Green Beans With Banana Genes

Introduction: Genetically modified organisms are exactly what they sound like. They are organisms that have been tampered with to create similar organisms with a few changed characteristics. Although farmers and other groups have been tampering with the genes of crops for a long time, it is now possible to insert a specific gene of interest into another organism. GMO's are created by using T.I. plasmids that contain the gene of interest. The T.I. plasmids go through transformation and the agricultural bacteria replicates its DNA. This bacteria is put into a plant cell which will eventually be grown into a GM plant. To identify GMO's the cell wall must be mashed up to create a wounded target. Whatever is being tested is then put into a hot H2O bath that breaks open the cell membrane. Next, instagene matrix is used to kill DNAse. With DNAse out of the picture DNA is open game. The next process, polymerase chain reaction, (PCR) replicates the DNA so we can identify whether or not it is genetically modified. PCR requires four ingredients, target DNA, nucleotides, the enzyme thermus aquaticus, and primers. Once the DNA has been replicated plenty of times, it's time to find out the answer. Found in 85% of GMO's, T.I. plasmids are the target that will prove if the organism is genetically modified. A gel must be run and if the GM band shows up then the organism is genetically modified, and if the plant band appears it is not. As it should be, genetically modified food is a controversial topic because both sides have strong points. Those in favor of GMO's argue they improve nutritional value, can be mass produced, and selective breeding brings out the best in foods. Those who oppose  GMO's have found the negatives in this process. Amongst their concerns are moral values in regards to tinkering with evolution, allergic reactions, and the problems that accompany a monoculture of products. Do the positives outweigh the negatives? Since GMO's are fairly new technology it's almost impossible to be certain. Our lab will consist of bringing in a food product from the store and doing all of the steps above to discover whether or not that food is genetically modified. Since so much of today's food is genetically modified, I believe our food will also prove to be a GMO.

Results/Observations: Our final gel had a band in every single lane. Since the first lane, test food with plant primers appeared, we know that DNA extraction worked. The second lane was test food with GMO primers. The band appearing in this lane proved that our first test food was in fact GMO. The third and forth lanes had the same results but were just a different food. The fifth lane was a GMO positive control DNA with plant primers. The fact that a band appeared in this lane shows that PCR was successful. Lane six was a GMO positive control DNA with GMO primers which reinforced that PCR worked. Finally lane seven contained just a marker. The band in this lane proved that gel electrophoresis worked.

The Glowing Belly of a Sea Jelly

Introduction:
In this lab we will be completing a genetic transformation by taking the gene that codes for Green Fluorescent Protein (GFP) and inserting it into the DNA of bacteria. Green Fluorescent Protein is found in sea jellys and we will take it to create glowing bacteria. Bacteria contains plasmids which are circular pieces of DNA. These plasmids usually contain genes that code for traits in bacteria and have the ability to transfer back and forth between bacteria. We will be inserting pGLO, a plasmid that codes for the GFP gene into the E. coli cells. The new genetically modified E. coli cells will then glow. To get the pGLO plasmid through the cell membrane we will need to use a solution of CaCl2 and use heat shock. Then to get the newly transformed cells to grow we will provide nutrients and incubate them. This will eventually make the cells start to express their fluorescent gene.

DNA Chips: Genes to Disease

       Introduction:
A microarray is a tool that helps scientists look at thousands of genes at a time. This enables them to see to what extent the genes are expressed in certain tissues. Microarrays are commonly used to compare tissues. The mRNA extracted from the samples are labeled with colors such as red and green. The mRNA is then applied to the DNA chips and the spots on the microarrays show which genes are expressed. Whichever color appears on a certain spot shows whether the gene is on in that sample. Combinations can create (for example with red and green) yellow spots revealing that the gene is on in both of those samples. Intensity is also important because a dull red spot and a bright red spot are two different things. The bright one shows that the gene is turned on more than the dull one. A helpful analogy is to think of the spots like lights with dimmer switches. This can be applied to cancerous and noncancerous tissues to see which genes are on in each showing the difference between the two. We will be studying the expression of six different genes in normal lung and cancerous lung cells. The end results will show us which genes have been expressed to produce more RNA in cancerous lung cells and which genes have been repressed from producing mRNA in normal lung cells.

Records Put On Record

Introduction:        
       Every person in the world has their own unique DNA fingerprint DNA fingerprinting can help to identify and compare individuals. Much of every individuals DNA is the exact same. This makes it difficult to distiguish different people. Microsatellites are used to make this identification easier. Microsatellites are short pieces of DNA that repeat many times in one's DNA sequence. Any biological material can be used for DNA fingerprinting such as, body tissues, body fluids, and hair. Even some dired material such as blood stains can be used. To create this DNA fingerprint from the DNA restriction enzymes must be used.
        Restriction enzymes act like small DNA scissors. These enzymes recognizes specific base pairs that tell it to cut the DNA at that point. The spots in which the enzymes make the cuts are called restriction sites. This can result in many different pieces or fragments along one DNA strand. Once the DNA has been cut it can be seperated by the size of the fragments. This seperation is created by using a process called Agarose gel electrophoresis. This process consists of inserting the DNA into an agrose gel slab and passing an electircal current through it. The DNA fragment (which are negatively charged) are attracted to the postively charged end. This is the point in the process that creates the seperation. The bigger DNA fragments are unable to pass through the gel as easily as the small fragments consequently causing them to not travel as far. All of the fragments that are the same size come togethor to form bands. Once the gel is stained we can see these bands. This final result of the way that they line up is the DNA fingerprint.

Results/Observation:
       Lane 4 or sample number 3 ended up matching the the crime scene DNA from lane 1. All of the other lanes had differing results with the strips being at different places along the gel. The crime scene matched perfectly to sample 3 which happened to be the sample from Katie Records.

Discussion:
       The gel ended up working correctly and the restriction enzyme obviously did its job as the molecular scissors. The smaller pieces moved farther along the gel as expected compared to the larger fragments that didn't make it as far. Some possible sources of error could have been the loading dye not weighing down the sample and the DNA floating out and mixing with the other DNA. Another source of error could have occurred when undergoing the difficult task of inserting the samples into the small slots in the gel. Although some incidents did occur, we were able to work past these and receive the correct results.  
                                                                    
Sources:
McGuigan, Brendan. "What Is DNA Fingerprinting?." wiseGeek. wiseGeek, 08/9/2010. Web. 25 Oct 2010. <http://www.wisegeek.com/what-is-dna-fingerprinting.htm>.

Petroleum No More

Introduction/Procedure
Enzymes which are generally proteins, speed up the rate of chemical reactions. They have specific three dimensional structures and reduce the energy needed to carry out a chemical reaction (otherwise known as the activation energy). Since the enzymes reduce the amount of activation energy the reaction occurs at a quicker pace. Enzymes do not chemically react with the substrate so they can continually help to convert reactants to products. Changes in pH and salinity negatively affect the enzymes productivity. Another factor in the speed of the reaction is heat. More heat, therefor faster moving  enzyme and substrate molecules, causes more collisions and speeds up the reaction. Most enzymes function best at medium temperatures  however there are of course exceptions. The enzymes "natural habitat" is a good reflection of what are optimal temperatures for the enzymes to operate under. Another component to the speed of reaction is concentration of molecules. Until the point of excess, enzymes will speed up the reaction if there are more molecules. This knowledge of enzymes will help us in our lab because we are using cellobiase, (an enzyme) to break down cellobiose to glucose. Also our knowledge of how pH, temperature, and concentration affect reactions will come into consideration when we analyze how these affect our break down of cellobiose. This ability to break down celluloses into glucose is used by biofuel industrys in search of an alternative to petroleum. The glucose can be converted to ethonol which can be used to power engines. In our lab we are not trying to solve the worlds pollution problems, merely trying to understand the process. We are going to use cellubiase to break down cellubiose into glucose. During the process we will take part of the solution at different times in the reaction and attempt to use a stop solution to take "snap shots" of the process. Using p-nitro to turn the glucose a color visible to human eyes, we will be able to see glucose in the making. I predict this will be a successful lab but precision will be necessary throughout.

Results/Observations
During the experiment every later interval progressively became a stronger yellow color. In the beginning the yellow was hard to see and closer to a clear color. Towards the end the last tube that we transfered it into turned a very strong yellow color.  This was also true when we replaced the enzyme with mushroom extract. The results seemed to be nearly identical to the previous days tubes.

Discussion:
This means that the experiment did end up working. The cellobiose inside the main tube was being broken down into glucose and the results were obvious. It also proved that the mushroom acted just like cellobiase in that it also produced the glucose. Although our lab ended up working errors could have occurred during the process such as maybe a certain mushroom doesn't act like cellobiase. If it didn't break down the cellobiose then the p-nitro would have no glucose to turn yellow and we would have to results to look at.

Genetic Jewelry

Intro/Procedure:
DNA, short for deoxyribonucleic acid, is in all living things. It carries genetic information responsible for features such as skin, eye color, height, blood type, exc. Every one of our cells carries these instructions. The DNA is found in the nucleus of all cells except red blood cells.The shape of DNA is a double helix with bases on the inside and phosphates on the outside. The bases (adenine, guanine, cytosine, and thymine) are paired together. Adenine always pairs with thymine and guanine always pairs with cytosine. Everyone's DNA is 99.9% the same and it's that .1% that makes the difference and unique qualities of individuals. A section of the DNA, genes, carry the information to make proteins.  DNA can be used for testing for traits, cloning, crime scene investigations, and more. Our lab is an attempt to precipitate or extract our own DNA and then put it into a necklace. To extract the DNA we first must get some of our cells. After loosening cheek cells and putting them in saline solution which keeps the cells "happy", we use a lysis buffer to break open the membrane (phospholipids). We then use protease (an enzyme that breaks down proteins) to kill possible threats to the DNA (DNAse and Histone). After hot water is used to speed up this process cold ethonal precipitates the DNA.

Results/Observations:
We were successfully able to extract DNA from our cells and put it into a necklace. When doing the lab little could be seen inside the tube until the ethonal was added. Once the ethonal was added and we swished the tube around the DNA strands became visible.

Discussion:
There is not much to analyze other than the DNA was precipitated due to protease successfully killing anything that may have harmed the protein and then the ethonal worked and the DNA became present. Although the lab worked, things such as using wrong amounts of protease or ethonal could have ruined the results. Overall this was a fun, successful,and not too difficult lab.

     Food For Thought

Introduction/Procedure

Bacteria the most abundant life form on earth, was discovered in 1676 by Anton van Leeuwenhoek. Bacteria are prokaryotes, or single celled organisms. It is often referenced with disease and other negative effects. A few devastating break outs of disease due to bacteria such as the Bubonic plague have put a bad picture in our head. Thus many antibiotics have been created to help prevent any future tragedies. The truth is very little bacteria can harm you. The human body is full of bacteria that actually help you to survive. Bacteria are even present in many of the foods we eat. One of these foods is yogurt. In our lab our purpose is to make yogurt and use Koch’s postulates. Yogurt is essentially milk with added bacteria. The bacterium added to the milk takes in the milk sugars (lactose) and creates lactic acid. This lactic acid drops the pH causing the milk to curdle. We are going to attempt to use Koch’s postulates to prove or disprove which microbes cause the “yogurtness disease”. I hypothesize that this will prove correct and microbes will be the cause. 
                               
                            Results/Observations
Tube 1: Positive control, milk, smells like sour milk, texture is liquid. 
Tube 2: Negative control, yogurt, smooth texture, smells like yogurt. 
Tube 3: Milk and e. coli, milk, smells terrible, liquid texture.
Tube 4: Milk and ampicillin, smells like milk, liquid texture.


                           Discussion
    Tube one had no chance of turning into yogurt because it was just sour milk. The negative control turned into yogurt. Milk and e. coli didn't become yogurt because e. coli isn't the right type of bacteria to make the milk curdle. Milk and ampicillin stayed milk because antibiotics don't help either. Some possible sources of error could have been a contamination where other unwanted bacteria gets in the tubes.