Introduction:

Genetically modified organisms are organisms that have had an alteration in their DNA made inorder to to make the organism exhibit a desired trait. This can be used to have a variety of benificial affects on crops and other ogranisms.

 The organisms can be given such benificial traits as being drought tollerant, frost resistant, pest resistand and be given traits to last longer. This helps farmes grow larger crops and keeps the foods for longer without spoiling. GMOs are made when the desired trait from one organism is identified, isolated, and put into a plasmid. This plasmid is then insertrd into a tumor inducing (TI) cell which is then inserted into a plant cell where it will be able to creat the new genetically modified organism.

     Genetically modified organisms can be identified by using two different prosedures. Enzyme-linked immunosorbent assay (ELISA) is one prosedure that can be used to identify GMOs. In this process antibodies are used to identify different protines that are produced by GMOs this process is cheap and accurate but can only be preformed on fresh produce. Another from of identifying MG foods is by identifying the tumor inducing cell that is used in 85% of GMOs.  

Glowing Bacteria

Introduction:

Taking one trait from one organism has the ability to create a variety of beneficial outcomes. In order to carry out this process you must you must figure out the desired gene take out the part that codes for the trait and implant into the DNA of the other organism. To do this process you must take a restriction enzyme to cut the DNA at the correct locations and then join the strands back together using DNA ligase.

DNA Chips, no they're not a new Frito Lay product

Introduction:
     DNA chips can play a vital role uncovering which genes play a role in causing different types of diseases. These chips are made with around 30,000 spots where each one contains a specific code that the DNA fragments can bind to. Once the chip is completed all of the gene locations are known on the chip so when the spots change color the gene which is being expressed is known. When the chip is done the RNA from two different things such as healthy lung tissue and cancerous lung tissue is added each having been labeled with either a green or red tag. the sections then bind to the DNA chip at sections where the sections of mRNA correspond with the various locations on the chip. The chip can then be red by examining the light given off by the chip. Where there are only red or green only one of the mRNAs would have expressed that trait. Where there was a yellow spot both cells would have expressed that trait. If the spot remains black then the gene was not expressed by either.Through all of these the amount of light given off from one of the spots can vary by how strongly the gene is expressed.

Procedure:
    The first step is to obtain the slides, while doing so we need to make sure not to touch the surface of them. Then we will take the DNA tubes from the hot water bathe and put 15 nanoliters of each tube into each of the spots on the slide. We will then take a Hybridization Solution and add 15 nanoliter of that to each spot to help with the dyeing process. We will then examine the slide and see what color each spot turns. The blue dry shows the lung cancer, the pink dyes show healthy lung cells, the purple represents spots where both are expressed and clear means no genes were expressed.



Discussion:
1: Pink healthy lung cells express this gene
2: Purple this gene is expressed in both healthy and cancerous lung cells
3: Blue Expressed in cancerous lung cells
4: Clear no Genes expressed
5: Pink healthy lung cells express this gene
6: Blue Expressed in cancerous lung cells

We could have had error in many places. If we were to contaminate a spot by dipping one of the tips of the micropipet into one spot and then dipping it back into one of the tubes would contaminate all of the solution and give us faulty results. Also pipeting more or less of the solution could lead to a change in the intensity of the color.

Daring Nucleotide Adventures: Lafayette

Introduction:
     DNA fingerprinting is a process in which scientists can use Restriction Fragment Length Polymorphism to distinguish one individuals DNA from another. The process creates unique banding patterns of DNA as the DNA moves on an agarose gel. In order to create the bands the longer strands of DNA is cut into segments by restriction enzymes that recognize certain sequences of base pairs. Because the Lengths of the DNA segments are different lengths the will move at different speeds. The smaller segments will be able to move faster because they are lighter and will move faster because the electric current will affect them more so the negatively charged DNA will travel faster toward the positive end. While the DNA will move across the It will do little good without a dye because This process is called agarose gel electrophoresis. DNA can be gathered from body tissue, body fluids, hair follicles, and other biological materials. If the amount of DNA is not enough PCR techniques are used to carry out the test. In our lab we will use DNA fingerprinting to identify whose DNA was found at the crime scene. In the real world more complicated methods are used that are more precise to match the DNA of suspects with DNA found at crime scenes.

Procedure:
     To carry out this lab we first get the crime scene DNA as well as the DNA from each suspect. We then will need to add enzyme to each micro testube. We will then centrifuge the testubes so that all of the liquid accumulates in the bottom of the test tube. We will then put that in a 37 degree Celsius water bath so the enzyme is able to perform its job. After the test tubes have spent 45 minuets in the warm water bath they will be moved to the refrigerator so that the enzymes and DNA stay in tact. The next day we will remove them from the refrigerator and add loading dye so we can see the solution and so that the solution is heavier and will sink into the wells. We will then pipette the DNA and loading die into the wells. Once we have all of the DNA loaded we will run the gel and will be able to see the loading dye move but will be unable to see the progress of the DNA. In order to reveal the DNA we will then remove the gels and place them onto a tray that we will fill with Fast Blast DNA stain and will leave them for over night. the next day we will return and see which suspects DNA matches the DNA found at the "crime scene".

Results/ Observations:
     Upon returning we examined our gel which we had run the gel electroforesis on and this is what we saw:

Discussion:
     As we examined the gel we concluded that the bands created from the DNA collected at the crime scene matched the DNA from the suspect 3 which was Katie Records. So we concluded that it was Katie Records DNA that was found at the scene of the crime. There are several different possible sources of error in this lab. One of the most obvious but also one of the easiest ways to produce a false result would be to accidentally but the wrong DNA in a test tube or by putting the wrong DNA into the wrong well. there can also be errors in loading such as not getting all of the material from the test tube into the well. Shaking the test tubes too violently could cause the strands of DNA to break which would also produce faulty results.

Enzymes Make the Weels Go Round

Background:
     Enzymes are the driving force behind the production of biofules. They help to catalyze the reaction and speed up the reactions in order to make the production of biofules a realistic option. Enzymes are proteins that take the substrate in a reaction which fits into the enzyme in such a way that it is the only thing that could bind to the that site. Once the substrate had bond to the enzyme the activation energy for the reaction is lowered because the substrate is positioned in a way that it is easy for the reaction to occur. Once the reaction has taken place the enzyme moves on to another substrate that it can bind to to help facilitate the reaction. While enzymes are an important part of the reaction temperature and the concentration of all the molecules can either speed up or slow down a reaction. While higher temperatures cause the reaction to occur faster because all of the molecules are colliding more often if the temperature becomes too hot it will begin to break down the individual molecules. Concentration of the substances can also effect the reaction as the increased number of molecules will cause them to collide more often.

Purpose/ Objective:
     In industry scientists look for the fastest and most efficient ways to carryout reactions. In this lab we will eaxamine how quickly cellulose is broken down by different cellulases. We will test both cellubiase and enzymes found in mushrooms.

Procedure:
     For the lab the first step is to put stop solution into all of the curvettes. The stop solution will denature the enzymes halting the reaction, it will also turn the p-nitrophenal yellow revealing how much of the reaction has taken place. Next, we will need to take some of the substrate, the molecules that will be involved in the reaction, and add it to both the enzyme reaction test tube and the control test tube. We will then need to add some buffer to the solution in the control test tube that will then be put into the start cuvette. There should be no change in color in this test tube. We will then need to add some enzyme to the enzyme reaction tube. While adding in the enzyme we will need to start the timer. We will then need to add some of the solution in the enzyme reaction tube to each of the cuvettes at set intervals. We will repeat this process on the second day but on the secondary we will first need to extract part of the mushroom to serve as our enzyme. to extract the mushroom we will add extraction buffer and then grind the mushroom with a mortar and pestle. Then using the centrifuge we will separate out what we will need for our reaction to use as the enzyme.

Hypothesis:
     I think that there will be no change in color in the start or stop cuvettes because they were never in contact with the enzyme. I also think that the cuvettes will increase in darkness as the experiments because they will have experienced more of the reaction before coming in contact with the stop solution.
Results:
Day One: Cellubiase

Day Two: Mushroom used as enzyme

The first day we had color in all of our cuvettes this could have been leftover from the previous class if it was not washed out thoroughly enough. Also the Mushrooms appeared to have become dark quickly and then did not change much this could be because all of the substrate was used up in the reaction.

My Own Darring Nucleotide Adventures

Deoxyribonucleic acid carries genetic information in all living things. This genetic information is held in the double helix structure composed of a sugar called dioxiribos, a nucleic acid, and one of four bases. The four bases are adenine, guanine, thymine, and cytosine which always pair together in the same way adenine with thymine and guanine with cytosine. These bases code, thought the order of the bases, how each protein should be made. DNA is contained in the nucleus of every cell. In the nucleus the long strands of DNA are organized in chromosomes. There are a total of 46 chromosomes in the nucleus which contain all the genetic information. With in the DNA strands there are different sections which code for different things these sections are called genes. While all the information for all your cells is contained in each one each cell, each cell only uses some of the information to perform whatever function it is responsible for. It uses the information stored in the DNA by creating mRNA which can travel through the cytoplasm in the cell. Transporting the Information to various ribosomes who can use the information to create proteins. In this lab we hope to synthesize DNA from our cheek cells. Extracting DNA is a process that can be used in a variety of applications including identification in crime scene investigation, cloning and testing for genetic traits.
     In order to carry out this lab the first step will be to loosen cheek cells from the inside of our mouths. The next step will be to rinse our mouths out with a saline solution whose salinity is equal to the salinity of the fluids in our bodies by doing this the solution will maintain isotonic equilibrium.The next thing to do will be to put the solution into a test tube and add a lysis buffer that will break open the phospholipid membrane changing the hydrophobic membrane to a hydrophilic substance. Once the membrane is broken down Protease will be added to break down the dnace another protein contained inside the cytoplasm of a cell that breaks down DNA molecules. Next the test tube will be put into a hot water bath to act as a catalyst for the enzyme that will break down the dnase. Finally once the test tubes are removed cold ethanol will allow for the DNA to percipitate out of the solution much like a supersaturated solution of sugar and water would produce a solid as it is cooled from it hotter temperature that allowed more sugar to be mixed in. We then extracted the DNA using a DPTP to put the DNA in to a necklace.
     In my lab I was able to precipitate a large amount of DNA when compared to the rest of my lab table. i think this came from my excellent technique in removing cheek cells from my mouth. I think I used the proper amount of force being able to extract a lot but not causing myself to bleed. One possible source of error in the experiment would have arisen if the lysis buffet was added to long before the protease it would have broken down the phosphilipid membrane and expose the DNA to the dnase that would destroy it making it impossible to precipitate the DNA. Another Problem could have come about if the hot water bath was to hot. If that were the case it could have denatured many of the proteins and harmed the DNA.

Yogurt, its Alive: Testing Koch's Postulates Through the Growth of Yogurt Bacteria

2. Introduction
a,b) Bacteria are found almost everywhere. Soil, water, animals, plants, and humans all offer bacteria with the environments that they need to thrive. Out of the unimaginable number of bacteria only a small fraction cause infection. While this percentage is small pathogens have have a major impact on humans. In order to combat these diseases scientists tried to discover the cause of these diseases and Lear n how they were transmuted. Anton van Leeuwenhoek was the first person to examine bacteria under a microscope. As time passed and more research was done Robert Koch developed his postulates. His first postulate requires people to find the bacteria that is found in sick patients but not healthy ones. In his second postulate the bacteria must be isolated and grown. In this third postulate the bacteria must be put into a healthy individual to see if the individual becomes infected. For his final postulate the bacteria must be isolated again against the original to prove it is the same bacteria causing the infection. This allows doctors and scientists to identify the particular pathogen that is causing a disease.

c) In our experiment we will take milk and use it to represent the human body and that when the milk thickens up it is a sign of that disease. We will test the yogurt bacteria to see if it is responsible for the milk turning to yogurt. In our experiment we will have both a positive and negative control. The negative control will only contain milk and the positive control will contain milk and yogurt. We will also then have one test tube in which yogurt and ampicilin are added to the milk and one test tube in which E.coli is added. We will use an inoculation loop to add in the yogurt and then will add in one drop of ampicilin. we will also use an inoculation loop to mix the E.coli into its proper test tube. The tubes will then be left to incubate at 37 degrees Celsius for 24 hours so that the bacteria will have time to grow. At that point we will make our observations and collect our data.

Results/Observations
Here is one video of our lab table doing the lab unfortunately we lost most of our footage.

In doing our lab we saw the growth of yogurt in the positive control which contained just milk and yogurt. In the other test tubes there was no growth of yogurt bacteria that would help to preserve the milk by producing lactic acids that lowers the pH of the substance in the test tube helping to preserve it. When testing the test tubes pH all were around 6 except for the positive controls whose pH was around 4. An other observation that also supported the conclusion that the positive control test tube produced yogurt was that there was a precipitate that formed in the bottom of the test tube.
There were several sources of possible error that could have occurred throughout the lab. One possible source of error would be if we were to accidentally put yogurt bacteria into the test tube which contained E.coli. Doing this would result in a false positive in that test tube as the yogurt bacteria would grow and not the E.coli. Another possible source of error would be if you were to get ampicilin into some of the wrong test tubes which would kill the bacteria in that test tube preventing any bacteria culture from growing.