PCR!!

If only it was PBR right? (: (Professional Bull Riding) but no. This is almost as interesting, without the screaming fans, angry animals, and cowboys.


I did an online Bacterial ID Lab that was intended to identify the bacterial sample given.

First of all you have to prepare the DNA sample that is to be used. This involves placing the bacterial colony in a microcentrifuge tube and inserting the digestive buffer. The tube has to sit for several hours until the sample is ready. Following that you have to heat-inactivate the digestive enzymes which will denature and inactivate them. Add counterbalance and spin down cellular debris for removal from the sample. Then the wanted DNA is supernatant. Transfer the supernatant to the PCR tube and the sample prep is complete!!



Next step is to use PCR to make copies of DNA sequences. To do this you have to add a PCR master mix solution to all of the tubes. To set up a positive control reaction, you have to add control dna to one tube. For negative reactions you must add de-ionized water to one tube. Then insert both of them into the PCR machine. The short strands are desired DNA strands from PCR thermal cycling process.



NEXT: Purify the PCR product. To do this you have to set up the microconcentrator column and add a buffer solution to the column, then add the PCR product to the column. Put the positive and negative controls on ice until needed again. Add counterbalance to the tube and put it in the centrifuge. After a while DNA is trapped into the column and you need to loosen it into a new tube. Invert the column into the new tube (turn it upside down) and add a buffer. Now put centrifuge assembly to collect DNA into a collection and wait patiently.



PCR sequencing prep is next. First you have to dillute the PCR product to increase the volume. Add distilled water to purify the PCR product. The green and blue strip tubes contain PCR reaction mixtures, so now you can add purifed PCR product to them. They are now ready for PCR amplification so put it in the PCR machine. The Sequencing prep is complete!



Second to last step is DNA Sequencing. You must load the auto sequencer and insert the tubes. In my case the first tube read tacggtagcgtaatgcc. And that completes the DNA sequencing event.



The last step is to analyze the sequence. Copy the output from the DNA sequencer and past it on the ncbi website. The ncbi website searches through it's massive database and eventually comes up with results. The bacteria was identified as bartonella henselae.

DNA Sequencing Activity

This graph represents how alike Abby, Bob, and Carol are alike to Norm, or the Normal DNA.

• Abby only had one difference from Norm. Norm had GAG, but Abby had GTG, otherwise known as a point mutation. This also changed the protein from Glu to Val. This could lead to disease, or other problems because of this change. 
• Bob also only had on difference from Norm. Norm had AAG, but Bob had TAG, another point mutation. This also changed the protein from Lys, to the signal that the protein stops, also read as "stop!" Clever huh? This change causes the protein to become too short, otherwise known as truncation mutation.The stop causes Bob's protein to become three amino acids short because the DNA stops. This could cause some major problems for Bob in the future.
• Carol is the most different from Norm. She has 14 differences, creating the lowest percent of similarity. Her DNA is actually really similar to Norm, except that with the fact that she's missing a base, it made everything shift over, creating new codons within the frames. The frame shift has huge consequences on Carol because all of the proteins are different than Norm. This can cause drastic consequences for Carol and her health. 

Interesting Fact: 99% of DNA changes, do not cause problems for the person!

This is pretty interesting actually, I didn't understand that this is how DNA and diseases, etc can play out. I thought it was a lot more complex, but on the surface it doesn't look that difficult. It's crazy how all three of them have a disease risk, just because they're DNA is different. 

Pedigree Analysis

A while ago, we became "genetic counselors" for Greg and Olga, a couple who wanted to have kids, but was terrified of the fact that they're children could be born with a genetic disease. They were concerned because they had the Factor VIII deficiency disease throughout both sides of their families.

This particular post taught me that autosomal recessive diseases skip generations, while autosomal dominant diseases don't skip generations. Autosomal recessive disease is when there is one mutated allele and one normal gene. It has a 50% chance of being transmitted. All children of the infected people will be carriers no matter what. The disease is either transmitted by either the father or the mother. Both sexes have an equal chance of getting the disease, unless it is a sex-linked disease. Recessive diseases are never inherited directly because recessive diseases are only inherited by the y. Women can't display sex-linked genes, but they can be carriers. Greg and Olga could be a carrier for this disease because people in their family have the disease. In this activity Greg has a high chance of being a carrier, he can pass it to his sons, and his daughters could become carriers. His daughters could also have children that could possibly get the disease. Consanguineous means relating to or denoting people descended from the same ancestor. The advancement of technology can really harm the future of the kids with these genetically inherited disease. If a parent finds out that their unborn child has a disease, they are less likely to carry through with the pregnancy in order to "try again." Also, insurance companies would have to be forced to accept all children, no matter of their health because every disease could be "pre-exsisting."

The world of genetics is definitely a complicated one, that could cause a lot of problems, or great advancements in the future.

FLASHCARDS!!!!!!!

Study Study Study!!!


FLASHCARDS!!   <------ click THAT!! It could save your life.... or at least your test scores.

Baby Lab

To better our understanding of genetics and genes, most of us paired up to make a baby. We looked at each other to determine traits, then flipped a coin to determine genotypes. Kiel and I paired up for this activity and had a very... interesting... baby. I learned a lot in this activity. I learned that even if you think you know what your baby will look like, it doesn't necessarily mean that's how it'll happen, because genotypes are completely random. This is how our baby turned out ---->
Another interesting fact is that even if me and Kiel decided to "have another baby," the probability that the new baby would look like this baby is very unlikely. They may look alike but not exactly alike.
I think this activity was a lot of fun, because we got to learn about phenotypes and genotypes in an interesting way.

DNA Extraction from Wheat Germ

1. Place 1 gram of raw wheat germ in a test tube.
2. Add 20ml of hot tap water and mix constantly for 3 minutes
      Observation: The "wheat germ soup" looked like watery, old bread. It turned the water a cloudy color.
3. Add 1 ml of detergent and mix gently every minute for 5 minutes without creating foam.
     Observation: After adding detergent to the mix, the wheat germ soup turned yellow. It looked a lot like chunky old Mountain Dew. At this point the cell membrane is dissolving so that we can later extract the DNA.
4. Remove foam.
5. Slowly pour 14ml of alcohol down the side of the test tube so that it forms a layer on top of the solution. Don't mix the two.
     Observation: The alcohol made the solution form four layers. The layers are: wheat germ, detergent, a while layer, and the clear alcohol. At this step, the DNA is precipitating at the water-alcohol interface, pulling the DNA out of the wheat germ. At the water-alcohol interface, DNA is forming a white layer(DNA).
6. Let the tube sit for a few minutes as the DNA rises. Remove the DNA with a wooden stick.
     Observation: The DNA looks a lot like a small wet piece of paper, or in Chapin's words, "a booger."

Self Analysis: Chapin and I had a lot of fun with this lab because we got fast results and the results we got were very interesting. I never knew you could extract DNA with simple household items. I never even knew that wheat germ had DNA!

Eugenics Paper

Eugenics "Paper" on Prezi