Is This Food Genetically Modified?

GMOs are organisms that have been scientifically altered in some way to make it "better." An example would be making a crop resistant to certain environmental factors or stresses. If a crop could only grow during the summer because of its inability to tolerate cold weather, a gene from something that lives in cold weather and insert it into a plant. This seems like it would be the fix for all of our problems, however, there is more to it than just that. For example, say a gene from fish was inserted into corn DNA and someone who is allergic to corn picks up a piece at the supermarket and becomes extremely ill because it is not required to have a GM sticker on food in the United States. However, in other countries around the world these foods are required to notify customers by placing a sticker on the item. There is also a potential for a "superweed" to be created on accident which would ravage the world's food supply. These controversies are similar to the ones raised on testing Genetic modification in humans. What if a Frankenstein is created? What about zombies? Although most Geneticists are fairly confidant nothing like this will happen, the general public remains worried.

In the GMO identification lab we are testing a food to see if it contains the Tumor Inducing plasmid that over 90% of all Genetically Modified foods contain. This is used in the real world setting to determine whether or not a food has been modified.

To do this we will have to amplify a certain strand of DNA by using Polymerase Chain Reaction. The PCR requires 4 things for it to work. DNA Polymerase must be present to perform the replication of the Target DNA. Next, you must have a Primer to seek out the certain sequence of DNA that is to be replicated. Third, there has to be a large supply of the four Nucleotide bases and fourth you must have the target DNA that you want to replicate. Before the PCR is used we have to extract the DNA of the plant that is going to be tested. To do this we use a mortar and pestle to break up the cell wall of the plant. Then, it is placed in a 99 degree Celsius water bath, this will break up the Cell and Nuclear Membrane. Once the Nuclear Membrane is gone the DNA will be free, however; in the cell there will be DNAse which will destroy the DNA. To prevent this we must add Instagene matrix beads, which disable the DNAse, immediately after removing the sample from the water bath.

Bioluminescent Nightlight

Sea Jellies possess the mystifying ability to glow in the dark. This is due to the presence of the Green Fluorescent Protein. Stanley Cohen and Herbert Boyer were the first scientists to create a recombinant DNA plasmid. They took a gene that coded for a protein in frogs and inserted it into a bacterial plasmid. They did this using a restriction enzyme and a process called heat shock which forces the recombinant DNA through the bacteria's membrane. They then tested the bacteria and it had been tricked into producing frog protein.

We will use these same principals in an attempt to insert the pGLO gene into E. coli bacteria to make them glow in the presence of UV light. To do this we must first create the recombinant DNA using a restriction enzyme and then pipetting the Gene of Interest into the newly cut DNA. We will force them to accept it using the heat shock method of making them very cold then very hot rapidly. Once the new plasmid is in the E. coli we will place it on 4 plates. One will contain only food and will have un-altered bacteria on it which will be the experiment control. Another will have bacteria without the gene and grown on a plate with Ampicillin on it which the bacteria will be vulnerable to without the GOI. The next plate will have the gene with Ampicillin added to it, the bacteria should be resistant to the anti-biotic because of the ampR gene inserted into the plasmid with the GOI. The final plate will have The gene ampicillin and aravnose which is what will cause the bacteria to glow in the presence of UV light.

The bacteria were able to grow and the results were as expected with only one of the plates able to glow, and one plate with no bacteria on it due to its inability to withstand the ampicillin.

DNA Chips Show the Genes

Microarrays can be used for evaluating thousands of genes at one time. A simple red, green or yellow dot can tell us many things about genes. Each dot represents a different gene and each color represents how the gene is expressed in the cells of the scientists choosing. For example, perhaps the scientist is experimenting with normal skin cells and cancerous skin cells. If the dot for a certain gene is green that means it is expressed in healthy cells but not in cancerous cells. If the dot is red, it is expressed only in cancerous cells. Finally, if the dot is yellow, it is expressed in both healthy and cancerous cells and therefore probably has nothing to do with the cancer.

We experimented with healthy lung cells and cancerous lung cells. We had 6 different genes that we were testing. We carefully pipetted all 6 genes into their places on the microarray slide, and then added a dye which changed colors to either red, blue or purple. Then we examined each space for its involvement in the cancer. The genes that are only expressed in healthy cells are somehow involved in the cancer because for whatever reason they are not being expressed in the cancerous cells. Therefore the only genes not involved in the cancer were the ones that showed up as a combination of red and blue.

Crime Scene Investigation

The field of DNA profiling is relatively new, however, it is already being applied with great success by law enforcement. Using restriction enzymes to "cut" the DNA at certain points different sized strands of DNA are produced. This is called Restriction Fragment Length Polymorphism. Restriction enzymes are a naturally occurring bacterial defense system. They destroy invasive DNA by cutting it into small parts that will be harmless to the host. Using this technique allows the strands to be separated. Once separated the nucleotide sequence will be checked for similarities to suspects DNA nucleotide sequences. Any biological material that is found at a crime scene can be tested in this fashion and compared to suspects DNA in an attempt to solve a crime. Once the strands are separated they are placed on an agarose gel and electrified. The DNA has a negative charge so it will move towards the positive pole of the gel. The DNA can then be checked against suspects DNA to determine the perpetrator.

First, we removed the DNA samples and placed them in a centrifuge. Then we added 5 microliters of loading dye, which makes the DNA and also makes the sample heavier. Then we loaded the DNA samples into the wells in the agarose gel. Then we turned on the power to separate the samples with electricity. Then we waited 2 days and then placed the gel on a white box to examine the samples.

We concluded that suspect 3, Chloe, was the murderer. We saw that the DNA marks in her track matched the ones of the DNA that was found at the crime scene. These markings were fairly straightforward and easy to read. However, we could have possibly contaminated samples by using the same pipette tip or placing DNA in the wrong well.

Biofuel

Lately, people are trying to develop more environmentally friendly fuels. Biofuels are fuels made out of organisms that have been genetically modified. We are performing a lab that will test the effectiveness of a certain biofuel. We are testing it by adding it to a strong base at various increments of time. The strong base will react with it and cause it to turn yellow, so, the more yellow the beaker the more energy is in that beaker. Depending on how long it takes to become a dark yellow we will know how effective this biofuel really is. Also on the second day, we will grind up a mushroom, a decomposer, and add it to the solution. This should speed up the reaction time because of its enzymes. Our group predicted that the amount of glucose in solution will increase until a certain point when the reaction will run out of reactants and stop.

Breaking down cellulose is fairly simple as demonstrated in these steps: First we add cellobiase to the cellulose which breaks apart the cellobiose that is made up of 2 glucose molecules. The 2 glucose molecules can then be used as fuel. We will be testing how efficient this reaction is. We will do this by adding .5 mL of the created solution to .5 Ml of p-nitrophenol which will stop the reaction and change the glucose to a yellow color allowing us to easily determine how much glucose has been produced.

The results of the reaction appear to prove our hypothesis. The solution appeared darker in the 2 minute tube than it was in the 1 minute tube. However, after that the increase in color was miniscule if there was any at all. This could be for two reasons, either we didn't add enough p-nitrophenol or the reaction had actually slowed to an almost complete stop.

Precipitating DNA

DNA is a molecule that all living things have. It carries information for cells to perform the tasks that they are created for. DNA also carries genetic information which controls all a person's inherited traits such as height, eye color and hair color. 99.9% of every single person's DNA is exactly the same; the .1% difference is what makes every person different. The purpose of this lab is to precipitate our own DNA. Commercial uses of this type of lab could be to Study, compare, map or sequence DNA. It could even potentially be used in cloning.

The procedure of this lab is very simple. First we loosened cells on our cheeks by chewing them and then extracted them by rinsing our mouths with saline solution. Then we break open the cell walls with the lysis buffer which dissolves oil-based substances. Next, the protease is added, protease breaks down proteins. We destroy the proteins to destroy the enzyme, DNase, which digests DNA. Now the DNA can be precipitated without being destroyed by the DNase. DNA has a negative charge which would allow it to be soluble in water, so we add salt and the NA+ ions bond with the DNA neutralizing it. It will also allow the DNA to come together instead of repelling due to charges. Finally, cold ethanol is added which makes it even harder for the DNA to dissolve in the solution and the DNA will precipitate enough to be seen. Then we extracted the DNA from the solution and placed it in a necklace.

Our lab worked as it was supposed to and all of us had more than enough DNA in our test tubes. Due to our success we can assume that we did everything right, however, some possible things that could have gone wrong are: We could have not added enough protease and the DNase would have consumed all the DNA or we could have not harvested enough cells.

How Does Bacteria Taste?

Microorganisms have been around since the beginning of Earth, but we still have much to learn about them. However, we do know a few things about them. Most people associate bacteria with disease and infection, however only a very small percentage of bacteria can actually act as pathogens. Most bacteria are actually helpful to us as humans. That is why we hear about things like pro-biotics which promote the growth of so called "good" bacteria. A man named Koch developed a few postulates which are now used in modern day science in identifying bacteria and pathogens. We will test Koch's postulates by making yogurt, adding E. coli to some and Ampicillin to some and determining the outcome. We are also practicing how to handle microbes or our microbial technique such as using inoculating loops and agar plates.

We started with 4 tubes filled with milk and then we inoculated one with only yogurt bacteria, one with yogurt bacteria and ampicillin, one with E. coli and leaving only milk in one. We then left the tubes in an incubator overnight to allow the bacteria to grow. We predicted that the yogurt tube would be the only one with actual yogurt in it. We also hypothesized that the tube with yogurt and ampicillin in it would be milk, and that the tube with E. coli in it would be milk. The tube with only yogurt and milk did in fact end up as yogurt, while the tube with the ampicillin-yogurt mixture was more of a combination of yogurt and milk. We correctly hypothesized that the E. coli would end up as milk. The tube with E. coli ended up with a rancid smell, while the two tube with yogurt in them had a yogurt smell, and the milk tube smelled like spoiled milk. We then tested the pH of the tubes with Litmus paper they were all neutral except for the yogurt tube which was between 4 and 5.

The tube with only yogurt ended up as yogurt because it was the only addition to the milk in that tube. The tube with yogurt and ampicillin ended up as a mixture of milk and yogurt because the anti-biotic either didn't have enough time to eliminate all the yogurt bacteria or there was not a large enough amount of it to completely destroy the bacteria that was creating the yogurt. The E. coli tube ended up looking like milk and smelling very spoiled, this is because the bacteria multiplied overnight spoiling the milk. There were a few possible sources of error that could have altered our results, we could have used an inoculating loop that had been contaminated somehow, such as with the bleach that was being used. Another source of error could have been misreading the litmus paper. Also we could have not mixed the mixtures up enough with the vortex.