Microarraynalysis Results

In this experiment we found that there were two genes only turned on in cancerous cells(1 and 5) and two genes on in healthy cells (3 and 6). One of the other spots held a gene that was not turned on in either cell(4). The other was colored purple(2) and therefore on in both the cancerous and healthy tissues. The 4 differences of color between the two healthy blue genes and the red cancerous genes shows that the cancer cell is missing too necessary genes that probably kill unhealthy cells, and have two different cells turned on that probably send signals for the cancerous cell to continue to multiply. Sources of error could conclude from the short amount of time number 2 stayed purple or from the dye not being in high enough concentration. In conclusion this lab went very well.

Microarraynalysis Healthy and Cancerous Genes

In microarray analysis genes of comparing factors such as cancerous and healthy DNA are put onto DNA chip. The DNA chip would be used to analyze complementary DNA made from mRNA isolaed from cancerous and noncancerous tissue. The samples are flagged with dyes and the extent to which a flagged gene adheres to its complement reveals which genes show up in cancerous tissues as well as noncancerous tissues. This information is all processed by a computer and saves a lot of money and time. A single microarray can have more than 30,000 spots of DNA, each being a different gene. Some genes are not transcribed to RNA and eventually protein in cancerous cells and some are made too much of in cancerous cells. Finding the exact genes can help medical personal to create drugs to directly treat and eliminate cancer. We are personally using 6 genes in this lab for our microarray.

CSI Acalanes Results and Discussions.

Through electrophoresis, Katie Records DNA was matched to the DNA found upon the body of poor Trevor. The patterns in the DNA were exactly the only for Katie's DNA. The lab was really fun to carry through. Placing the DNA into the gel took a manner of precision and it really felt like we were practicing biotechnology for a living. The different coloring added to the long and short strands made it easy to identify. It was interesting that almost all the DNA samples had similar strand sections except for different strand. I believe some possible sources of error could be the partial breaking down of the DNA samples due to waiting overnight for the next class period. Also our table had the positive and negative ends mixed up and although I think we did it the right way it could be possible that we screwed up. Overall this was a very successful lab and I feel I learned a lot.

CSI 94549 Who killed Kenny?

Intro

Today DNA profiling does not only use fingerprints but any part of the suspect with DNA in it. Restriction enzymes are used to cut fragments of the DNa at specific sites and the resulting strands carry different lengths. DNA profilers can then use agorose gel electrophoresis. This process seperates DNA fragments by size by adding a blue color which attracts to the shorter strands and a cyan color that attracts to the longer strands. The lectrophoresis places DNA through a gelatin and has a direct current pass between wire electrodes. The DNA fragments are negatively charged and therefore are attracted to the other side or positive pole. Smaller DNA fragments can move easier through the gel and get farther. Based on the length of the strand a persons DNA pattern can be obtained. Humans can be up to 99.9 % identical DNA but that difference can still be huge. It is not likely to find two people with very similar DNA sequences in the same place. DNA testing is used to identify remains of soldiers killed in combat and currently frees 1/3rd of all sexual assault suspects. DNA testing can alos be used to identify different versions of the same disease. It can also determine whether a bone marrow transplant takes place and can show the relatedness of animals.

 DNA profiling was first discovered by Alec Jeffrey in 1984. DNA profiling is an encrypted set of numbers that reflects a persons genetic makeup. A buccal swab is used to pick up the DNA and avoid cross contamination. DNA can be picked up by anything, blood, semen, and other fluids/ tissues. Todays profiling is based on the number of repeat bases or short tandem repeats.

 Procedure

In this CSI lab 5 suspects will be taken and one will be the theoretical killer of a student. There DNA will be taken and using enzymes taken from ecoli they will cut the DNA into different sized strands. This will happen within an incubator for 45 minutes at 37 degrees Celsius the temperature that the ecoli generally lives at in the small intestine. After the incubation we shall add loading dye to the tubes of DNA. We will place the agarose gel in the the electrophoresis apparatus. The shorter strands in will reach closer to the positive end and visa versa. After 30 minutes the strands will be removed and dyed by either cyan for the shorter strands and blue for the longer strands. Based on the pattern of the DNA we will match it to the murderer.

Biofueling Future Generations

Introduction

 Backround: In this lab we are exploring the world of creating biofuels from plants. The process uses enzyymes and bacteria to create a finished product. Enzymes are proteins that speed up chemical reactions without actually being consumed. Increasing temperature can speed up reactions but if enzymes are neccessary the temperature has to be at a specific range to be effective. Most enzymes function at a range between 20-40 degrees Celsius.In this lab we are taking the sugars found within cellulose within the cell wall of plants. In this reaction cellulases will break down the cellulose into strands of glucose. Ethanol was the first type of biofuel to be created but because of its low yield of energy, scientists have begun to search for more effective solutions. Our lab is a miniature version of this research and in order to make sure detect that our lab was successful in creating glucose we are adding a seperate substrate called p-nitrophenol which when added to a basic solution, will cause the solution to turn yellow. On the second day of this lab we will dealing with mushrooms that are naturally decomposers, which should break down the cellulose just as effective. Today most gas stations contain 10 percent ethanol within the regular gasoline.

Hypothesis: I believe that adding mushrooms on day two  will speed up the reaction because mushrooms are naturally decomposers and therefore will do their job effectively and increase the reaction rate.

Procedure: In this lab we are taking cellulose from plants and introducing an enzyme called cellobiose which creates two glucose molecules bonded together. If we wanted to make ethanol we would then add cellubiase which would break the molecule into two glucose which we would then create into fuel and burning the fuel would create energy. Instead we are adding an alternative substrate which will make a glucose molecule and Pnitrophenol. The addition of a strong base will begin to turn the solution yellow and throughout the reaction we will add some of the solution to a number of vials.

Results: In the lab adding enzymes to our substrates did not change anything on the macroscopic level. Only when the base was added did the product turn yellow. On day two the mushrooms extract did the exact same thing and therefore should contain similar enzymes for breaking down the cellubiose. Some possible sources of error could have been, leftover products from the class before us, changing the rate of reaction slightly, or different conditions from day one to day 2. 

DNA Analysis

After following the directions I received visible DNA within my necklace. I did not get a lot of DNA to show up, and think this was due to shaking my tube too hard. I shook the tube twice because I was distracted and almost skipped a step. Other possible sources of error may have been cross contamination of the pipettes by other classes, or the cold day could have skewed the process some.

DNA procedure

In his lab we are extracting cheek cells from our mouth. We spit the salt solution with the cells into a cup and then put it into a a test tube. A lysis buffer is added to break apart the cell, and then protease is added to break up the protein. We incubate the protease, and then afterwards add cold alcohol so the DNA strands bunch up. A necklace is made and then we get to wear it!

DNA: Taking A Part of yourself

DNA is what life is made of. All organisms contain DNA and the different genes within DNA give them their individuals traits. DNA is in a double helix structure and the bases connect A to T and C to G. Each base is connected to a phosphate and a sugar. A nucleotide has all three. The four chemical letters make genes which contain information to make proteins. DNA is made into structures called chromosomes and every human has 2 pairs of 23. DNA is found within every cell except for red blood cells. DNA doesn't directly make proteins first messenger RNA copiesbthe genes needed and then carries them to the ribosomes within the cytoplasm. The ribosomes process the information and put together the needed amino acids to make needed prote ins.

Yogurt Discussion

In our data the first test tube contained only milk and came out as a ph of 6. I found this interesting because the second tube with yogurt and milk was also at a ph of 6. The yogurt tube was starting to smell like yogurt but the first tube didn't smell like much. I theorize that bacteria floating in the air changed the ph slightly. Tube 3 containing the yogurt and ampicillin came out with a ph of 7. This makes sense because the ampicilin added must have killed off the bacteria within the yogurt changing the acidity of the solution. Tube 6 containing the ecoli came out with a ph of 7 which surprised me. I believed the ecoli would devour the milk and begin to bring the ph down. I knew they wouldn't turn it to yogurt but I thought there would be more change. The control cup of fully formed yogurt contained a ph of 4 which easily made sense. Some possible sources of error for this lab would be maybe not tightening the cap enough, or the test tubes were not in the incubator for long enough.  

Yogurt; Milk, Bacteria, Science!

Yogurt: A Yummy Bacterial Experiment

Until the 1800s microbial diseases were a mystery. This all changed after robert koch worked with diseases. He developed a postulate that we use today. It consists of identifying a disease, isolating it, implementing it into a healthy subject and successfully take out bacteria of the same origion now in the once healthy person. This can be used for good bacteria as well especially because most bacteria are not harmful. They are also the most populous form of life. Bacteria don't have a nucleus and move with tiny flagella. There are three types of bacteria, round, rod, and spiral shaped. Bacteria divide as fast as 15 minutes and can become billions overnight. In our lab we will be dealing with bacteria with different types of cell walls as well. The lactic acid bacteria that make the yogurt are gram positive, while the ecoli we are adding in a separate container is gram negative. We are using anaerobic bacteria that make lactic acid and do not require oxygen. This keeps harmful bacteria from eating the yogurt because it's acidic. In most countries a product may only be called yogurt only if the finishing project contains live bacteria. In our lab we will experiment with bacterial strains found in the yogurt sample and use it to create more yogurt out of fresh milk. There will be four tubes the first containing just milk, the second containing just yogurt, the third will contain yogurt and ampicilin which is an antibiotic and finally the fourth tube will contain ecoli in the milk solution. For my hypothesis I believe that the solution with milk only will remain unchained, the tube with milk and yogurt will begin to change, the tube with ampicilin and yogurt will kill of the yogurt bacteria, and the ecoli and milk will begin to smell rotten