Discussing The Strategic Use Of Microarrays In The Study Of Lung Cancer Genes

A) Results: From the gene chip our lab group was able to determine that: Genes 1, 2, and 5 were active in in the cancer cells, Genes 2,3, and 6 were expressed in cells obtained from healthy tissue, and also that Gene 4 was express in neither the healthy cells nor the cancerous cells. We were able to tell this becauseof the colors of each gene on the slide. Genes 1 and 5 were pink (pink means expressed only in cancer), Genes 3 and 6 were blue (blue means only expressed in healthy cells) , Gene 2 was purple (this represents expression in both healthy and cancerous), and Gene 4 was clear (expressed in neither).

B) Sources of Error:
- Not enough of the cDNA was added, and the true color of the gene was not shown.
- The genes from the gene chip were not accurate, and we tested the expression of the wrong gene.
- We pipetted too much of the cDNA, and the slide overflowed, thus we were unable to get an accurate reading of the expression of the certain gene.
- We left the gel in the pipette for too long so it hardened and less than 20 microliters was exposed to the slide.

Translating Diseases; The Strategic Use Of Microarrays In The Study Of Lung Cancer Genes

A) Microarrays have simplified how scientists study gene expression in thousands of cells. This new technology detects patterns in transcription and translation, and aids in the understanding of the normal and abnormal aspects of cell function. The process of using Microarrays to analyze/study genes involving lung cancer include: creating a DNA chip, and using the DNA chip to analyze complementary DNAs isolated from both cancerous and noncancerous tissue (the same tissue). The Microarray will then indicate the differences between the two corresponding genes. This will be an indication of the extent to which transcription occurred. Some scientists have indeed observed that some genes are not transcribed as much in cancer cells as in healthy cells, and that some genes are not transcribed as much in healthy cells as in cancer cells.

B) The purpose of this experiment is for our lab table to use Microarrays to study Genes Involved in Lung Cancer. This will hopefully give our group a better understanding of the causes of the disease on a genetic level, and thus allow us to speculate with possible methods to prevent or cure it.

C) In this experiment, our lab table will be studying six genes using a Microarray. We will prepare the Microarray by spotting six different gene sequences onto a glass slide. Then we will obtain DNA tubes from a 70 degree water bath, and spot the appropriate gene solution onto the correct areas of out slide. To hybridize the Microarray, our group will add fifteen microliters of hybridization solution to each spot. We will then wait and observe our results when they appear.

D) Although we have the six genes that we are to study, making predictions is not possible because we do not have the background knowledge to hypothesize our results. However, I am quite certain that our group will accomplish something worthwhile, and we will learn valuable facts about gene expression and the effects of cancer on this.

The Sticky Ends Justify The Means Discussion

A) During Day one of the lab, our lab table acquired the DNA of the five suspects, and the DNA found at the crime scene. The purpose of the experiment was to identify the culprit by matching the DNA found at the scene with the DNA of the five suspects using Restriction Fragment Length Polymorphism. After acquiring the DNA, we added restriction enzymes to the tubes, flicked/tapped them, and placed them in a hot water bath for 30 minutes. On Day two we ran the newly cut DNA through a gel, and visually compared the samples using loading dye to stain the DNA (make it visible), and attracting the fragments to the positive end through Gel electrophoresis. Gel electrophoresis functions by pulling fragments of DNA (negatively charged) through the gel matrix towards the red end (positive), run to red. On Day three, our group was able to compare the DNA of the five suspects with the DNA found at the crime scene. We were able to positively identify Chloe Krey as the culprit in this crime scene.

B) Possible Sources of Error:
- We did not add enough loading Dye so the DNA fragments were not visual.
- Accidentally scraped off a skin cell into a test tube, and my DNA was analyzed instead of a suspect's DNA.
- We did not add enough DNA to the tube, and thus not enough substance was present for DNA to become fully visible.
- Accidentally added the wrong suspects DNA into the wrong well, and the wrong suspect was 'proven' guilty by the DNA evidence.
- Accidentally added the food coloring in place of the Loading Dye, and the DNA was not properly stained thus leading to an inaccurate reading.

The Sticky Ends Justify The Means; The Strategic Use of Restriction Enzymes In DNA Fingerprinting

A) DNA fingerprinting has revolutionized how crimes are solved, and has also aided in other applications. Since described in 1985, Restriction Fragment Polymorphism (RFLP) has acted as the factotum for DNA fingerprinting/profiling, and currently Polymerase Chain Reaction (PCR) is in use. The Restriction Enzymes are vital to the functionality of DNA fingerprinting. Restriction Enzymes are obtained from E-Coli, and the enzymes act as a natural defense against viruses. Restriction Enzymes work by cutting DNA at palindromes. To compare the desired strands of DNA, it is ran on a gel. The DNA differences are the fragments of different lengths. Running DNA on a gel produces different results, because gel electrophoresis is the use of electricity on a gel, giving it both a positive and a negative end. DNA has a slightly negative charge, so the fragments run to red. In the case of DNA, the smaller fragments go farther and the larger fragments remain closer to the original well.

B) The purpose of this experiment is to match DNA from a crime scene. During the experiment, our lab table will be attempting to match the DNA of the suspects with the DNA found at the crime scene. We hope to analyze the DNA correctly and receive experience in the field of crime solving.

C) The use of Restriction Enzymes in this experiment is vital. To analyze the various sample of DNA, and to successfully determine the culprit we will be using six samples of DNA: one from the crime scene, and five other tubes which contain DNA samples from suspects 1-5. We will be pipetting the restriction enzymes into the different tubes. We will then make a gel  (add correct ingredients, and mix it) and run the various samples with a dye to make the fragments visible on the gel. The smaller fragments will move farther, and the success of the lab will depend on the similarities between the crime scene DNA and the DNA from one of the five sample tubes. The Variables of this experiment will be the five DNA samples, and the control will be the DNA from the crime scene. We will attempt to visually compare and identify the controls with the variables to figure out which variable most matches the control.

D) The hypothesis cannot be produced at this time, because I have no knowledge of the suspects or the crime. However, I do predict success for my lab group and I as we use DNA fingerprinting in our special CSI lab.

Prolonging Life with Life Discussion

A)  Throughout day one the lab, our group attempted to record the effectiveness and efficiency of cellobiase on an artificial substrate which represented cellobiose. One day two of the lab, our group measured the effectiveness and efficiency of edible mushroom in turning cellobiose into glucose. We measured the rate of conversion from the artificial substrate (acts as cellobiose) to glucose by adding a strong base. The strong base turns the artificial substrate yellow, and stops cellobiase. To measure reaction rate, we labeled five tubes and added a fixed amount of artificial substrate and cellobiase (day 1) and a fixed amount of artificial substrate and our mushroom (day 2)., and added the strong base at set points in time. This allowed our group to discover that both were approximately even when it came to efficiency. Overall, my hypothesis was correct. The cellobiose was converted into glucose efficiently by both the cellobiase and the mushroom solution on both day one and day two of the lab.

B) Possible Sources of Error:
- When adding the strong base, we could have added it at the wrong time messing up the correct coloration of yellow.
- Failed to grind the mushroom up enough, thus the majority of the enzymes remained unable to produce glucose.
- Not enough cellobiase was added, thus a slower conversion occurred and inaccurate readings were obtained by our group.
- The centrifuge was not spinning for long enough to fully separate the mushroom solution, not enough of the mushroom was added to accurately convert the artificial substrate.
- Too much cellobiase was added, so the artificial substrate was converted too rapidly for our group to notice a change after three minutes.

Prolonging Life With Life; Extending The Future By Exploring Possibile Benefits Of Biofuels

A) The current fuel system is subject to change. The global economy is dependent on petroleum, which is a polluting natural resource which is destined to run out. Although the future seems bleak for the global economy, there is hope in alternate fuels. Some of the most promising of the prospects to replace gasoline are biofuels. Biofuels are the classification for fuels derived from biomass. In the wall of plant cells lies a polymer with a lot of potential named cellulose. Cellulose cannot be broken down naturally by animals, and this is the reason why it's importance for energy has not become relevant until now. Cellulose is broken down by the cellulose enzyme which is present on the inside of Protists. Enzymes are beneficial to reactions because they speed up chemical reactions and are not consumed with the reaction, so they can be used again and again. The majority of enzymes are proteins, and have a specific 3-D structure. For a chemical reaction to take place, the active site (site of chemical reaction) binds to the substrate (the reactant of the enzyme catalyzed reaction). The process is sped up because the substrate is positioned in a way which allows the transition state of the reaction to become stabilized, and the activation energy is lowered to allow quicker reaction rate. However, the conditions of enzymes must be kept within an optimal range, (the right pH, the right temperature, and the right level of salinity). For centuries, termites have broken down cellulose and used its energy as fuel, and not until recently, scientists discovered how the termites were able to accomplish this feat. The termites have a protozoan called Trichonympha living inside their abdomen, and the trichonymphba has a bacterium named Rs-D17 that lives inside it and produces cellulase enzymes, including cellulase. Cellulase enzymes convert the cellulose into cellobiose, which is converted into two glucose molecules by the enzyme cellobiase. Biofuels work by using glucose (energy) obtained from cellulose to power their engines.

B) For our class, the purpose of this experiment is to measure the enzymatic activity of cellobiase, and to identify the optimal conditions for the enzyme. This also acts as a real world example of the possibilities behind enzymatic studies, and the relevance in the possible future. For industry, the research of Biofuels can offer an alternative energy which would be more sustainable than petroleum. The biofuels offer a new future for industry, one which could make life less polluting, more sustainable, and more reliable.

C) The lab will start with a one milliliter pipette of cellulose. Cellulose is broken down by bacteria, protists, and fungi, so we will use enzymes derived from these sources to convert cellulose into cellobiase. Cellobiase is composed of two glucose molecules, and will be the substrate of the experiment. Cellobiose will be placed in a test tube along with Cellobiase, an enzyme which breaks down cellobiose into single glucose molecules. To measure the effect of the cellobiase on the cellobiose, we will substitute the cellobiose with an artificial substrate. The artificial substrate will be composed of Glucose and P-Nitrophenol. At various time points, we will add a strong base to the test tube which kills cellobiase, and turns P-Nitrophenol yellow. This will allow documentation of the coloration of the test tube, and we will be able to drw a conclusion from this data. For extended exploration in this experiment, we will bring in mushrooms to test which mushrooms are better decomposers. We will grind up the mushrooms, and add them in place of the cellobiase (add them with the Glucose and P-Nitrophenol). This part of the experiment will give us a greater understanding of the cellobiase content in the foods that we eat, and also in some of the mushrooms that we see.

D) I believe that the cellobiase in Day 1 will make glucose disappear faster than the ground mushrooms which we will add in day 2. The controls of this experiment are the Cellobiase and the artificial substrate (Day 1), while the variables of the experiment will be the ground mushrooms and artificial substrate (Day 2). The cellobiase acts as the control, because cellobiase will definitely separate the artificial substrate at a quicker pace with its higher concentration. The ground mushroom acts as the variable in this case, because we are unaware of the cellobiase concentration within the organism, and we are charting the difference between cellobiase and the mushroom.

DNA Precipitation Lab Discussion

A) Discussion:
The resluts of the DNA precipitation lab were approximately what I had predicted. My earlier predictions included that I would receive a transparent little knot of precipitated DNA, and that part was true. My group and I performed every part of the procedure correctly, and precisely, which allowed each of us to obtain favorable results.

B) Possible Sources of Error:
-Ate a chicken sandwhich during brunch, and precipitated the DNA of a chicken.
-No cheek cells were extracted from mouth, so there was no DNA to precipitate.
-Lab table member accidently contaminated the lysis buffer pipette with his or her DNA by dipping pipette into their test tube.
-The inverting of the tube was not intense enough, and the lysis buffer was not thoroughly mixed in. Thus the cell membranes were not dissolved and the DNA never left the cell.
-We did not add enough Protease, and the DNASE survived to kill all of my DNA.
-The inverting of the tube with the protease was too intense, and all of he DNA stuck to the sides of the tube.
-I accidentally removed the tube from the hot water bath too soon, so the necessary chemical reactions did not occur.
-Read the directions incorrectly, and added 10 microliters instead of 10 milliliters.
-When placing the precipiataed DNA in the supercool class necklace, applied too much pressure to the glass case itself and the glass broke in my hand.

Our Own Slice Of Immortality; The Extraction and Precipitation Of Our DNA

A) For all living  organisms DNA is present, and for some, DNA is the code for life. However, not until fairly recently have scientists known DNA's genetic importance. In human beings DNA codes for such traits as hair color, eye color, height, facial features and blood type. In 1953, James Watson, Francis Crick and discovered the structure of DNA with the help of Rosalind Franklin. The scientists built a model of DNA, which was the first accurate model of its time. Their model described that DNA a double helix, connected by four nitrogenous base pairs, adenine, thymine, guanine, and cytosine. Each base is connected to a sugar and a phosphate group, which act as the backbones of the structure. The entire unit is called a nucleotide. The DNA of the cell is found in the nucleus of almost every cell of the human body (because an enzyme called DNASE evolved to kill all DNA outside of the nucleus in case the DNA was viral). The DNA is coiled up around histones (proteins) and organized into structures called chromosomes. There are 46 chromosomes in human cells, and all of the genetic information contained in the 46 chromosomes represents the genome. A gene is a section of DNA which codes for a certain trait. Humans receive their DNA from their parents, half from the father, and half from the mother.

B) The purpose of this experiment is to precipitate our own DNA. Precipitating our DNA will make it visual, and we will have the chance to view our very own DNA. This allows us to compare it, and would allow us to test it, clone it or sequence it.

C) To precipitate our DNA, the first objective we must complete is to extract our cheek cells by rinsing our mouths vigorously with a 0.9% saline (isotonic) solution. The solution will allow for quick extraction, and the cells will not burst in an isotonic solution. We will then add the lysis buffer (soap), and invert the tube several times to mix in the buffer completely. The lysis buffer will break open the cell membrane by dissolving the phospholipids in the plasma membrane. After the addition of the buffer, protease will be added and the tube inverted to spread the Protease throughout the test tube. Protease had the purpose of destroying DNASE before DNASE can kill our DNA. DNA has a negative charge, and water has a positive charge. Because of this, DNa is hydrophilic (attracted to water) and will dissolve in water. To counter this, we will add salt which will neutralize DNA's charge. Without a negative charge, DNA will become hydrophobic and non-polar. Our DNA will then be placed in a hot water bath to speed up the reaction time and break open the cell membrane. To finish this process we will add cold ethanol to precipitate the DNA. Ethanol is the preferred substance because of it's lower freezing point. It will become colder while staying a liquid.

Yogurt Lab Discussion

A) The predictions that my lab table gave were approximately what we received as results. In tube 1 (the milk), the milk never transformed into yogurt, because there was no addition of a probiotic. Tube 1 was acting as a control, a basis for what the milk was to look and smell like, and also to give the lab researcher an idea of the texture. Some of the physical properties of tube 1 include: a semi-liquid texture, a smell of slightly sour milk, a white color, and a pH of 7. In tube 2, the milk and the addition of the yogurt (the probiotic), transformed the milk and yogurt into yogurt. Tube 2 was a variable, because the results of the milk added to the yogurt could have either changed or remained the same. The purpose of a variable is to measure the transformation and possible change that a certain experiment could cause. The properties of tube 2 include: a semi-solid texture, a smell of yogurt, a white color with a transparent film at the top, and a pH of 4. Tube 3 was composed of milk, yogurt, and ampicillin. This tube was also a variable in this experiment, as we were trying to figure out if yogurt could be produced with the addition of an antibiotic. The end result was no, because the ampicillin killed the bacteria in yogurt which did not allow the transformation from milk to yogurt to occur. The physical properties of tube 3 include: a semi-liquid texture, a smell of sour milk, a white color and a pH of 7. In our final test tube, tube 4, we tried using a different type of bacteria to make yogurt. This was also a variable, because E.Coli is another type of bacteria, and our lab group was attempting to find if any type of bacteria could create yogurt. E.Coli did not produce yogurt, some of the physical properties of tube 4 are: a semi-liquid texture, an unattractive smell (bad smell), a white color and a pH of 7. The yogurt up in the front of the classroom is worthy of mentioning, as it acted a control for tube 2. The yogurt had a pH of 4, and a yogurt smell, a white color, and a semi-solid texture. Our table succeeded in creating yogurt.

B) Possible Sources of error include:
- Accidentally adding ampicillin to tube 2, which causes all the bacteria to die. Which means no yogurt is produced.
- We used the same yellow rod to add yogurt to all 4 of our tubes, and we add ampicillin to tube(s) 1, 2, or 4 on accident.
-The vortex could have shaken the tubes so violently that the ampicillin stuck to the roof of the tube and we created yogurt in tube 3.
-The hot water bath was so hot that the DNA strands in the bacteria's nucleoids denatured, thus making the process of yogurt making impossible.
- The hot water bath was not hot enough to pasteurize the yogurt, so bad bacteria survived and spoiled the milk or yogurt
- The vortex did not move enough to thoroughly mix in the contents of tube 2, tube 3, or tube 4 so either yogurt was not produced, ampicillin did not come into contact with the yogurt and yogurt was produced, or the E.Coli was just pooled at the bottom
- We dropped all of our tubes on the ground and bad bacteria entered all of the tubes and spoiled the various results

Exploring the Technological and Biological Factors in the Process of Yogurt Making

A) For hundreds or even thousands of years, Yogurt has been a delicious treat enjoyed by humans all over the planet. Yogurt is a food of mysterious origins, and has been an early example of biotechnology. However, the process of yogurt making is very different than one would think. Bacteria plays a major role in yogurt production, thus making it an important topic. Bacteria is the most populous and successful form of life on earth, and has played a large role in human history. Although only a surprising minority of bacteria is known to cause disease, pathogenic bacteria in the form of cholera, typhus, tuberculosis, and the bubonic plague have caused the suffering and death of millions. However, the bacterium that we are to be using for our yogurt is a type that is not harmful towards humans.There are many distinct shapes of bacteria, such as coccus (spherical), bacillus (rod-shaped) and spirillum (spiral). These different types of bacteria reproduce through binary fission, which allows them to divide every 15-20 minutes. The yogurt we shall be producing is a pro-biotic, meaning that it is designed to aid the helpful bacterium which reside in the stomach of humans along the stomach and small intestine.

B) Our purpose for this experiment will be to test Koch's postulate (which has four steps: find microbe present in all sick people, culture the micrrobe, inoculate a healthy subject with the microbe, culture the same microbe from the newly sick), and practice the microbial technique.

C) To make our yogurt, we will scald the milk to 80 degrees Celsius (pasteurize) to kill spoilage bacteria, then we will cool down the milk, add the yogurt and wait for 24 hours. The way this process is completed, is that the milk sugar, lactose, is converted into lactic acid. This decreases the milk protein, casein, and turns the milk from a semi-liquid to a semi-solid. This process is known as curdling.

D) The controls of this experiment will be tube 1, which is the negative control, and tube 2 which is the positive control. The variables of the experiment are tube 3 and tube 6, because tube 3 is indicating the yogurts reaction to ampicillin, and tube 6 is monitoring the growth of E-Coli. My predictions for this experiment are that tube 3 loses the benefits of a pro-biotic, and tube 6 grows into a healthy medium.