of PCR amplifies the

sequence for better observation.

PCR has three steps: denaturing, annealing, and elongation. During denaturing, the DNA

is denatured into two single strands after being heated in a water bath of 94 degrees C. DNA is

then cooled to 59 degrees C to let the primers anneal, or bond to the DNA. The primers will bond

faster to the template DNA because they are shorter than the original template DNA. The third

step is to heat the samples to 72 degrees C which lets the DNA polymerase to thrive while

allowing the DNA polymerase to add nucleotides at the 3’ end of the primer. This elongates the

3’ strand of the DNA for a complementary copy. This one cycle is then repeated around forty

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PCR Detection of GMOs 6

times with a thermal cycler (PCR machine). The aluminum block inside the machine allows the

sample to be heated and cooled to allow the reaction to happen multiple times to replicate the

DNA. That way, gel electrophoresis can be used to actually see this amplification.

The master mixes used in Day Three of the lab are used as controls. The Plant Master

Mix (PPM) has plant primers to make sure that the sample used is of plant origin. The GMO

Master Mix has GM primers in it which can be used to check if the sample truly is a GMO or

non-GMO. To test the samples, an agarose gel plate must be made. A 1.5% agarose gel is used in

this part of the experiment because it is a gel that is less permeable to the samples. This creates

resistance to the bands that are created from the electric current making them easier to see with

their definition, by separating the bands more evenly. The gel as an agent to let the samples run

through it and to “paint a picture” of what the sample is. To actually see the bands, Ethidium

Bromide (EtBr) must be mixed into the melted agarose gel mix. This is so when the gel is

stained, and when put under a UV light, the bands will be fluorescent to determine how far the

sample traveled, allowing the sample to be identified as a non-GMO or a GMO. The UV light is

needed because the EtBr is visible in only UV light. Orange G dye is added to each sample as a

marker for each sample to appear on the gel. To be able to compare each marker, a molecular

weight ruler (DNA standard) is also added to each sample along with the Orange G dye to see

whether the PCR samples are supposed to be the correct size. In this lab, the ruler has 1000, 700,

500, 200, and 100 bp.

If the test sample is genetically modified, it will give a positive result with both primers

because the test sample is both a plant and genetically modified. If the sample is not genetically

modified, then the sample should have a positive reading for the plant primer, but a negative with

the GMO primer, denoted with a band at 200 bp. Considering that the test sample is corn, it is

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PCR Detection of GMOs 7

most likely genetically modified because it is produced in such large quantities and corn is used

in many products such as cornmeal or feed for animals.

Materials and Methods (5 points):

Materials Day 1:

-2 screwcap tubes with 500 uL InstaGene matrix

-DNase- and RNase- free distilled water

-Plant based food samples

-Non-GMO control sample

-Clean knife to cut larger food sample

-Balance and weigh boats

-Disposable plastic transfer pipets

-Mortar and pestle

-Marker

-Mini centrifuge

-Water bath (around 95-100 degrees C)

-Micro centrifuge

-Floating micro centrifuge tube holder

Methods Day 1:

Before starting, check to see if the InsteGene matrix in the micro test tube is thawed out

and on ice. Take two screw cap tubes and label one “non-GMO” and the other “test” with the

table number.

Testing the non-GMO:

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PCR Detection of GMOs 8

Weigh out 0.5g of the GMO-free oatmeal as the “certified non-GMO” control on a

weighing boat. Pour the oatmeal into a clean mortar. With a disposable plastic pipet, add 2.5 mL

DNAase- and RNase- free water to the mortar. Grind the sample with the DNAse- and RNase-

free water until a “slurry” is made. Add an extra 5 mL of the DNAse- and RNase- free water to

the mortar and again mix well until the mixture can be pipetted. Add 50 uL of the slurry to the

screwcap tube labeled “non-GMO” with the same transfer pipet in the last step. Cap the tube and

shake well.

Testing the Sample:

From the previous sample, make sure to clean and dry the mortar well before starting this

part of the experiment. Weigh out 0.5g of the test food on a weighing boat. Transfer sample to a

clean mortar. Using a clean transfer pipet, add 2.5 mL of DNase- and RNase- free water to the

mortar. Grind with a pestle until a “slurry” forms. Add another 5 mL of DNase- and RNase- free

water to the mortar until the mixture can be pipetted. Add 50 uL of the slurry to the other

screwcap container with the InsteGene matrix labeled “test” with the same transfer pipet in the

last step. Cap the tube and shake well. Wash the mortar and pestle with 10% bleach to disinfect

it.

Processing Both Samples:

Place the two screwcap tubes (the non-GMO and the test tubes) into a floating rack and

gently place into a water bath set at 95 degrees C for five minutes. Remove the rack with the test

tubes from the water bath after five minutes and then place into a balanced mini centrifuge and

spin for five minutes on maximum speed. Remove tubes from the centrifuge and store tubes in

the freezer or refrigerator until Day Two.

Materials Day 2:

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PCR Detection of GMOs 9

-Micro centrifuge

-Ice bath

-GMO master mix (red tube on ice)

-Plant master mix (green tube on ice)

-GMO positive control DNA (clear tube on ice)

-Test food DNA (from Day 1)

-6 PCR tubes

-Sharpie

-2 (20 ul) micropipets

-2 (20ul) pipet tips

-thermal cycler

Preparations:

If not thawed already, thaw the two samples (non-GMO with the InsteGene matrix and

the test with the InsteGene matrix) from the previous day. Centrifuge the two samples for five

minutes to separate the supernatant (liquid with the genomic DNA) and the pellet (the solid

contents that settles at the bottom that is comprised of “cellular debris and Instagene matrix).

Label the six PCR tubes 1-6 with the table’s number. Add the designated DNA samples with the

designated Master Mix as denoted by the table taking care to keep the samples on ice. Add the

master mix first to each tube. Afterwards, with a fresh pipet tip each time, add the DNA as

directed by the table below:

Tube Number DNA Master Mix

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PCR Detection of GMOs 10

1 20 uL non-GMO food control 20 uL Plant Master Mix

(green)

2 20 uL non-GMO food control 20 uL GMO Master mix (red)

3 20 uL test food DNA 20 uL Plant Master Mix

(green)

4 20 uL test food DNA 20 uL GMO Master Mix (red)

5 20 uL GMO positive control

DNA

20 uL Plant Master Mix

(green)

6 20 uL GMO positive control

DNA

20 uL GMO Master Mix (red)

Table courtesy of PCR Detection of GMOs Day Two “PCR amplification of target DNA sequences.”

Do not transfer any of the pellet with the InstaGene beads to the new tubs. If it is difficult

to obtain the pure supernatant, centrifuge again to separate the mixture from the supernatant from

the pellet. To aid in mixing, while pipetting the DNA into each designated Master Mix, pipet up

and down to mix the new solution thoroughly.

Thermal Cycler:

Place the samples into the thermal cycler and use the program “GMO-BioRad.”

Hot start 94 degrees C 2 minutes (1x)

Denature 94 degrees C 1 minute Repeat 3 steps

sequentially (40x)

Anneal 59 degrees C 1 minute Repeat 3 steps

sequentially (40x)

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PCR Detection of GMOs 11

Elongate/ Extend 72 degrees C 2 minutes Repeat 3 steps

sequentially (40x)

Final Extension 72 degrees C 10 minutes (1x)

Hold 4 degrees C Infinite (1x)

Table courtesy of PCR Detection of GMOs Day Two “PCR amplification of target DNA sequences.”

Day 3:

-Agarose gel (1.5%) in a water bath

-EtBr (Ethidium bromide)

-Gloves

-Samples from Day 2

-About 300-350 mL running buffer (1 x TAE for agarose gel)

-1 vial Orange G loading dye

-1 vial PCR molecular weight ruler

-1 2-20 ul adjustable-volume pipet

-20 ul pipet tips

-Gel electrophoresis chamber

-Power supply

-UV light box

-UV goggles

Making the Agarose Gel Cast (for Electrophoresis):

Take care to wear gloves during this part of the experiment. Into the gel casting tray,

make sure that the well is tight so the agarose will not spill out when poured into the mold. Rest

the comb towards one end of the gel in one of the rungs making sure the comb is straight across.

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PCR Detection of GMOs 12

While wearing gloves, add 5 uL of the EtBr (Ethidium bromide) to the bottle of melted agarose

(1.5%). Gently mix together. Pour the new mixture quickly and carefully into the mold, taking

care to not move the comb or to create air bubbles. If there are air bubbles, take a clean pipet tip

and drag the small bubbles to the longer edges of the gel. Let the gel solidify at room

temperature. When the gel is solid, carefully remove from the mold and slide into the

electrophoresis chamber. Fill the chamber with the 1X TAE buffer until the gel is covered and

the lid can still be sealed.

Loading the Samples:

With a fresh tip each time, add 10 uL Orange G loading dye to each sample. Mix well by

pipetting up and down with the same tip used to transfer the dye. Again with a fresh tip each

time, put 20 uL PCR molecular mass ruler to each tube. Separately add 20 uL of each sample

into the wells in the agarose gel made by the comb. Starting from the left, add the respected

samples to the gel taking care to fully submerge the pipet tip into each well and to not pierce the

gel with the pipet tip or to pull up too fast while loading each well to prevent contamination:

Lane Sample Load Volume

1 Sample 1: Non-GMO food

control with plant primers

20 uL

2 Sample 2: Non-GMO food

control with GMO primers

20 uL

3 Sample 3: Test food with

plant primers

20 uL

4 Sample 4: Test food with

GMO primers

20 uL

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PCR Detection of GMOs 13

5 Sample 5: GMO positive

DNA with plant primers

20 uL

6 Sample 6: GMO positive

DNA with GMO primers

20 uL

7 PCR molecular weight ruler

(MWR)

20 uL

8 EMPTY 20 uL

Table courtesy of PCR Detection of GMOs Day Three “Gel Electrophoresis of PCR products.”

Gel Electrophoresis:

Set up the gel electrophoresis chamber with the corresponding colors to the machine. Run

the agarose gel at 125v for at least 30 minutes. Do not let the orange dye bleed off of the gel.

Gel Analysis:

Put on UV goggles and disposable gloves. Carefully slide the agarose gel onto the UV

light box. Turn on the light box and observe the patterns.

Results (10 points):

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PCR Detection of GMOs 14

Lane Sample # bands Band sizes (bp)

1 Sample 1: Non-GMO

food control with

plant primers

1 450

2 Sample 2: Non-GMO

food control with

GMO primers

0 --------------

3 Sample 3: Test food

with plant primers

1 450

4 Sample 4: Test food

with GMO primers

? ?

5 Sample 5: GMO

positive DNA with

plant primers

1 450

6 Sample 6: GMO

positive DNA with

GMO primers

1 200

7 PCR molecular

weight ruler (MWR)

5 1000

700

500

200

100

Table courtesy of PCR Detection of GMOs Day Three “Gel Electrophoresis of PCR products.”

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PCR Detection of GMOs 15

Discussion/Conclusions (10 points):

The experiment was conducted to find if the test sample was a GMO or a non-GMO

food. Using a fresh plant sample, it is easier to find if the food is a GMO or a non-GMO because

there is less processing done to it. DNA is extracted from it by manual grinding. This released

DNA is then elongated by replicated so that the sequences can be seen with the gel

electrophoresis process. The gel seemed to be a smudged with the bands. This could be because

of the evidence of primer dimers.

Primer-dimer formation “is an undesirable situation that leads to the inhibition of target

DNA amplification” (Dora 765). This can “become competitive enough to suppress the desired

product formation” (765). Primer dimers appear in gel electrophoresis. This can distort the

results of the gel plate because it makes the results harder to see. Changing the temperatures for

the water bath or the voltage for the current during the gel electrophoresis could help eliminate

the presence of primer dimers. Primer dimers mean that the results cannot be conclusive and

cannot be used to see if a sample is a GMO or a non-GMO.

The first lane was “Sample 1: Non-GMO food control with plant primers.” There was

one band in this lane at the 450 bp mark. This makes sense because the sample tested was a plant

and at around 455 bp, there should be a band. There should not be any other bands in this lane

because this was a pure sample, or a control to compare the test sample and the other control

with.

The second lane was “Sample 2: Non-GMO food control with GMO primers.” There

were no bands in this lane. This result makes sense because the control, or the non-GMO food

should have no GMO products in it, making the GMO primer useless. There should have been no

other bands in this section because this lane was just to confirm that the non-GMO food provided

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PCR Detection of GMOs 16

as a control was indeed a non-GMO food. If the food was a GMO, then there would be a band in

this lane.

The third lane was “Sample 3: Test food with plant primers”. There was one band in this

lane at around 450 bp. This result makes sense because the test sample was indeed of plant

origin. This band was also very apparent which helps confirm that the DNA replication and

amplification was successful to allow the band to appear.

The fourth lane was “Sample 4: Test food with GMO primers.” It is unknown whether or

not there was a band in this lane because the area seems to be smudged. This means there was no

definite band and no way to see to confirm if the test food had GMO primers in it. Without

knowing if the food had GMO primers, there is no way to tell if the test sample was a GMO or a

non-GMO.

The fifth lane was “Sample 5: GMO positive DNA with plant primers.” There was one

band in this lane at the 450 bp mark. This should have happened because the GMO positive

should have been of plant based origin. There should not have been any other bands in this lane

because the only thing that was being tested in this lane was if the food was a plant or not.

The sixth lane was “Sample 6: GMO positive DNA with GMO primers.” This lane had

one band. This lane should have had one band at the 200 bp mark. This makes sense because the

200 bp band means there are GMO primers in the mixture. And since this sample had GMO

positive DNA, it should have had a band here.

The seventh lane was the “PCR molecular weight ruler (MWR)” This lane had five

bands. These bands should have appeared at the 1000, 700, 500, 200, and 100 marks. The gel

plate had these five bands to show that this standard is a valid measuring tool to look at the bands

in the agarose gel.

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PCR Detection of GMOs 17

Primer dimers were observed on the gel plate because it there were multiple shadows in

lane four. This means that there were some sources of error in the experiment. One error that

could have occurred could be from the pipet tips being contaminated. With many pipet tips being

used, it could have been possible to mix up the samples. Another mix up that could have

occurred would have been from not labeling the right screw tubes with the right names. This

could have mean getting a result that could have been misinterpreted as another and leading to

false conclusions.

While grinding the samples, not washing the mortar and pestle thoroughly between each

sample (the non-GMO and the GMO positive), the non-GMO could have been contaminated

with the GMO positive or vice versa. Also, not grinding the samples enough could have been

another possible error because it would have not allowed the DNA to be completely extracted for

the second day. Not using DNase- and RNase- free water also could attribute to errors. Using

regular water, or even distilled water could have led to the denaturing of the DNA too early

which would have been detrimental to the PCR process.

During the extraction of the DNA from the supernatant, some of the pellet (with the

InstaGene matrix) could have been pipetted up and transferred. This would have hurt the

experiment because the beads in the complex would have removed certain cations that Taq

polymerase needs to work.

Creating the agarose gel could have also had many sources of error. If the gel was not

mixed well enough with the EtBr, then the gel would have had glowing splotchy places which

would not reflect the bands well. Bubbles from pouring the gel in the mold would have hindered

the passing of the current through the gel. If the gel was not immersed completely in the buffer,

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PCR Detection of GMOs 18

this would have also not allowed the current to completely pass through the gel for a clean band

at the end.

Pipetting the samples into the gel could have had some errors like missing the well and

injecting the sample into the buffer. This would contaminate all of the other wells and samples. If

the pipet tip was stabbed into the gel and pierced the gel, this would also make the sample bleed

into the other wells leading to more contamination between the standards and the samples.

If the samples were not completely centrifuged after each extraction and mixing, then this

could have contaminated the samples with each other, giving the samples a false positive where

there should not have been. This process could have been easier if there could have been slightly

larger quantities or clear screw tubes so it would be easier to see the supernatant separate from

the pellet at the bottom.

There was one point in the Orange G dye process where a pipet was double dipped into

the original tube. This was remedied by stopping all of the additions and getting a new sample

from the instructor to make sure that no samples could have been contaminated.

For people who are intent on living healthy, knowing the process of PCR, or even ELIZA

could test which foods are GMO positive. PCR testing could be used to isolate DNA sequences

to see if certain foods have diseases or could have harmful effects on humans. In the future, tests

like these could be more easily accessible with more immediate results with something like test

strips.

This experiment was inconclusive because there was no definite band in lane four. This

means that even though the other standards were definite, there was no way to identify if the test

sample, fresh corn, was a GMO or a non-GMO. The hypothesis for the experiment is proven

false because the corn could not be determined as a GMO.

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PCR Detection of GMOs 19

Stance on GMOs:

I believe that GMOs are relatively harmful things. I dislike how in the United States the

policies on stating on if a food is a GMO, it does not have to be listed depending on the

percentage that has been actually genetically modified. Companies such as Monsanto profit on

genetically modifying crops, and are in such control of the agriculture business, that they are

unstoppable. I believe that it should be a choice whether or not someone wants to eat a food that

has been genetically modified.

In terms of foods that have been processed that have ingredients that could have been

genetically modified, I think it is fine only because of the processing may have killed or

completely changed the composition of the food so it would not be so detrimental to my health.

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PCR Detection of GMOs 20

References (5 points):

Brahmbhatt, A. (Director) (2015, April 15). PCR Detection of GMOs (Genetically Modified

Organisms). Lecture conducted from , San Diego.

Brahmbhatt, A. (Director) (2015, April 22). PCR Detection of GMOs (Genetically Modified

Organisms) . Day Two (PCR Amplification of Target DNA Sequences). Lecture conducted from

, San Diego.

Brahmbhatt, A. (Director) (2015, April 29). PCR Detection of GMOs (Genetically Modified

Organisms). Day Three (Gel Electrophoresis of PCR Products). Lecture conducted from , San

Diego.

Dora, D., Kocagöz, T., & Öner, F. (2008). Synthesis and Cloning of a Small Bacillus Pheromone

Gene (ComXRO-B-2) by Primer-Dimer Formation with PCR. Turkish Journal of Chemistry,

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