Fishing For Answers

In this lab, we will use the power of Proteomics to identify which species of sea creatures are most closely related. Proteomics is the study of proteins and by running proteins from various species on a gel, we can observe the bands to see which are most closely related. Which is more closely related to a squid, this blobfish or a crab? We can find out through PROTEOMICS! There are three main steps in this lab. First we will denature (unravel) the proteins. Next we will run them on a gel just like we have run DNA on gels in previous labs. Finally, we will study the gel to compare species. The more similar the bands are, the more closely related the species are. This method is especially useful to scientists who are comparing species. For example, this is how they discovered that chimpanzees are more closely related to humans than they are to gorillas.

Sequence What Your Mama Gave You

Every living thing has DNA unique to it that they pass down from generation to generation. However, few people know about mitochondrial DNA which is passed down only through the maternal line. This DNA is found only in the mitochondria, which evolved from bacteria. This is why it is different from normal DNA. Examining mitochondrial DNA helps in tracing ancestry because it remains exactly the same in every generation. In this lab we will extract our mitochondrial DNA and amplify it using PCR. From these results we can send it to be analyzed and see our sequence.

Disease Testing Results

After doing electrophoresis on our DNA, we found that everyone at our lab table was unaffected by the disease.

I Think We Should Get Tested...

By analyzing your genes and such through a process called disease gene testing, it is possible to see if you have a disease. In many diseases, early detection is crucial so this technique is incredibly important in today's society.
The first step in this process is to collect DNA to be processed. After swabbing our cheeks, we will use a 95 degree Celsius water bath to break open the cell wall and the nuclear membrane of the cell. Just outside the nucleus are enzymes called DNAse that protect the cell from viral infections. However, this enzyme will also try to attack the DNA we are trying to extract so we must use instagene matrix beads to kill them and protect the DNA. After doing a DNA Polymerase Chain Reaction (PCR) to mass produce the DNA we collect, we will do electrophoresis of the PCR products. Based on the lines that show up, we can tell if we are affected by the disease, carriers, or disease free.

Frankenplants: Friend or Foe?

Science has advanced to the point where it is capable of adjusting the genetic makeup of organisms. Genetically modified organisms (GMOs) range from crops to bacteria but they all have one thing in common, they are not strictly natural. Many people fear GMOs simply because they do not understand them, but is this fear justified? To answer this question, we must first understand GMOs. To genetically modify an organism, scientists put a tumor inducing plasmid with a gene of interest into a cell. From there, the cells will replicate and create an entirely new and unique organism. In this lab, we will use a technique to identify GMOs. First, we will use a mortar and pestle to break open the cell walls of the plant. Then, using a 99 degree Celsius water bath, we will break open the cell membrane and the nuclear membrane of the cell. Just outside the nucleus are enzymes called DNAse that protect the cell from viral infections. However, this enzyme will also attack the DNA we are trying to extract so we must use instagene matrix beads to kill them and protect the DNA. After doing a DNA Polymerase Chain Reaction (PCR), we will do electrophoresis of the PCR products. Based on the bands that show up on the gel, we will know if the plants we tested contain a T.I. plasmid which is found in 85% of cells. To prevent erroneous data, we will also test to see if the plants contain plant fiber, which all plants do. This way, if a band does not show up in either the T.I. lane or the plant fiber lane, we can assume the lab failed instead of that it is not a GMO. While there are many benefits of GMOs such as increased resistance to insects, frost, or disease, there are also many risks attached to them. People fear for the evolution of "superbugs" that could become resistant to all pesticides and destroy crops. Some people also have allergies to some proteins put into GMOs. Although there are many pros and cons to GMOs, nobody can be sure at this point in time of what the repercussions could be from these enhanced organisms.

Glowing Bacteria: The Future is Bright

Genetic transformation is a process in which one can change an organsim through the genes. Scientists recently began experimenting with this process to give new characteristics to living organisms by combining genes. By cutting, circular strands of DNA called plasmids with restriction enzymes, certain genes can be taken out and then combined with other cut plamids. DNA ligase is then added to seal the new strand and the new plasmid is completed. Scientists have many applications for this technique such as gentically engineering plants to be resistant to frost, insects, disease, etc. In this lab, we will first use a transfer pipet to transfer 250 µl of transformation solution (CaCl₂) into two tubes, one labeled +pGLO and the other labeled
-pGLO.  Then, after placing the tubes on ice, we will use a sterile loop to pick up bacteria from our starter plate and submerge them completely in each tube (using a different loop for each). Then we will ad 10 µl of plasmid DNA directly to liquid into just the +pGLO tube and flick the tube gently yo mix. Next we will return both the tubes to the ice for 10 minutes. After labeling four agar plates, we will begin to heat shock the tubes. By moving them from ice to a 42 degree celcius water bath, the phospholipid bilayer of the bacteria will stop repelling the plasmids and they will be able to enter the bacteria.  Then we will add 250 µl of LB nutrient broth to each tube. Finally, we will use new pipets to transfer 100 µl of each tube onto the appropriate plates and spread it around. The normal, untransformed bacteria should be killed by the ampicillin but the transformed bacteria has a resistance to this antibiotic. Therefore, this plate will glow a fluorescent green under UV light.

Biofuels: Fueling the Future

In our society, gasoline is becoming one of the most used and most expensive substances. Gasoline prices can rise dramatically, and we are at their mercy. However, there is a light at the end of the tunnel. A new concept, biofuels, have scientists working to find an alternative source of fuel. What are biofuels? Plant fiber contains a lot of sugar, but it is locked away securely. Scientists use enzymes such as E. Coli to break down these fibers and consume the sugars. (The molecule combined by an enzyme is called the substrate.) When this occurs,  substances such as ethanol are released, and these can be used as fuel. This idea is very important in today's world so that we can eliminate our dependence on oil. In this lab, we will combine cellulose, a plant fiber, with an enzyme called cellobiase that breaks down cellulose. Cellulose is comprised of two glucose molecules bonded together. When the enzyme breaks this bond, two individual glucose molecules are released and can be used as fuel. However, we are not able to see how fast this reaction is occurring. In order to observe the reaction's speed, we will add a mixture of cellobiase and an alternative substrate into five separate containers. This mixture creates glucose and P-nitrophenol. To these containers we will add stop solution at different time intervals. The stop solution will kill the cellobiase, essentially taking a snapshot of the reaction. The stop solution will also turn the P-nitrophenol yellow. By adding this at different time intervals, we can observe the differences between each container. Depending on the intensity of the yellow coloration, we know how far along the reaction is. On the next day, we will grind up mushrooms, creating a fungus extract, to add to the solution. Fungus contains many enzymes so adding this will speed up the reaction. We will compare different types of fungi to determine which type speeds the reaction up the most.