Still Sick

So I'm still feeling a bit under the weather. And teaching all day today didn't help. I woke up this morning all sore, I so didn't want to get out of bed. But talking all day didn't help either.

About three weeks ago I wrote up a proposal for a grant that is given by UWF for Graduate Student Research. I was looking at getting money for my thesis. Which currently looks like I'll be doing something about Detection of Marine Viruses in Ectocarpus sp. It's interesting because it is thought that about 50% of the Ectocarpus in the world in infected by a virus known as the EsV-1. What is not known, or at least there aren't any articles that I have found, is there an ecological impact that EsV-1 has on the population. Because of the cell wall that plants have it is difficult for any virus or bacteria to infect a plant. Infection usually occurs when the cells have been damaged breaking the cell wall. With Ectocarpus during sexual reproduction the cell wall on the gametophytes is quite thin allowing the virus to infect the plant. The viral DNA will incorporate in and when Meiosis occurs there are 2 out of 4 plants infected. There was a recent article published that had sequence the entire viral genome. Which is a big help in my study. What I plan on doing is taking primers for the viral DNA, a primer is basically a strand of DNA that is homologous to the viral DNA. One thing you can do with a primer is attach a epiflourescent that will fluorescent in UV light. Using a microscope you can do physical counts of the glowing dots. There is a limitation with that. First, when putting organisms under a microscope they never cooperate, so you can get stacking, which will throw your numbers off.

Another way of dectecting the amount of virii in Ectocarpus is to use a technique called PCR or Polymerase Chain Reaction. There is a nice little animation here that shows you wants occurs during PCR. Basically what PCR does is amplify the DNA in a sample. Because DNA is double stranded, usually, when you heat it up it will break apart leaving you with two single strands. Using a special enzyme called Taq Polymerase, cultured from a bacteria that was found in a hydrothermal vent. You can take a primer, bind it to your DNA and make copies from where you primer binds till the DNA ends. Normally you would use two different primers, if you have an idea what you are looking for you will know what is at the beginning and end of the DNA that you wish to amplify. So with two primers you anneal them, bind them to a single stand of DNA, and allows for the Taq Polymerase to create new strands of DNA. In one step you have gone from 2 strands on DNA to 4. If you repeat this several times you have a nice log of growth of the number of DNA strands. The other reason that you use two primers is that DNA is read two different ways, if you watch the animation you'll get a better idea. It is read by the enzyme in 5' to 3', this refers to the way DNA is chemically bonded. If you are really interested I suggest taking a Genetics course. Because the Taq Polymerase reads from the primer onwards it does not get the entire strand of DNA. If you look at the other strand of DNA the same thing happens, so what happens is your desired piece of DNA that you want to amplify is the only part that is being fully copied. Now repeat this about 75 times and you have your desired DNA amplified. The makeup of DNA carries a negative charge. This allows you to take your amplified sample and run it through a gel that will separate the DNA by size. A gel can be made of many things, usually Agarose from a red seaweed. The way a gel sets up it has pores in it. When a electrical current is run through the gel the DNA will migrate towards the cation. You can control the pore size of a gel by controlling the percentage of agarose in the gel. The more agarose in the gel the smaller the pore size. Applying the charge smaller pieces of DNA will migrate towards the cation faster than large pieces, because it's easier for smaller pieces to move through the pores. You can separate the DNA by size, if you know the size of your DNA you can use a high speed centerfuge to separate the different pieces of DNA so you have the one that you want. The great thing about PCR is it uses small quantities. I'm talking about μg of material, which is 10^-6 of material.

So that's what I'll be doing with my grant money.

I don't Understand Women

So there is a girl in botany class, damn you ethics. I swear she flirts with me all the time. Well today she was talking about her boyfriend and then she began to flirt with me. God I just wish I knew what the fuck women were thinking.