Today, scientists use a process called microarray to find differences in gene expressions, since it allows scientists to see a specific gene in a cell. Which makes it alot easier to find these differences because you don't have to look at the entire genome to find what your looking for. Definition: DNA microarray is thousands of microscopic spots of DNA oligonucleotides, which have specific probes on them. Scientists today, use these microarrays to find specific gene sequences that cause human health problems such as skin cancer, breat cancer and etc.
Steps for the Microarray:
1. Isolate DNA.
2. Pelimanary chains reactions make more genes.
3. Then a robot spots individual gene sequences into specific addresses onto a DNA chip
4. Then the mRNA from the tissue of interest is dyed red and also the mRNA from a second tissue of interest is dyed green.
5. Finally these mRNAs are put on the chip and analyzed.
For our Microarray lab we followed these same procedures to determine which six genes we had ( ODC1, C4BPA,FGG,HBG1,CYP24 and SIAT9), caused lung cancer, from the two samples we have from a cancerous cell and a healthy cell.
Thursday, November 18, 2010
Monday, November 1, 2010
CSI: Crime Scene Investigation Lafayette
Background: Scientists today, use a bacterial defense mechanism called the restriction enzyme. A restriction enzyme is basically like a "restriction scissors" that make cuts at certain areas in a sequence of base pairs that are recognized by the enzyme. This enzyme has derived from viruses that eject their DNA into a cell, and use the restriction enzyme, as a bacterial defense. A restriction enzyme, basically slides down a DNA molecule, until it starts to recognize a specific sequence, this then causes the enzyme to stop sliding and cut the strand off that is recognized by the restriction enzyme. Once this happens scientists take this specific strand and place it into a process called agarose gel electrophoresis, which separates the strand so it can then be observed. This process is done, by placing the DNA fragments into an agarose gel slab, which is placed into a chamber filled with conductive buffer solution, then a direct current is passed between wire electrodes at each end of the chamber. Since DNA fragments are negatively charged, they are going to move towards the positive poles in the electric field. Once this happens, the agarose gel acts like a "molecular sieve" which smaller DNA fragments move easier than larger fragments. Some time after, the smaller fragments will have traveled further than the larger pieces, creating single bands of DNA at certain places, which are then stained so the bands can then be seen. This is just like DNA fingerprinting from crime scenes, but they use radioactive probes that are specific to certain nucleotide sequences and then compare the DNA of different people.
Purpose: Our purpose for this lab is to figure out who committed the crime by using a forensic DNA
fingerprinting kit.
Lab instructions: 1. First we labeled micro test tubes CS (crime scene), S1 (suspect one), S2 (suspect two), S3 (suspect three), S4 (suspect four), S5 (suspect 5).
2. Then we took a DNA sample form each stock tube and placed the specific DNA samples in the corresponding tubes (using a 10 pipet).
3. Then we used a centrifuge to mix the components together.
4. Next we placed our tubes in a foam micro tube and incubated them overnight in 37 C water.
5. Then we added 5 hl of loading dye in each tube.
6. Then we added each sample in its specific well in the agarose gel, while it was in the electrophoresis apparatus with 275 ml of buffer solution.
8. After that, we turned on the electrophoresis chamber for 3 minutes and then turned off the apparatus.
9. Next, Mr. Chugh stained our agarose gel with 120 ml of 1x Fast Blast DNA staining it overnight.
10. The next day we saw our end results of our lab.
Observations and Results: Once our agrose gel was complete I could easily see deep blue strands of DNA in certain places on the gel. In our end results, we came to a conclusion that suspect 3 or Chloe had to have done the because, the DNA strands from suspect 3 (Chloe), was closely related to the one found at the crime scene. Though we were sure that our results were correct, we could have accidentally not put enough of the DNA in well # 3, since the DNA strands in 3 were very faint and hard to see where the location of the strands were in the agarose gel.
Agarose Gel Electrophoresis
Purpose: Our purpose for this lab is to figure out who committed the crime by using a forensic DNA
fingerprinting kit.
Lab instructions: 1. First we labeled micro test tubes CS (crime scene), S1 (suspect one), S2 (suspect two), S3 (suspect three), S4 (suspect four), S5 (suspect 5).
2. Then we took a DNA sample form each stock tube and placed the specific DNA samples in the corresponding tubes (using a 10 pipet).
3. Then we used a centrifuge to mix the components together.
4. Next we placed our tubes in a foam micro tube and incubated them overnight in 37 C water.
5. Then we added 5 hl of loading dye in each tube.
6. Then we added each sample in its specific well in the agarose gel, while it was in the electrophoresis apparatus with 275 ml of buffer solution.
8. After that, we turned on the electrophoresis chamber for 3 minutes and then turned off the apparatus.
9. Next, Mr. Chugh stained our agarose gel with 120 ml of 1x Fast Blast DNA staining it overnight.
10. The next day we saw our end results of our lab.
Observations and Results: Once our agrose gel was complete I could easily see deep blue strands of DNA in certain places on the gel. In our end results, we came to a conclusion that suspect 3 or Chloe had to have done the because, the DNA strands from suspect 3 (Chloe), was closely related to the one found at the crime scene. Though we were sure that our results were correct, we could have accidentally not put enough of the DNA in well # 3, since the DNA strands in 3 were very faint and hard to see where the location of the strands were in the agarose gel.
Tuesday, October 12, 2010
Enzymes and Biofuels
Background info:
General information about Enzymes: Enzymes help speed up the process of chemical reactions, and are able to work again and again, converting reactants into products, since they do not react with substrat.(Substrat is the reactant in an enzyme-catalyzed reaction.)
Cellulase: Cellulase is the structural polysaccharide found in the cell walls of plants, that is only contained in plants because it's the source of sugars for the plant. Though animals cannot produce cellulose, some animals that eat plants, have a bacteria that produces cellulose. For instance cows produce cellulose because they have a bacteria called Bacteriodes succinogenes, that produces cellulose for them.
Cellulose practical uses: Cellulose today, is used in the bio fuel industry to create ethanol that can help run cars, planes and more. Cellulose is converted into ethanol by extracting the cellulose from a plant's cell wall then converting it into a sugar, and finally the product is changed to ethanol through microbial fermentation.
Purpose: Our purpose for this experiment is to gain more research about the reaction rate in the presence of an enzyme.
Lab instructions:
First we label five curevttes E1-E5, then we put stop solution in all the curvettes. Because we are adding the stop solution, it will dentaure the enzyme reaction, which will cause p- nitrophenal to turn yellow. Since this solution will turn yellow, it will show how much of a reaction is happening. After this, we will then add substrate to both the enzyme reaction tube and the controlled tube. Then, we will add a buffer to the controlled test tube and then put this solution in the curvette labeled E1. After, we then add some of the enzyme reaction solution to the curvette and then start our timers. After this, we will then add more enzyme reaction to each curvette at set times. On day two of the lab, we used a mushroom as our enzyme instead, by extracting the enzyme in the mushroom with the centrifuge.
Hypothesis and Results: I think the curvettes that have had the longest length in contact with the reaction solution, will be a more darker yellow, while the ones that weren't in contact with the reaction solution, will have a light yellow color. My hypothesis was correct, as we put the solution in the curvette and let it set for a longer time, the more yellow it would turn,which meant more of the product was being produced. Though, we believe our end results were very accurate it, we could have had one mistake, which could have been using dirty curvettes that weren't thoroughly washed from the last period. We also learned that the reaction of the enzymes would soon end because the enzymes would lose recources to make more product, since we saw this in the mushroom lab.
General information about Enzymes: Enzymes help speed up the process of chemical reactions, and are able to work again and again, converting reactants into products, since they do not react with substrat.(Substrat is the reactant in an enzyme-catalyzed reaction.)
Cellulase: Cellulase is the structural polysaccharide found in the cell walls of plants, that is only contained in plants because it's the source of sugars for the plant. Though animals cannot produce cellulose, some animals that eat plants, have a bacteria that produces cellulose. For instance cows produce cellulose because they have a bacteria called Bacteriodes succinogenes, that produces cellulose for them.
Cellulose practical uses: Cellulose today, is used in the bio fuel industry to create ethanol that can help run cars, planes and more. Cellulose is converted into ethanol by extracting the cellulose from a plant's cell wall then converting it into a sugar, and finally the product is changed to ethanol through microbial fermentation.
Purpose: Our purpose for this experiment is to gain more research about the reaction rate in the presence of an enzyme.
Lab instructions:
First we label five curevttes E1-E5, then we put stop solution in all the curvettes. Because we are adding the stop solution, it will dentaure the enzyme reaction, which will cause p- nitrophenal to turn yellow. Since this solution will turn yellow, it will show how much of a reaction is happening. After this, we will then add substrate to both the enzyme reaction tube and the controlled tube. Then, we will add a buffer to the controlled test tube and then put this solution in the curvette labeled E1. After, we then add some of the enzyme reaction solution to the curvette and then start our timers. After this, we will then add more enzyme reaction to each curvette at set times. On day two of the lab, we used a mushroom as our enzyme instead, by extracting the enzyme in the mushroom with the centrifuge.
Hypothesis and Results: I think the curvettes that have had the longest length in contact with the reaction solution, will be a more darker yellow, while the ones that weren't in contact with the reaction solution, will have a light yellow color. My hypothesis was correct, as we put the solution in the curvette and let it set for a longer time, the more yellow it would turn,which meant more of the product was being produced. Though, we believe our end results were very accurate it, we could have had one mistake, which could have been using dirty curvettes that weren't thoroughly washed from the last period. We also learned that the reaction of the enzymes would soon end because the enzymes would lose recources to make more product, since we saw this in the mushroom lab.
Wednesday, September 15, 2010
DNA Extraction
DNA, also known as Deoxyribonucleic acid, is a molecule found in every living thing, and carry's all the genetic information of a living thing. DNA is responsible for making a person have a certain eye color, hair color, skin color, your height, and more. DNA is a double helix, which looks like a twisted ladder. DNA is made up of bases containing adenine, guanine, thymine and cytosine, in which Adenine and Thymine always pair with one another and Guanine and Cytosine always pair with each other. These bases or chemical letters are responsible for making organized messages that are understood by genes. Once this information is sent to the genes, the genes then make proteins, which are the basis of all your bodies structure and function, about 40,000 genes can be found in the human genome. Another molecule called RNA, helps duplicate DNA, so it can then be brought to the ribosomes. Once at the ribosomes, they help decode the genetic information and add certain amino acid to the proteins, to finally make cell traits. DNA can be found in the nucleus of every cell in the human body and animal bodies.
Our purpose during this lab, is to precipitate DNA ( dissolve DNA) so we can observe our own DNA and study it.
Our purpose during this lab, is to precipitate DNA ( dissolve DNA) so we can observe our own DNA and study it.
Tuesday, August 31, 2010
Intro
Bacteria are microscopic single celled organisms that can be seen only with the help of a microscope. Bacteria cause many diseases because they increase in number of bacteria rapidly, because of binary fission, which is the splitting and dividing of bacteria. Though many people think all bacteria are harmful to humans, in actuality, only a tiny portion of bacteria are capable of causing diseases. Some diseases caused by harmful bacteria are cholera and tuberculosis, but because of the development of antibiotics, most bacteria related illnesses are very low and treatable. The other bacteria which are beneficial to humans, actually live inside our intestines, helping digest our food and also help produce food products such as cheese, yogurt, pickles and yogurt.
Yogurt is produced by scalding milk at 80 C, then adding yogurt bacteria when it is at a cooler temperature, then after 24 hours you have YOGURT. Yogurt is produced because the bacteria in the yogurt, eat the milk proteins, which converts it into lactic acid, causing denaturation, which makes yogurt into a solid mass. In result of denaturation, all bad bacteria is killed and close to a billion good bacteria are left in the yogurt, making yogurt a great probiotic.
Our purpose for creating the yogurt, in our lab is to help prove Koch's postulates, which is to prove that a disease spread from a host is the same disease when someone is inoculated by the host. Since Koch's postulate is to find the microbe in all sick people, but not in healthy people. Then Step 2 is to culture that microbe, then step 3 is to inoculate a healthy person with the microbe. In our procedure milk is the healthy person and yogurt is the microbe. Then step 4 is to culture microbe from the new sick people and check to see that it is the same.
In our procedure, we are going to have 4 tubes, a negative control (milk), a positive control (yogurt), a tube with yogurt and ampicilla, and another tube with milk and ecoli. After these are mixed, we are going to put these tubes in an incubator at a temperature of 37 C for at least one or two days.
Our end results of our data showed that our negative control tube 1, became very watery rather than producing yogurt. In this tube their was only a small solid chunk and the rest was watery, and looked clear with a little foul smell. Our next test tube was test tube # 2 Positive control, which turned into a yogurt substance because it was very solid and had a white solid color with a yogurt smell. Our next test tube #3 which was yogurt and ampicillin, which was very watery, but had a pure white color. We guess that this test tube was unable to make yogurt because the ampicillin killed all the necessary bacteria to make yogurt. In test tube # 6 which contained E.coli, had a very watery texture with a pure white color. Which made me think, that possibly the E.coli added to much bad bacteria or just killed all the good bacteria. In all I think our lab was very accurate and had no mistakes because it matched our hypothesis for the end results.
Yogurt is produced by scalding milk at 80 C, then adding yogurt bacteria when it is at a cooler temperature, then after 24 hours you have YOGURT. Yogurt is produced because the bacteria in the yogurt, eat the milk proteins, which converts it into lactic acid, causing denaturation, which makes yogurt into a solid mass. In result of denaturation, all bad bacteria is killed and close to a billion good bacteria are left in the yogurt, making yogurt a great probiotic.
Our purpose for creating the yogurt, in our lab is to help prove Koch's postulates, which is to prove that a disease spread from a host is the same disease when someone is inoculated by the host. Since Koch's postulate is to find the microbe in all sick people, but not in healthy people. Then Step 2 is to culture that microbe, then step 3 is to inoculate a healthy person with the microbe. In our procedure milk is the healthy person and yogurt is the microbe. Then step 4 is to culture microbe from the new sick people and check to see that it is the same.
In our procedure, we are going to have 4 tubes, a negative control (milk), a positive control (yogurt), a tube with yogurt and ampicilla, and another tube with milk and ecoli. After these are mixed, we are going to put these tubes in an incubator at a temperature of 37 C for at least one or two days.
Our end results of our data showed that our negative control tube 1, became very watery rather than producing yogurt. In this tube their was only a small solid chunk and the rest was watery, and looked clear with a little foul smell. Our next test tube was test tube # 2 Positive control, which turned into a yogurt substance because it was very solid and had a white solid color with a yogurt smell. Our next test tube #3 which was yogurt and ampicillin, which was very watery, but had a pure white color. We guess that this test tube was unable to make yogurt because the ampicillin killed all the necessary bacteria to make yogurt. In test tube # 6 which contained E.coli, had a very watery texture with a pure white color. Which made me think, that possibly the E.coli added to much bad bacteria or just killed all the good bacteria. In all I think our lab was very accurate and had no mistakes because it matched our hypothesis for the end results.
Subscribe to:
Comments (Atom)