Sushi

Proteomics is the study of proteins and in particular the structure and functions. When combined with genomics it becomes the study of evolution. A similar number of genes is required to make a worm and a person because genes can be different sizes and code for multiple proteins. Proteomics can be used to determine how closely related certain organisms are through the structure and function of their proteins.

In this lab, we will be comparing many different sea organisms to determine their relationships on an evolutionary scale.

Mitochondrial DNA

The Mitochondrial DNA Genome was sequenced in 1981, decades before the complete Human Genome was 

sequenced. It was much easier to sequence because it contains only 37 genes which are only involved in the production and storage of ATP.

 There is a non coding section of approximately

 1200 nucleotides which is called hypervariable because of its extremely high

 mutation rate. In the 

1980s a group of scientists traced the ancestry of all modern humans to Africa around 200,000 years ago. 

The results of the lab are somewhat troubling. According to our gel, I do not have any ancestry. Joe's band was the darkest so he was the most successful in extracting the DNA. Another source of the error could have been Michael destroying the gel while removing the combs.

Oh No Not a Genetic Disease

DNA testing was developed in the past few decades, and has been growing more effective, especially since the turn of the century. The tests use certain techniques to test and check to see if a person has a gene that predisposes them to get a disease. For this reason only certain genes have to be tested. The tests are performed by taking a sample of the patients cells and then isolating a gene of interest to test for. This gene could be for anything not just a disease. There are 3 possible results to the lab either homogenous negative, homogenous positive or heterogenous. We will be able to distinguish between these results by using 3 controls, one for each different result and comparing the gel electrophoresis results from the test to these controls.

First, we have to extract the DNA from our cheeks. To do this we have to take a swab of our cheek. Then to break open the cells to get access to the DNA. To do this we have to break open the cell membranes which we will do by raising their temperature to 95 degrees celcius. then we immediately have to add the cells to a solution containing Instagene Matrix beads to disable the DNAse. The DNAse is in the cell to prevent foreign DNA from entering the cell, but we need to disable it so it doesn't destroy the DNA we are trying to test. Then we will prepare the DNA for PCR by adding Master Mix which contains nucleotides, DNA Polymerase and the template strand of DNA. Then the tube is placed in a thermal cycler to raise the amount of DNA exponentially. Then we will prepare an agarose gel to electrophorese the DNA and use the results to determine who has the "disease".

The results of the Gel running showed that all four members of our lab group were, in fact, diseased. This can be seen by looking at lanes 5,6,7 and 8 which all display the same bar as lane 3 which is the -/- control lane. We are all extremely traumatized.

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.