Michael R. Pina's Lab Notebook

Lab Notebook

Week 2

a) At around base 80, the upper (blue) DNA sequence has AC whereas the lower (yellow) DNA sequence has GG in the last exon.

b) No, they don't all have to have the same DNA sequence, they just don't have any of the correct pigment sequences or they do not have a promoter region.

c) All of them share the first two exon sequences, labeled in purple and teal; it is in the third exon sequence where they differ. This region is likely responsible for the different colors.

In order to create a blue flower to cross with the red flower, I loaded the Green-2 flower and arbitrarily changed some of the bases in the yellow sequence so that the new folded protein was white, creating a blue flower.

When I crossed my new blue flower with the pre-existing red flower, I got some purple but it was not true breeding. After some thought, I went back to both the blue and red flowers and observed the differences in their upper and lower sequences in order to change both of the DNA sequences so that they were true breeding red and blue, respectively. Crossing these 2 true breeding red and blue flowers yielded all purple flowers.

I was not able to isolate a purple flower that would produce all purple flowers when self-crossed so I began to observe the biochemistry and noticed that Tyr and Phe were the determinates for color in the flowers where Tyr produced blue and Phe produced red. Using this information, I began to play around with the DNA sequence, deleting, adding, or changing certain base pairs (around 80) to see the outcome. Finally, I thought to add both Tyr and Phe together which yielded a mutant purple flower. Mutating both the upper and lower DNA sequences allowed for a true-breeding purple flower.

Week 3

In class activity

What I know about HIV so far

HIV is a human pathogen that targets the immune system. It uses white blood cells as hosts; the white blood cells burst after being infected and thusly the immune system is compromised. The HIV virus itself does not actually kill anyone, rather people who otherwise become sick while they have the virus cannot fight off the disease (such as influenza). The virus is transmitted through the exchange of human tissue such as blood or other bodily fluids. When the number of HIV virus cells go beyond a certain percentage in humans, it is referred to as AIDS. There is no known cure for the virus as of yet, just some treatments that don't always work.

What I would like to know

1. What is it about the virus that makes it so difficult to treat?
2. How did the virus evolve to attack the immune system of its host?
3. What is the most recent advancement that has been made in hope of finding a cure?

Becoming an instant expert with PubMed

• Query functions much like Google.
• Click on a search result to get an abstract. The book mentions something about clicking on an author but that feature doesn't seem to be available any longer. The abstract can be saved in a number of ways by clicking the "Send To" link.
• Alternatively, you can choose one or more articles in a given page by selecting the check-mark boxes next to them. You can still use the "Send To" feature even for multiple articles.
• After clicking on an article you can choose to show the abstract, summary, etc. by clicking on "Display Settings."
• At the top right corner there's a link that says "Full Text Article in PudMed". From here you can view the full article, save it in a PDF, etc.