DNA Detective Work

 Unless you have a twin, no one in the world has a DNA sequence identical to yours. Although 99 percent of the DNA is the same in all humans, certain segments vary widely. Differences in these segments are detected through DNA fingerprinting. A small amount of tissue, such as blood, hair, or semen, is all that is needed to create a DNA fingerprint. The sample is cut up using enzymes and the segments are separated by size through gel electrophoresis. DNA is made visible either with radioactive probes or by staining. This reveals a pattern of bars: the DNA fingerprint. If the two DNA fingerprints match, they probably came from the same person. If they don't match, they certainly came from different individuals. In recent years, a number of people convicted of crimes have been exonerated based on DNA evidence.

Activity

In this exercise, you will learn the basics of DNA fingerprinting and consider the use of DNA in criminal investigations.

Part 1.

Use your browser to go to NOVA’s web site about “Killers Trail,”  the story behind the man who inspired the Fugitive TV series and later the movie version starring Harrison Ford:

http://www.pbs.org/wgbh/nova/sheppard/

Click on the “Chronology of a Murder” section and read about the events that led up to the murder trial of Dr. Sam Sheppard.

1.                 In your opinion, what role (if any) did newspaper stories and editorials have in the outcome of the original trial of Dr. Sam Sheppard?

1.     In my opinion the rle of newspaper stories and editorials played a major part in the outcome of the original trail of Dr. Sam Sheppard. Because of the pressure the police and jury felt from the attacks from the media, they unlawful arrested Sheppard just to please them. The media complained or questioned something they did what they could to please them. Even if it ment putting an innocent man in jail with out a proper trial.

Go back to the Killers Trail homepage and select ”Create a DNA Fingerprint.”

Read about the crime and the suspects then go on to part 2. Answer the following questions about the technique as you go through the simulation:

2.                 What is the function of the restriction enzymes in DNA fingerprinting?

1.     The restriction enzymes work like scissors to cut the long DNA molecules at different locations. Where the enzymes ut depends on the code within the DNA molecule and the code within the enzymes.

3.                 What is the function of  the agarose gel electrophoresis step?

1.     Acts as a molecular strainer, allowing smaller pieces of DNA to move through more easily than larger pieces.

4.                 Why is a nylon membrane used to blot the DNA?

1.     The DNA is sucked into the membrane as liquid traveled up from the gel toward an absorbent material that was placedover the membrane.

5.                 What does a dark spot on the X-ray film indicate?

1.     Your fingerprint

Part 2.

Use your browser to go to Frontline's "What Jennifer Saw" at

http://www.pbs.org/wgbh/pages/frontline/shows/dna/.

The material on this site is about a man convicted of rape but later exonerated by DNA evidence. To read a summary of the case, choose the link to Ronald Cotton's wrongful conviction, then choose "Summary of Cotton's Case."

In the interviews section, read the interviews with DNA expert Peter Neufeld and lawyer Barry Scheck.

Answer the following questions:

6.                 What evidence was initially used to convict Cotton?

1.     A photo identification was made by one of the victims.

2.     A police lineup identification was made by one of the victims.

3.     A flashlight in Cotton's home resembled the one used by the assailant.

4.     Rubber from Cotton's tennis shoe was consistent with rubber found at one of the crime scenes.

7.                 What did the DNA evidence show?

1.     That Cotton was not the rapest and that another inmate in prison for similar crimes had committed the rapes. He ven addmitted it to another inmate but the superior court refused to alow known to the jury.

8.                 How could DNA fingerprinting be used to prevent a false conviction if a case like this was being tried today?

1.     DNA fingerprinting gives us hardcore edvidence on weather or not someone committed. This way those who are innocent won’t be put way for something they didn’t do.

9.                 What percentage of convicts are unjustly convicted of sexual assault cases, according to Neufeld and Scheck?

1.     25%

10.               The O.J. Simpson trial was one of the most visible trials that attempted to use DNA evidence.  In the end, the DNA evidence was not satisfying to the jury, who acquitted Simpson.  What do Neufeld and Scheck believe about the impact of the O.J. Simpson trial on the use of DNA evidence?

1.     They talked about how though DNA helps in keeping innocents from being wrongflly convicted they can still be wrong, but it depends on if the person working on it makes a mistake.

The Human Geneome and Genetic Disease

THE HUMAN GENOME AND GENETIC DISEASE

In 2001, the Human Genome Project completed the sequencing of the entire human genome. A byproduct of this effort was the identification and mapping of more than 1,000 human disease genes. The large amounts of data generated by the Human Genome Project have been organized and made available to scientists and the general public via several databases. Online Mendelian Inheritance in Man (OMIM) is one example. OMIM is a catalog of human genes and genetic disorders developed for the World Wide Web by the National Center for Biotechnology Information (NCBI). The database contains information about the research history of the disease gene, inheritance patterns, a clinical synopsis of the disorder, and information about the molecular nature of the mutation or defect that leads to the disorder.

Activity

In this activity you will access the resources provided by the National Center for Biotechnology Information and research the details of a genetic disease using OMIM.

Part 1

Use your browser to go to

http://www.ncbi.nlm.nih.gov/

http://www.ncbi.nlm.nih.gov/

Under the section "Genetics and Medicine" choose "Genes and Disease."

Choose the section near the bottom titled Chromosome Map and read the introduction to chromosome mapping.

*What are the three main parts of a chromosome, as viewed under a microscope? 

      a.Three main parts of a chromosome when viewed under a microscope are two special chromosomes, X and Y, that determine our sex, special units of chromosomal DNA, and the center of each chromosome, centromere.

It will be handy to know these as you are looking at maps of chromosomes- these will be part of the “address” for each gene!

Select the X chromosome from the list of chromosomes on the right side of the page and read the summary of the genes found on the X chromosome.

*List at least four human diseases that have been mapped to the X chromosome.

      a.Hemophilia

      b.Alport Syndrome

      c.Menkes Syndrome

      d.Fragile X Syndrome

Click on the Map Viewer link at the very bottom of the page (Featured: Mapviewer)or click here:http://www.ncbi.nlm.nih.gov/mapview/

http://www.ncbi.nlm.nih.gov/mapview/

Notice that this database has information about the DNA and proteins for many species (including platypus!).

Choose the latest build for human (homo sapiens) chromosomes.

Select the X chromosome.

At this point you will be looking at the most current map of the known DNA sequences on the human X chromosome! And yes, its complicated  : )

You can browse through the map of the X chromosome if you wish, zooming in and out. You may find the “You are here:” diagram on the left side of the page to be handy (or not).

Perhaps an easier way to experience the map of the X chromosome is to do a search for one of the disease genes that you discovered earlier. Do that now using the search box above the chromosome map.

Once you get the results, click on the Map Element that looks most promising to you. This link will take you to a more detailed map of the X chromosome showing where the disease gene is located.

Click on one of the reference numbers for that gene to see if you can get some useful information about it (and there will be a lot of scientific nonsense, so keep digging or find a summary!)

*Read the summary section for that gene to find out what functions, processes, and components it is thought to be involved in (what’s it do?).  

Part 2

Hemophilia A

a.Function:  a deficiency of the blood clotting protein known as Factor VIII that results in abnormal bleeding.

b.Process: Mutation of theHEMA gene on the X chromosome causes Hemophilia A.

c. Components: X-linked disorders such as Hemophilia A are far more common in males. The HEMA gene codes for Factor VIII, which is synthesized mainly in the liver, and is one of many factors involved in blood coagulation; its loss alone is enough to cause Hemophilia A even if all the other coagulation factors are still present.

Return to the Genes and Disease table of contents where you began this exercise (http://www.ncbi.nlm.nih.gov/books/NBK22183/).

Choose a topic from the menu at the left (Cancer, Immune System, Metabolism, and so on).

Read the introduction to the disease type you have chosen, then choose a specific disease to study.

Read the information about the disease you picked and use it to answer the following questions:

*What disease did you choose and what gene is/genes are associated with this disease?

      a.The disease that I chose is called Rett Syndrome. The genes that are associated with RTT are mutations in the gene MeCP2

*On what chromosome are these genes/is this gene located?

      a.Found on the X chromosome.

Use the link at the side of the disease page to go to the OMIM entry for the disease you chose.

*Read the text section and the clinical synopsis in the OMIM entry and answer the following questions:

• When was the disease first reported in the scientific literature?

·       Rett , a Viennese pediatrician, first described Rett syndrome after observing 2 girls who exhibited the same unusual behavior who happened to be seated next to each other in the waiting room. (Around 1966-1977)

• What are some of the clinical symptoms of this disease?

·       a period of clear developmental regression followed by limited recovery or stabilization. Other main criteria include loss of purposeful hand skills, loss of spoken language, gait abnormalities, and stereotypic hand movements. Although deceleration of head growth is a supportive feature, it is no longer necessary for diagnosis. Exclusion criteria include other primary causes of neurologic dysfunction and abnormal psychomotor development in the first 6 months of life.

• What lab findings (gene function or biochemical data) are associated with the disease?
• an MECP2 mutation, that resulted in decreased, but not absent MECP2 function.

• What type of inheritance governs this disease?

·       family recurrences of Rett syndrome comprise only approximately 1% of the total reported cases; the vast majority of cases are sporadic.

Bacterial ID Lab and Questions

Completing this virtual lab and answering the following questions helps meet Standard 3: Lab Skills.

First, go to:

http://www.hhmi.org/biointeractive/vlabs/bacterial_id/index.html

In this virtual lab you will assume the role of a lab technician in a modern molecular biology laboratory.  As such, you are responsible for providing lab results to medical doctors for use in diagnosing their patients.  Be sure to follow the steps of the procedure in order and to make use of the notes on the right side of the computer screen.  As you work through the lab, answer the following questions:

1. As the medical technician in charge of this investigation, what are you trying to determine about the tissue sample provided to you?

I am trying to determine if I can grow bacterial colonies on a solid medium culture dish.

2. How did you prepare the DNA to be used in this investigation?

            You take a wire loop and extract the bacterial colony from the dish. Then you transfer the bacterial colony into the microcentrifuge tube. From here you add digestive enzymes to your sample. You add digestive buffer to the same tube. Once that is done you let the tube sit for several hours. Once the hours are done and your sample is ready you heat-inactivate the digestive enzymes. Now you will spin down cellular debris for removal from your sample.  You then transfer the superantant to the PCR tubes. Then your sample preparation is complete.

3. Describe how PCR is used to make copies of DNA sequences. Use the animation and notebook entries in the PCR Amplification step to guide your answer. Note that you may replay the animation as needed.

The PCR separates the strands of DNA, annealing the primer to the template, and the synthesis of new strands. This takes less than two minutes. Each step is carried out in the same vial. At the end of a cycle, each piece of DNA in the vial has been duplicated. The cycle can be repeated 30 or more times, and each newly synthesized DNA piece acts as a new template.

4. Summarize the technique used to purify the PCR product.

            First you set up the microconcentrator column. You add buffer solution the the column. Now add the PCR product of the column. Now place the tubes on ice. Then load the column into the cenrifuge. Now you need a new tube to invert the column. Now add buffer solution to the inverted column. Discard the first collection tube.Load the inverted column into the centrifuge. The column is no longer needed, so discard it. The PCR product had been purified.

5. What is produced during the sequencing prep PCR run? Use the animation and notebook as needed in thinking through your answer.

            Copies/ sequences of DNA will be produced.

6. Describe how the automatic sequencer determines the sequences of the PCR products.

            They stop the sequence at a certain point and then continue to the next section. They repeat this process thousands of times.

7. What does BLAST stand for?

            BLAST stands for Basic Local Alignment Search Tool.

8. What conclusions did you make using the results of the BLAST search?  Did these conclusions support a clinical diagnosis for the patient (what disease did they have)?

            It was very easy to find what was mutated in the DNA. Yes and they had Bartonella henselae.

GATTACA Questions

For the last three days we have been watching the movie GATTACA to give us a better idea of DNA.

1. The following terms were used in the movie. How do they relate to the words we use: degenerate and invalid?

         De-gene-erate-Were the people who weren’t specially modified.

         In-valid-they used in-valid to show that the persons Dna does not match those who work in GATTACA because they have workers DNA

         Borrowed Ladder-They defined borrowed ladder as a person using someone else identity to do what they can’t because of “defect” in their body. For example Vincent ued Jerome as a borrowed ladder because Vincent had a heart problem and eye sight issues, but everything was fine with Jerome’s heart and eye sight, therefore Vincent borrowed Jerome’s identity to become a navigation piolet for GATTACA.

2. Why do you think Vincent left his family, tearing his picture out of the family photo, after winning the swimming race against his brother?

            a.Vincent left his family to persue bigger and better things because he was tired of always being told that he couldn’t accomplish anything because he was born through concivement.

3. Describe the relationship between Vincent and Anton.

            a.It was decent relationship, but Vincent was jealous of Anton because he was essentially the perfect human, since Anton was made through science.

4. When Jerome Morrow said to Vincent/Jerome, “They’re not looking for you. When they look at you, they only see me,” what did he mean? Can you find any parallels to this type of situation in real life?

            a.Jerome ment that since they had his DNA on file and because Vincent took on Jerome’s identity.

5. Choose your favorite character from the film. Explain why you choose that person. Would you want to be that person? Why? Why not?

            a. My favortie character would have to be Vincent because like him I have a lot of medical conditions, that my doctor tells me might prevent me for doing actual work. Desite this I plan on working after college.

6. At the end of the film, you are told that the Doctor knew about Vincent all along. Why did the Doctor go along with the fraud? What would you have done if you were the Doctor?

            a.I believe that the doctor went along with Vincent pretending to be Jerome because the doctor didn't believe that people should be labeled because of the way they were born. If I was the doctor I would have kept quite and even offer my help.

7. The technology to do what was done in the movie is definitely possible within the next fifty years. Do you think that Vincent’s world could eventually happen in America? Why?

            a. If science keeps progressing the way does, I believe that it will become possible for America to bring Vincents world to life. Even now people still want the perfect baby so that desire may manifest Vincents world into a reality.

8. What do you think is wrong with the society portrayed in "GATTACA"? What is right?

            a. I think whats wrong with society portrayed in GATTACA is that they don’t give people identities. The gentically enigneered people in GATTACA were what was deemed as normal compared to the supposed in-vailds who were seen as an inferior part of the human race, as they were “god children” someone who was concieved. I believe that Vincent was right in his goal of becoming one of GATTACA’s navigation officers, despite his supposed heart condition.

 

9. What were the screenwriters trying to tell us through the episode of the 12-fingered pianist? Is anything wrong with engineering children to have 12 fingers if, as a result, they will be able to make extraordinarily beautiful music?

            a.I don’t really agree with engineering children to 12 fingers because it could affect the childs up bringing. Some may think it’s right to alter someones DNA to produce the result they want.

10. You and your spouse are having a child and are at the Genetic Clinic pictured in the movie. What characteristics would you want for your child and what would you ask to be excluded? Why would you make those choices?

            a. If I was to have a child who was genteically altered then I would chose for the child to have the characteristics it would naturally be born with with the exception of having the eye color change to blue.Consing medical conditions I would have the chances of my child having the same medical conditions as me as I know the difficulties that my child would face.

 

11. Picture yourself as either Vincent, Jerome, or Anton. Would you have acted the same or done things differently if you were in the same world as them?

            a.I would have probly done the same as Vincent as I would not have liked to have my future decided just because I was born different. I would fight the achieve what I want and not let anyone tell me otherwise.

12. How does the society in GATTACA resemble the type of society America was during the height of the eugenics movement?

            a.Everybody wanted genetic babies insteas of making one because they want their kid to be the perfect baby compared to random results that the baby could get form being concieved.

DNA Lab

In Biology class, since we were learning about DNA and the molecule itself, our teacher decided that it would be a good idea to do an extraction lab! The lab consists of wheat germ, HOT water, alcohol and  dry powder of laundry detergent. I will explain the steps and then show pictures as I continue to tell you what is happening or what happened.

Steps:

1) We needed 1 gram of wheat germ to add to a 50 mL test tube.

2) We needed to place the wheat germ into the test tube after getting the right amount.

3) Now we needed to collect 20 mL of HOT water and mix constantly for 3 minutes.

           - After mixing the solution for 3 minutes it should start to look like and icky dark yellow color with crushed cheerios.

4) After mixing we needed to add 1 mL or a scant 1/4 teaspoon of dry powder laundry detergent and mix gently every minute for 5 minutes. We had to try and not create and foam.

5) Use an eyedropper,pipette, or a piece of paper bowl to remove any foam from the top of the solution.

6) Tilt the test tube at an angle. SLOWLY pour 14 mL of alcohol down the side so that it forms a layer on top of the water/wheat germ/detergent solution. Do not mix the two layers together. DNA precipitates at the water-alcohol interface ( the boundary between the water and alcohol). Therefore, it is crucial to pour the alcohol very slowly so that is forms a layer on top of the water solution. If the alcohol mixes with the water, it will become too dilute and the DNA will not precipitate.

7) Let the test tube sit for a few minutes. White, stringy, filmy DNA will begin to appear where the water and alcohol meet. You will usually see DNA precipitating from the solution at the water-alcohol interface as soon as you pour in the alcohol. If you let the preparation sit for 15 minutes or so, the DNA will float to the top of the alcohol.

   You can usually get more DNA to precipitate from the solution by using one of the DNA-collecting tools (such as a glass or paper clip hook) to gently lift the water solution up into the alcohol. This allows more DNA to come in contact with the alcohol and precipitate. You may find it helpful to pour the water/ detergent solution into a clean test tube, leaving behind the wheat germ, before adding alcohol.

8) Use a glass or paper clip hook or a wooden stick to collect the DNA.

9) Once finished collecting the DNA clean the test tube and the lab area and put away the materials.

After we finished the lab we needed to answer questions. After I show you the questions I will show you pictures of the lab and I will tell you the step we were at when the results happened.

Questions/ Observations:

1) What does the "wheat germ soup" look like?

        The wheat germ soup looked like ramen noodle soup with bread crumbs.

2) How does its appearance change as you add the detergent and swirl it in?

        The wheat germ soup started to turn a brighter yellow as I was continually stirring it. 

3) What do you think is happening at this step?

        The detergent is having a chemical reaction to the wheat.

4) Describe the appearance of the mixture just after you add the alcohol?

        You can see the two layers of wheat germ soup and alcohol.

5) What do you think is happening at this step?

        The DNA is leaking into the alcohol from the wheat germ.

6) What do you observe at the water-alcohol interface?

        The formation of DNA is starting.

7) What does DNA look like?

        It looks like white sticky strings.

Those were our observations of the lab as we were going through the steps. Once we got to the final step we took pictures.

This is the first picture we took. The dull yellow substance is the wheat germ soup. The clear substance is the alcohol. It is layered over the wheat germ as instructed. Now the white stringy stuff is the DNA. It reminded me of cobwebs or really thin, white string. This was the completed results as are the other two pictures.

In this picture you can see the DNA a little better. Kind of weird looking huh? It could also remind you of mucus. Ewww! 

This is the last picture we took and it shows the DNA much better than the others. Like I said before they still remind me of cobwebs stuck together. I hope you enjoyed learning about our DNA lab and I hope you give it a try yourself. 

DNA Structure

For the past week in biology we have been learning and understanding about the structure of DNA(Deoxyribonucleic Acid) the geneic material inside all cells, and what each part was. DNA consists of sugar, phosphate, nitrogenous bonds, hydrogen bonds, and A, T, C, and G. The ladders that make up the DNA structure is called nitrogenous bases: A stands for Adenine and it is always paired up with T or Thymine. The same can be said for C(Cytosine) and G(Guanine). The ladder shape twists into a way that it forms a double helix.  The arrangement of two bases in the DNA molecule forms a base pair and each base pair is held together with a weak bond called a hydrogen bond. The subunit  of DNA has three parts: a phosphate  sugar, and nitrogenous bases these all together are called a nucleotide. Then when DNA makes a copy of its self its called replication.

The above picture is one that my group drew in class to show that we knew the structure of DNA and the terms that go along with it. On the drawing the triangle shape is sugar. The purple lines are phosphates. The brown circle in between the base pairs are known as hydrogen bonds. The yellow base is the  C (cytosine) base. The red base is the T (thymine) base. The black base is the G (guanine) base. The blue base is the A (adenine) base. The subunit of DNA has three parts: a phosphate, a sugar, and a nitrogenous base. This is also known as a Nucleotide. The backbones of the DNA molecule are made of alternating sugar and Phosphate bonds. The scientific name for the DNA molecule is called the Double Helix.