Archives for the Month of April 2008 on Christina Cajigas's Online Journal
More to do...
Other things I need to fix in my proposal:
PCR- Polymerase Chain Reaction: allows millions of copies of a specific DNA sequence to be produced in usually two hours. It bypasses the need for the use of bacteria.
Nuclear DNA content: the DNA located in the nucleus
“Purified” DNA: Means DNA samples that do not contain any other materials labeled “Junk” such as RNA and any other substances not pertaining to direct genetic mapping ( I need to ask Dr. Cullis more about this)
Variation in the Termination step: A thermocycler is used to vary the temperature in the solution so the ddNTP can bind to the template strand at different points. Each point in the strand represents a “letter” in a genetic sequence. Different ddNTP’s bind at different temperatures, so varying the temperature, allows them to bind in many places, therefore reducing the number of DNA templates needed for a complete and successful sequencing reaction.
The electropharigram shows the different wavelengths of color detected by the photocell , the peaks are seen and each peak represents a different letter (ACGT)
You said what?
One of the questions I talk about in my proposal involves the idea that part of this project is to develop new techniques for DNA purification. It was commented on my rough draft that I need to explain more about that key idea and develop it more.
“Also missing is a clear discussion of the data gained and how it will help address the fundamental questions in the proposed project.” So I figured the best way to tackle this is to free write, so here I go...
Here are the questions asked by Professor Hauck that need to be answered:
How will the data feedback into developing purification techniques?
As of now I am using a couple of techniques to purify the DNA and get rid of excess large pieces of RNA that cloud the sample.
We are using experimental amounts of Ribonuclease enzyme to help eat at the RNA and purify the sample. (Experimental means that a set amount of enzyme to add has not yet been determined as optimum). We also are using column filtration, to get rid of large pieces (Will this work? only trying will tell). And another technique is PCR through buffer solutions that will filter the DNA, that can be eluded, or removed from the filter through another solution. Optimum amounts for these solutions are still experimental and how much DNA that can be purified effectively at one time is still unknown.
2. What steps can be altered in response to new data?
We using gel electrophoresis to determine how pure a DNA sample is, or how clean it is. If bands corresponding to RNA show, then we have to continue, i.e., try same technique with different amount, or try another. That is what will be done in this experiment, to determine using trail and error what are the best amounts of solution to use for each technique for this kind of DNA.
okay now...to get this in my paper, and so that it makes sense...
Significance?
My rough draft is complete, all turned in but there is a lot I want to work on and fix.
It seems from my feedback, I need to relay more specifically the significance that sequencing the flax genome will have on the future of not only genomics in general. I want to emphasize the following:
-Studying that plant more closely and future implications that genetically modified (gm) flax crops could have in the future.
-A genetic sequence will allow us to see what makes up the genome and allow us to compare that genome with other sequenced plants, as well as allow us to discover if the flax genome really is as unique as we think it is, i.e.. does it really have low copy number sequences as we predicted
-Also this sequenced genome will allow us to see what makes makes flax oil polyunsaturated, i.e. study the composition and the implications of what makes it up with what it actually becomes, etc.
-Studying the genome will also allow us to get a better idea of how flax evolved, etc.
Just some ideas. Now to get them in my paper.