The View of Blue; The Use of Eliza to Determine the Health Status of an Individual

A) Since the beginning of time, the ability to differentiate between healthy and unhealthy individuals has literally saved lives. Early detection has also been a life-saver, and the use of the ELISA (Enzyme linked immunosorbent assay) test has only improved these logistics.  The Use of the Elisa test has been helpful in determining the status of individuals (healthy or unhealthy), and is important in the field of medicine today. The test is completed by adding an antigen and incubating it to allow binding to the plastic walls. The primary antibody is then added to the well and incubated to allow it to bind to the antigen. Unbound primary is washed from walls, and secondary antibody is added to wells to bind to primary antibody. Upon rinsing of unbound secondary antibody, enzyme substrate is added, and color change occurs for infected individuals, while it does not for healthy individuals.

B) The purpose of this experiment is to  discover who the "infected" members of our class are and tracing the original "infected" people. We will also get experience in the field of testing contagious diseases. If we understand the ability of the ELISA test and the possibilities of it, then we will have learned what we were supposed to, and we can take this knowledge into the real world with us.

C) As individuals, we are supposed to transfer our fluid with three other people. Upon completion of this, we are to transfer 50 micro-liters of our mixed fluid into 2 of the wells on the 12- strip well. We then wait for five minutes to allow our proteins to to bind to the plastic wells. After this objective is completed, we wash out the wells twice with wash buffer. Then the primary antibody is added into every well for about five minutes. The washing is completed twice upon completion of this objective as well. Again, more fluid is added into the wells (this time, secondary antibody). Washing with sample buffer is to occur three times after five minutes of waiting. Finally, enzyme substrate will be added, and blue coloring will appear if the individual is infected, and the solution will remain clear if the individual is healthy.

D) I predict that I will be a healthy individual, and that 15 people will be infected in my class.

Studying The Secret of Life; The Use of Proteomics In The Testing of Marketplace Sushi

A) Although life on earth is unable to function without one of the four important macromolecule (lipids, carbohydrates, proteins, and nucleic acids), Proteins are possibly the most important of the group when it comes to human life. Proteins are utilized by every organ of the human body, and carry out numerous important, specific functions which are vital to the human body. Proteins are not only linked with current human life, as they have played a large role in evolution and the past history of every species in the world. Proteomics is the study of proteins. Although the acalanes period three biotechnology class has used the process of genomics before in the classroom, they have yet to experience the use of proteomics in their studies. Proteomics can be used in the study of evolution, bodily functions, and numerous other important biological observations/experiments. The central Dogma of biology is DNA to RNA to Protein, with the main molecule being protein as it carries out vital tasks in the human body.

B) The purpose of this experiment is to analyze the muscle proteins (actin and myosin) in fish species to determine how closely related they are to each other.

C) To successfully complete this experiment, our lab table will need to complete a number of tasks. To extract the actin and myosin from the fish, we will need to grind up the muscle. Upon grinding up the muscle, we will run the proteins in a gel and visually compare them. The more similar the banding patterns of the fish, the more related they are, and the more different the banding patterns are, the less closely related the fish are to each other.

D) For this experiment, I predict that we will be successful. Although I am unsure of what fish we will be testing, and because of this I am uncertain about the results, I believe that the results will be accurate, and we will learn something new as a lab table.

Tracing Our Ancestry From Our Mitochondrial DNA Lab Discussion

A) In this experiment, our lab table was successful in completing the experiment. The gel and markings on it turned out to be fine, and the results proved our incredible success. After the errors of our last lab experiment which led to the burning of our gel (results) we worked together as a lab table to ensure that this experiment worked out and that our mitochondrial DNA was ready for sequencing after the recent extraction. All four of the visible bands were in the desired location indicating the success and glory of performing the experiment correctly.

B) Sources of Error:
- We could have ran the gel for too long and burned off our half again.
- Could have not rinsed mouth thoroughly prior to cheek cell extraction and sequenced the mitochondrial DNA of a chicken or a strawberry.
- Chelex beads missed the DNASE and the DNA was destroyed before sequencing took place.
- No cheek cells were extracted and there was not sufficient mitochondrial DNA for successful extraction.

Searching For Eve; Tracing Our Ancestry From Our Mitochondrial DNA

A) Although each cell's nucleus is generally known as the storage facility DNA, the mitochondria also contains several copies of its own genome. Inside the Nucleus is the organisms very own unique DNA (taken from the egg of the mother and the sperm from the father and created to make an entirely new sequence); however, mitochondrial DNA is taken directly from one's mother (is an exact replica of one's mother's mitochondrial DNA). The difference between these two also include: Nuclear DNA has 46 chromosomes, mitochondrial DNA has only 37 genes, and the mitochondrial DNA contains only 16,569 nucleotides. Genetic tests are done using Polymerase Chain Reaction (PCR), a process which takes small DNA sequences, uses a DNA polymerase, a primer, and nucleotides to accomplish its goal. The PCR amplifies a gene (a 440 nucleotide sequence), each from the same part of the mitochondrial DNA genome, thus, making it possible to compare each and every mitochondrial sequence allowing us to determine our relatedness, and in some cases, how long ago we shared a common ancestor.

B) The purpose of this experiment is to amplify a piece of our mitochondrial genomes for easy comparison with other students in the class. This will enable us to determine how related we are to each other, and allow us to figure out how long ago we shared a common relative.

C) To complete this experiment, our lab table will need to complete a number of tasks correctly. We will need to extract our DNA through cheek cell extrcation, which requires saline mouthwash for extraction. Upon extracting the cheek cells, they will need to be broken open which we will utilize a lysis buffer for. After breaking open the cells instagene matrix will be added to kill DNASE. Next we will utilize PCR (Polymerase Chain Reaction) to amplify the desired sequence of DNA. After PCR, we will use Gel electrophoresis. The Gel electrophoresis will allow us to determine how closely related we are to each other, and to hopefully see how we are related to Eve.

D) The objective of this experiment is to isolate our mitochondrial DNA, and to discover how closely related we are to each other and how long ago we shared our last common relative.

Disease Gene Lab Discussion

A) As it turns out, I have the genetic trait which causes the disease. Although this is not an actual disease, the process was still emotionally challenging, and I will take a long time to recover from this unfortunate diagnosis.

B) Sources of Error:

-Period 4 ran the gel for too long, so it melted thus destroying our actual results.

-We dropped the tubes after centrifuging once, and on the second time we centrifuged too much.

-We ran the gel the wrong way at first.

-We analyzed period 4's gel instead of our own, and the three of them were infact diseased instead of us.

-We analyzed the DNA of a strawberry seed instead of a cheek cell.

-We used insufficient time to vortex each sample.

More Than Meets The Eye; Identifying A Diseased Gene With PCR

A) DNA testing is when one uses science to discover more about themselves than is possible by looking at oneself. Such a test can decode one's entire genome and can thus indicates one's genetic future. Genetic tests are done using Polymerase Chain Reaction (PCR), a process which takes small DNA sequences, uses a DNA polymerase, a primer, and nucleotides to accomplish its goal. DNA tests are done for a variety of reasons, including: identifying other species, and discovering one's genetic future. PCR can be used to sequence a gene of interest and allow scientists to determine whether the gene is diseased (harmful) or not.

B) The purpose of this experiment is to determine whether each of us possess a "diseased" gene. The gene is not a real diseased gene, but it will offer insight into our evolutionary past and give us real world experience in the realm of genetic testing, thus teaching us the significance of such testing.

C) To complete this experiment, our lab table will need to complete a number of tasks correctly. We will need to extract our DNA through cheek cell extrcation, which requires saline mouthwash for extraction. Upon extracting the cheek cells, they will need to be broken open which we will utilize a lysis buffer for. After breaking open the cells instagene matrix will be added to kill DNASE. Next we will utilize PCR (Polymerase Chain Reaction) to amplify the desired sequence of DNA. After PCR, we will use Gel electrophoresis. The Gel electrophoresis will allow us to determine whether we are each individually carriers of this "disease" by visually comparing the Gel and the lanes within it to one another.

D) The objective of this experiment is to figure out whether we are the carriers of this "diseased" gene. I am unable to produce an accurate hypothesis at this moment, but if I was to attempt to do so, I would say that I am not afflicted with or a carrier of the "diseased" gene.

Genetically Modified Organism Discussion

Results: 

Our gel did not reveal the results of this test, so our experiment did not work. However, we were able to analyze the gel of fourth period table two, and the results indicated that their test food was not genetically modified. Their number three band corresponded directly with their number five band on the gel, thus indicating its organic status. Even though the test food appeared to be organic, Mr. Chugh's corn flower band (number four) corresponded with the number six band on the gel. This means that The cornflower (test food two) is genetically modified.

 

Sources of Error:

-Ran Gel for too long, so DNA and the loading dye ran off the Gel.

-Did not crush test food well enough, causing the chunks to be too big to fit into the pipette, which caused no lettuce to be analyzed by PCR or Gel Electrophoresis.

-Accidentally extracted leftover DNA from the previous class's mortar and pestle.

-Added too little loading dye, and the DNA is not visible on the gel.

-Missed the wells when adding the DNA into the gel.

Oh No GMO; Testing Our Favorite Foods To Inspect Prevalence Of GMOs In Agriculture

A) GMOs are genetically modified organisms, and their use in agriculture is increasing, and becoming harder to distinguish. Genetically modifying plants can make them more durable, as some of the traits they can gain from genetic modification include resistance to: frost, drought, disease, and insects. GMOs are made by placing a gene of interest into a tumor inducing plasmid, adding the plasmid into agro-bacteria through the method of heat shock, and infecting a plant cell with the bacteria. The plant cell will then divide and grow up into a large, healthy plant. Genetically modified organisms can be identified by taking a plant cell, and finding a specific gene sequence located in a tumor inducing plasmid inside of the plant cell. This process is made possible by Polymerase Chain Reaction (PCR), a process which takes small DNA sequences, uses a DNA polymerase, a primer, and nucleotides to accomplish its goal. The controversy behind GMOs is the possibility that they could in fact harm the public. One way is that by making plants stronger, scientists are in fact strengthening the bugs and weeds which feed on plants. For example, weeds that crossbreed with herbicide resistant crops could evolve into super-weeds, and bugs which feed on toxins in plants will no longer be susceptible to such poisons and evolve into super-bugs. Another way is the possibility of allergies or religious conflict that could arise from people unknowingly consuming plants containing proteins from an animal which is not revealed (ex. somebody allergic to fish eating frost resistant tomatoes and becoming deathly sick from the fish protein). GMOs can be a source for good, and could end world hunger and famine, yet the risks and potential dangers must be weighed before any such actions can be taken.

B) In this lab, we will be testing our various favorite foods to identify whether or not they are genetically modified. While doing this we will be policing our own food, and deciding for ourselves whether we really want to eat food which has been altered genetically. This can be applied to the population of the world, and could allow people to make this decision even if the foods are unlabelled.

C) To extract the DNA, we will be heating a hot water bath to 99 degrees Celsius. This should effectively burst the cell membrane. DNASE is a protein developed by Eukaryotic cells to kill DNA outside of the nucleus. To get around this problem, we will add Instagene. Instagene matrix beads are designed to kill DNASE, thus allowing us to perform the experiment. We will use a sequence of interest (from DNA) from the Tumor Inducing plasmid (one that would not occur naturally in the plant) through PCR, to identify if genetic modification has taken place. Special techniques that we will be using include the use of Polymerase Chain Reaction. Our controls of this experiment are the Non-GMO food control with plant primers, Non-GMO food control with GMO primers, the GMO positive control with plant primers, and the GMO positive control DNA with GMO primers. They serve as a comparison for the unknown pieces of vegetable or fruit, and also as an indicator of whether the experiment worked successfully or not. We will be using Gel Electrophoresis in this lab to visually compare the similarities and differences of GMO/Non-GMO foods with the foods that we brought in to experiment with. Depending on the food, we should have accurate results of how much food is genetically modified in our supermarket.

D) In this experiment, the main objective is to see how much of the food is genetically modified. So, the variables of this experiment will be the food we bring in to test (Test food with plant primers, and Test food with GMO Primers). My hypothesis for this experiment is that  both plants which we test will be genetically modified. I believe this because, 70% of the food in the united states is genetically modified, and odds are that both will contain some type of modification.

How To Make Your pGLO; Transformation Of Fluorescent Sea-jelly Genes Into Bacteria

A) Transformation is a genetic process which means change caused by genes, and involves the insertion of foreign DNA into an organism to change its trait. Transformation is carried out by restriction enzymes to cut plasmid DNA and insert new code in its place, and heat shock (rapidly heating and cooling cells with calcium chloride) which will move the plasmid (DNA which contains one or more genes which would be beneficial to a bacteria's survival) into the cell. It also is a key instrument of biotechnology, and is used in numerous ways, such as, bioremediation (the genetic manipulation of bacteria to digest oil from spills), and medicine (use of gene therapy to correct defective genes). Also, another use of Transformation is to make bacteria glow by inserting the Green Fluorescent Protein (from Seajellies) into bacterial cells.

B) The purpose of this experiment is to insert the GFP gene into a plasmid, and move the plasmid into bacterial cells. This will cause the cells to produce Green Fluorescent Protein, and they will glow brilliantly. We hope to have a flourishing fluorescent colony by the end of this experiment.

C) In this lab, we will have four petri dishes: +pGLO and LB/amp, -pGLO and LB/amp, -pGLO, and LB, and the +pGLO and LB/amp/ara. We will use Transformation, which is carried out by restriction enzymes to cut plasmid DNA and insert new code (GFP gene) in its place, and heat shock (rapidly heating and cooling cells with calcium chloride) which will move the plasmid (DNA which contains one or more genes which would be beneficial to a bacteria's survival) into the cell. The controls of this experiment are the -pGLO, and LB petri dishand the -pGLO and LB/amp. The variables will be +pGLO and LB/amp,and the +pGLO and LB/amp/ara. I predict that the +pGLO and LB/amp will be the only bacterial colony to exhibit fluorescent characteristics. This is because it contains the ampicillin resistance gene, and the plasmid containing the GFP gene.