DNA Fingerprint Web quest

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?

In my opinion I think that some people are stretching the truth about this and they are leaving facts out because they think he is guilty. But then there are some people that are thinking that Marilyn Sheppard needs justice and who is going to speak for her. It did say that on July 1989 Richard Eberling, an interior decorator and the former window washer at the Sheppard home, is convicted of aggravated murder in the death of Ethel May Durkin. But at the beginning it says that window washing company employee Vern Lund leaves town. Both guys are window washers at the Sheppards home and one guy had be convicted of murder and when they found Marilyn dead the other man left too.

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?

A-It cuts along different locations. The lengths of the fragments will vary from person to person because the code for every person’s DNA is different. Some of the fragments will be long, others will be short.

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

A-The agarose gel is thick, porous, Jell-O-like substance. It will act 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?

A-You do that because you just added probes to the nylon membrane, and what they do is attach themselves to DNA fragments on the nylon membrane.

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

A-The probes are now present at only a few locations on the membrane, exposing corresponding areas on the X-ray film.

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?

A-A photo identification was made by one of the victims, then a police lineup identification wa made by one of the victims. A flashlight in Cotton’s home resembles the one used by the assailant. Then the rubber from Cotton’s tennis shoe was consistent with rubber found at one of the crime scenes.

7. What did the DNA evidence show? 
   A-The DNA evidence shows that the samples from one victim were too deteriorated to e conclusive, but the samples from the other victim’s vagainal swab and underwear were submitted to PCR testing and showed no match to Cotton.

8. How could DNA fingerprinting be used to prevent a false conviction if a case like this was being tried today?
   A- DNA fingerprinting can be used to prevent a false conviction by the fact that there is a poor innocent person dropped their gloves on the floor and a criminal picks them up and commits a crime in those gloves then there is more of a chance of the criminal getting away with it because it would have the poor innocent persons DNA.

9. What percentage of convicts are unjustly convicted of sexual assault cases?
   A- 28%

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?
    A- They review cases of people who say that they have been falsely convicted and arrange for DNA test that may claim of innocence.
    
    

Bacteria Lab

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?

A-About the tissue sample is to identify a bacterial sample received from a clinician.

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

 

A-Well first the DNA consists of dissolving the cell wall with a digestive buffer, and what the buffer contains proteolytic enzymes that technically eat the cell wall. This will take about several hours. Then the DNA is contained in supernantant (the liquid) then transfred to the PCR tube.

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.

 

A-PCR is used to make copies of DNA sequences by the fact you first start off by adding PCR Master Mix solution to the sample of DNA. You then prepare negative and positive control reactions.  It is then put into a machine, and it determines the temp, the time, the cycle number, melt, anneal, and extend. The first step is to melt so it can separate the two DNA chains in the double helix by heating the vial containing the PCR reaction mixture to 95 degrees celcus for 30 seconds. Then the vial is cooled to 60 degrees celcus. At that temperature the primers will bind (anneal) to the single strand of DNA. The last step (extend) is to let the DNA extend the copy of DNA strand by rising the temp. to 70 degrees celcus for 45 seconds. When you do these three steps  each is carried out in the same vial, then at the end of  a cycle, each piece of DNA in the vial has been duplicated.

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

 

A-The technique that is used to purify the PCR product is the PCR Master Mix solution. What it is, water; a buffer to keep the mixture at the correct pH for the PCR reaction; large quantities of the four nucleotides adenine, cytosine, guanine, and thymine; large quantities of oligonucleotide DNA primers that bind the 16S rDNA region to indicate the replication process. What it does is basicly you mix the product with DNA mix it in the machine let it set and it makes copies of DNA.

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

 

A-The is produced during the sequencing prep PCR run is when the DNA replication starts. You have to melt, anneal, and extend.

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

 

A-When it is in the machine it determines the temperature, the time remaining, cycle number, melt, anneal, and extend.

7. What does BLAST stand for?

 

A-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)?

 

A-What BLAST does is it will start with the reference of the search program, which is the number of letters in the sequence and then the number of letters in the database. Then a graphic representation of the sequence matches, and a list of matches. There are a lot of sequences in the database and some of them are from the same species and therefore might be similar.

Pedigree Analysis

I let my mom try the PTC paper and she tasted it and didn't like the taste. I also then  let my dad try it and he could taste it to. I had tasted the PTC paper and I could taste it and it didn't taste very good. Then i went to my grandparents and gave it to them. My grandma tasted it and she didn't like it. But when my grandpa tasted it, he really didn't taste anything.

I had read an article about the blue skinned people of Kentucky. The Fugate progeny had a genetic condition called methemoglobinemia, which was passed down through a recessive gene and blossomed through intermarriage Susan Donaldson James had wrote in her articleMethemoglobinemia is a blood disorder in which an abnormal amount of methemoglobin. Hemoglobin is responsible for distributing oxygen to the body and without oxygen, the heart, brain and muscles can die, and it is unable to carry oxygen and it also makes it difficult for unaffected hemoglobin to release oxygen effectively to body tissues. Patients' lips are purple, the skin looks blue.Normally, people have less than about 1 percent of methemoglobin, a type of hemoglobin that is altered by being oxidized so is useless in carrying oxygen in the blood. When those levels rise to greater than 20 percent, heart abnormalities and seizures and even death can occur.But at levels of between 10 and 20 percent a person can develop blue skin without any other symptoms. Most of blue Fugates never suffered any health effects and lived into their 80s and 90s.

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/

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?

 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! The first one is the telomere which is the ends of the chromosome. The second one is the centromere which is the primary constriction of the chromosome, the centromere also divides the chromosome into a short arm (p) and a long arm (q). Then the chromatidwhich is a single molecule of DNA

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.

I was looking at chromosome 1 and it has UROD (Porphyria Cutanea Tarda) which is a group of acquired and familial disorders (passed on from generation to generation). Another disease is GBA (Gaucher Disease) which is an inherited disorder that affects many of the body's organs and tissues. Then there is GLC1A (Glaucoma), what this disease is technically when you are losing your eyesight. Then there is PS2 (Alzheimer Disease) this is when you lose your memory and you forget things that you have done. It happens when you get older.

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/

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 scientificnonsense, 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?).  

I was looking at the contig map and it shows the chromosomal placement of contigs that have been assembled at NCBI using finished and draft high-throughput genomic (HTG) sequence data. Any individual contig can be assembled from finished sequence (phase 3 HTG), draft sequence (phase 1 and 2 HTG), or a mixture of both.

Part 2.

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, thenchoose a specific disease to study.

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

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

I chose to look at cancer. The genes that are associated with this disease is that the predominant mechanisms for the cancers featured here are (i) impairment of a DNA repair pathway (ii) the transformation of a normal gene into an oncogene and (iii) the malfunction of a tumor suppressor gene. 

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

Well I had looked at the breast cancer article and where this cancer is located at is in the woman's breasts.

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?

It does not say but probably a long time ago because people were smoking back in the days and they probably started to have problems with their respiratory system.

What are some of the clinical symptoms of this disease?

Some of the clinical symptoms are inhalation of toxic agents, accidents, and harmful lifestyles, such as smoking. Infections, genetic factors, and anything else that affects lung development, either directly or indirectly, can cause respiratory symptoms.

What lab findings (gene function or biochemical data) are associated with the disease?

The respiratory function involves gas exchange — the transfer of oxygen from the air into the blood and the removal of carbon dioxide from the blood. Non-respiratory lung functions are mechanical, biochemical, and physiological

What type of inheritance governs this disease?

It has to do more with the lifestyle that you live in. For example say that you smoke, then you will end up having this disease because it is messing with your lungs and then instead of being healthy lungs, they will look black and it will be harder to breath.

Investigating Independent assortment

Mendel observed the effects of independent assortment when he carried out his dihybrid crosses. When he crossed two plants that bred true for different versions of two traits, the first-generation offspring all displayed the same phenotype (the dominant phenotype for both traits). However, when these plants were crossed, the second-generation offspring included four different phenotypes.

Mendel carefully recorded the numbers of phenotypes among the offspring of many dihybrid crosses. He found that certain combinations of phenotypes among the second-generation offspring occur in a 9:3:3:1 ratio, on the average. We now know that this pattern occurs because genes on pairs of homologous chromosomes are sorted out for distribution into one gamete or another independently of gene pairs of other chromosomes.

Activity

In this activity, you will first access the meiosis tutorial provided by the University of California, Santa Barbara. The tutorial demonstrates the random assortment of chromosomes into gametes. Next you will complete a tutorial quiz about independent assortment. This is part of The Biology Project from the University of Arizona.

Part 1.

Use your browser to go to the meiosis tutorial at

http://www.sumanasinc.com/webcontent/animations/content/independentassortment.html

Use the tutorial to learn how to determine which allele combinations are possible in two or even three trait crosses.

Part 2.

Use your browser to go to the independent assortment tutorial at
http://www.biology.arizona.edu/mendelian_genetics/problem_sets/dihybrid_cross/dihybrid_cross.html
Go through questions 1-9 of the tutorial. If you answer any question incorrectly, review the tutorial material and try again.

When you have completed this much of the tutorial, answer the questions below:

1. What type of gametes will be produced by a plant of genotype AaBb?

A- Dihybrid Involving Epistasis
2. What type of gametes will be produced by a plant of genotype aabb?
A-There would be 4 out of 16.


3. List all the genotypes you would find among the offspring of an AaBb x aabb test cross. 

A-A and a dominant B allele; the other half of the gametes get a recessive a and a recessive b allele.

4. What is the expected phenotypic ratio of the offspring of an AaBb x aabb test cross? 

A-1/ 16

5. List all possible gametes from a trihybrid individual whose genotype is RrSsTt.
A-It has parent one and parent two genes. The R genes are different chromosomes.

Gene's and baby lab

***The past few days in class we have been talking about genes and what traits the parents give on to their kids. So we finally made a chart and we made a baby. Using the create a baby table we found out that we had a son. After we finished the table we could find out our babies hair color, his eye shape and color. Also if he would have dimples, how his chin shape would be. and just about everything on his face. Now here is that chart on the left, that we used and made to create our baby.                                                                                                          
                                                                                                                                                                    
                                                                                                               
 ****After we charted everything and made our baby, our teacher gave us a piece of blank paper to sketch out the baby. We also had to use all the traits that we thought the baby would have, using the chart that we made. Here is a drawing of the baby that we made, i drew the baby on the right. Any my partner drew the picture on the left so you can see the differences and the things that look alike. 

                                                                                              

                                                                                                                                                                   ***So you can see the picture of me and my partner on the left. So you decide, do you think the pictures of the baby drawings resembles us..? Or did we draw a baby that doesn't resemble us at all.