DNA Sequencing!!! :)

DNA Sequencing Data!!!

While going through the DNA activity, an importance was to see which patient's sequence matched that of a normal one. In doing so, it was found that Abby and Bob had the most similar sequence to the normal. This would expect to have a normal state, which means most likely no diseases. Carol on the other hand had a very low percentage compared to the normal sequence. With this being said, she would most likely be more in the disease state. After review the sequences together, it was found that in Carol's DNA a letter was skipped somewhere along the way making everything else in her DNA shift. Just the slight factor of a letter being gone made a huge difference in this case for Carol.

Transformation Lab

Steps to the transformation lab:

1.) The first step was to get organized, and label all of our material. We labeled a green tube with a (+) for +pGLO and on orange tube with a (-) for -pGLO. The tubes were then placed into a foam rack, until needed. 

2.) Having both the green and the orange tube open, we used a sterile transfer pipet to transfer 250 ul of (CaCl2) also known as the transformation solution. After both tubes being filled with the transformation solution, the tubes were placed on ice to prepare for the next step.

3.) We then used a sterile loop to pick up a colony of bacteria from a starter plate. We placed an unknown amount of colonies in both the green (+) and the orange (-) tubes. 

4.) Soon after, we found ourselves waiting for the plasmid DNA solution. With a new sterile loop, it was a difficult task to get the plasma to fill the loop. Once it was finally filled, we inserted the plasma into the green tube (+) but not the orange tube (-). 

5.) The tubes were then placed in ice for 10 minutes. While we waited for the tubes on ice, we labeled our 4 agar plates with: LB/amp (+), LB/amp (-), LB/amp/ara, and LB.

6.) The tubes were then placed into the foam rack and placed into heat shock of 42 degrees for 50 seconds. After the 50 seconds were up, the tubes were placed back into the ice container for 2 minutes. 

7.) Once the 2 minutes were up, we then placed 100 ul of LB nutrient broth in both tubes. The tubes were then incubated for 10 minutes at room temp. 

8.) After the 10 minutes were up, we then used a sterile pipet for each plate, and added 100 ul of transformation and control suspensions into the appropriate plates. We then spread the suspensions evenly over the surface.

9.) The plates were then stacked together, and the stack was placed in the incubator at 37 degrees until the next day.

Expectations:

We expected to find the most bacteria on the LB, because it wasn't tampered with as much. We decided that the LB/amp and the LB/amp/ara would have genetically transformed bacterial cells, due to the fact that they have antibiotics. The +pGLO amp and the -pGLO amp we decided should be compared to determine if there was any genetic transformation that occurred. 

Results:

We drew what we saw on each plate, and placed our information into a data table. The -pGLO LB/amp came up with no colonies. The +pGLO LB/amp we found 2 colonies. The +pGLO LB/amp/ara had 6 colonies. The -pGLO LB had 8 colonies.

Gattaca Movie Review!

Here is a link to a glogster talking a little bit about what I thought of Gattaca.

Gattaca!!!

In the movie Gattaca, its a space agency that is supposed to be in the near future. At this agency, they are planning a trip to Saturn's moon Titan. In order to take the journey, you must have the right genetic makeup. Vincent Freeman wants badly to make the trip, but in Gattaca he is considered an "in-valid", which means he has defective genes. Vincent "switches" places with Jerome Morrow, right down to the nucleic acid. Vincent takes hair, blood, and urine samples from the real Jerome, to pass all of the required tests at Gattaca. Due to the fact that the real Jerome Morrow was crippled in some kind of accident, Jerome needs Vincent just as much as Vincent needs Jerome.

The scientific premise, like in most science-fiction movies, combines a mix of truth and fiction. In the movie, the alleles from parents are so chosen that the combination produces the optimal arrangement in terms of the child's genotype. But we know enough right now to realise that even in situations where there is a great degree of genetic predisposition, it is quite probable that that predisposition (positive or negative) is never realised. For more complex behavioural traits such as intelligence, aptitude test results would be a far better indicator than genetic makeup. In other words, any correlation people may find between a complex behavioural trait such as intelligence and genetics is for all practical purposes controlled by the environment, given the "edge of chaos" nature of such traits.




"What is disturbing about our genetic engineering capabilities today is no more disturbing than our medical engineering capabilities (and there are plenty of disturbing ramifications). The genetic component simply provides one additional way to discriminate in the real world, just as it is routinely done with age, sex, years of experience, education, and physical ability: Consider the physical and mental requirements for being an astronaut today, or even for admission to college. Information, of any sort, is a valuable commodity in this day and age, and the kind encoded in DNA is no exception. Humans naturally use information to discriminate. I would argue that for some of scenarios posited in Gattaca, the genetic information is far less reliable than physiological and psychological histories. "

Information from:
http://www.ram.org/ramblings/movies/gattaca.html

Bartonella Henselae

While doing a virtual lab on bacterial DNA, I was able to be a lab technician in a molecular biology lab and was responsible for providing lab results for use in diagnosing patients. On the certain DNa that I found, it came up with the bacteria Bartonella Henselae. Here is what was found:
Bartonella henselae Various species of Bartonella that are pathogenic to humans are transmitted via a vector, or directly from an animal reservoir. For example, B. bacilliformis via sandflies causes Oroya fever; B. quintana via body lice causes trench fever; and B. henselae via cats causes cat scratch disease (CSD). CSD typically manifests as swellings of the lymph glands, possibly with skin lesions at the site of inoculation and possibly accompanied by fever, fatigue, and other symptoms. Immunocompromised patients may be particularly susceptible and can develop a different disease, bacillary angiomatosis, as a result of infection by B. henselae or B. quintana.

Below are pictures of Bartonella Henselae:

How I was able to sequence the DNA:

In the first step, my objective was to:

• Prepare a sample from a patient and isolate whole bacterial DNA.
• Make many copies of the desired piece of DNA.
• Sequence the DNA.
• Analyze the sequence and identify the bacteria.

In Sickness and In Health

While doing the in sickness and health activity, it was found interesting that just because some people in your family might have a certain disease, there isnt a set chance that you or anyone else may get it. It was neat to see that some of them were just a spark and may not have appeared for any certain reason. While others either went to each generation or maybe even skipped a few but still continued a selevt pattern. It was amazing to see how different they all work.

Review:
While studying the information of the sickness and health, if a person was to have below 1% of the normal level of VIII, the smallest of cuts can cause uncontrolled internal bleeding. Why is this? Due to the fact of having a low level of VIII, causes the blood to be super thin. There is an injection of factor VIII that helps the blood to clot, making it less likely to cause uncontrolled bleeding. Internal bleeding, can cause complications such as: swelling, joint damage, and even an increased chance of neurological complications.  Very simple procedures can become too risky for a person with a low level of VIII. A person can either receive the injection of factor VIII monthly, or twice a year at a clinic. This is a therapy called prophylaxis.
A little bit more about factor VIII, its in the hemostatic system where the blood vessels have a huge role in a human beings survival. Hemophilia is the linked pattern of inheritance of bleeding diathesis. Due to the deficiency of factor F in the blood, hemophilia is caused. There was a test in the early 1900's and results found that normal plasma could shorten the blood clotting time of the hemophilic blood. It was soon found that a factor present in normal plasma showed to be effective to accelerate coagulation of the hemophilic blood. This was soon names the Factor VIII-C. Further testing is still to this day being tested and explored to see the roles of increased levels of factor VIII in a thrombophilic state. Factor VIII is a largely inherited disorder, with the proteins that are needed to form blood clots in the body is either missing or reduced. Studies show that around 30% of the cases of factor VIII show no family history of this disorder, although its the result of a spontaneous gene mutation. In some cases, the gene cane be "hidden". Numbers show around 1 in every 5,000 males have the factor. It doesnt affect a certain race or gender. The hemophilia gene is located on the X chromosome which everyone inherits. There is a product for people with VIII that is called desmopressin acetate (DDAVP) in order to treat small vuts.




Found this cool little bit of information!

Normal plasma levels of FVIII range from 50% to 150%. There are different levels of hemophilia: mild, moderate, and severe, depending on the amount of clotting factor in the blood:




People with mild hemophilia have 5% up to 50% of the normal clotting factor in their blood. Most patients usually have problems with bleeding only after serious injury, trauma or surgery. In many cases, mild hemophilia is not diagnosed until an injury, surgery or tooth extraction results in prolonged bleeding. The first episode may not occur until adulthood. Women with mild hemophilia often experience menorrhagia, heavy menstrual periods, and can hemorrhage after childbirth.



People with moderate hemophilia about, 15% of the hemophilia population, have 1% up to 5% of the normal clotting factor in their blood. They tend to have bleeding episodes after injuries and some without obvious cause. These are called spontaneous bleeding episodes.



People with severe hemophilia about 60% of the hemophilia population, have <1% of the normal clotting factor in their blood. They have bleeding following an injury and may have frequent spontaneous bleeding episodes, often into their joints and muscles
 
There are four possible outcomes for the baby of a woman who is a carrier. These four possibilities are repeated for each and every pregnancy:


1. A girl who is not a carrier

2. A girl who is a carrier

3. A boy without hemophilia

4. A boy with hemophilia

DNA

One may ask, what exactly is DNA?  Well, its the hereditary material in humans and almost all other organisms. Almost all cells in the human body have some sort of DNA. Where is it located? DNA is mostly located in the cell nucleus where it is also called nuclear DNA. Although most of DNA is located in the cell nucleus, there can also be some found in the mitochondria. Here it is called mitochondrail DNA. DNA is made up of 4 chemical bases. (A), guanine (G), cytosine (C), and thymine (T). Human DNA is composed of 3 billion bases. Over 99% of those bases are the same in every human being. The order determines the amount of information available. Which is used for building and maintaining an organism. Each DNA bases pairs up with one another. A with T and C with G, to form units that are called base pairs. Every base is attached to a sugar molecule and a phosphate molecule. Altogether, a base, sugar, and phosphate are called a nucleotide. Nucleotides are in strands of two that form a spiral which is called a double helix.  The double helix may look something like a ladder. The base pairs form the ladder's rungs, and the sugar and phosphates form the vertical sidepieces. DNA is able to replicate, also known as make copies of itself. Each and every strand of DNA in a double helix serves as a pattern for duplicating in the sequence of bases. This is very critical in cell division, due to the fact that each new cell needs an exact copt of the DNA present in the old cell.